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Burdennyy AM, Filippova EA, Lukina SS, Ivanova NA, Pronina IV, Loginov VI, Kazubskaya TP, Kushlinskii NE, Braga EA. DNA Methylation of a Group of Long Non-Coding RNA Genes at Different Stages of Ovarian Cancer Dissemination. Bull Exp Biol Med 2024; 176:495-500. [PMID: 38492100 DOI: 10.1007/s10517-024-06054-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Indexed: 03/18/2024]
Abstract
There are three types of metastases in ovarian cancer: lymphogenous, hematogenous, and peritoneal. Dissemination of the tumor in the peritoneum is directly related with the development of ascites and a poor prognosis. The purpose of this study is to determine changes in the methylation level of a group of long non-coding RNA (lncRNA) genes at different stages of ovarian cancer progression. The methylation level of 7 lncRNA genes (LINC00472, LINC00886, MAFG-DT, SNHG1, SNHG6, TP53TG1, and TUG1) was studied by quantitative methyl-specific PCR in 93 samples of ovarian tumors and 75 paired samples of histologically normal tissue, as well as in 29 peritoneal macroscopic metastases. Using the nonparametric Mann-Whitney test, a significant (p<0.001) increase in the level of methylation of the LINC00886, SNHG1, SNHG6, and TUG1 genes in the tumor tissue was shown. For the LINC00472, LINC00886, and SNHG6 genes, a significant relationship was found with the clinical stage (p≤0.001), as well as with the appearance of metastases for the LINC00472 (p<0.001) and SNHG6 (p=0.005) genes. There was a significant increase in the level of methylation of MAFG-DT and TP53TG1 (p<0.001) genes, as well as a decrease in LINC00886 (p=0.003) in peritoneal metastases relative to the primary focus. Methylation of the LINC00472 and SNHG6 genes can be considered as a factor in initiating ovarian cancer metastasis, and methylation of the LINC00886, MAFG-DT, and TP53TG1 genes as a colonization factor for metastases in the peritoneum. Thus, a relationship between methylation of a group of lncRNA genes at different stages of ovarian cancer dissemination was shown, which is important for understanding the mechanisms of these processes and for developing innovative approaches to ovarian cancer therapy.
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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
| | - S S Lukina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - N A Ivanova
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - I V Pronina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - V I Loginov
- 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
| | - N E Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - E A Braga
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
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Braga EA, Fridman MV, Burdennyy AM, Loginov VI, Dmitriev AA, Pronina IV, Morozov SG. Various LncRNA Mechanisms in Gene Regulation Involving miRNAs or RNA-Binding Proteins in Non-Small-Cell Lung Cancer: Main Signaling Pathways and Networks. Int J Mol Sci 2023; 24:13617. [PMID: 37686426 PMCID: PMC10487663 DOI: 10.3390/ijms241713617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial players in the pathogenesis of non-small-cell lung cancer (NSCLC). A competing binding of lncRNAs and mRNAs with microRNAs (miRNAs) is one of the most common mechanisms of gene regulation by lncRNAs in NSCLC, which has been extensively researched in the last two decades. However, alternative mechanisms that do not depend on miRNAs have also been reported. Among them, the most intriguing mechanism is mediated by RNA-binding proteins (RBPs) such as IGF2BP1/2/3, YTHDF1, HuR, and FBL, which increase the stability of target mRNAs. IGF2BP2 and YTHDF1 may also be involved in m6A modification of lncRNAs or target mRNAs. Some lncRNAs, such as DLGAP1-AS2, MALAT1, MNX1-AS1, and SNHG12, are involved in several mechanisms depending on the target: lncRNA/miRNA/mRNA interactome and through RBP. The target protein sets selected here were then analyzed using the DAVID database to identify the pathways overrepresented by KEGG, Wikipathways, and the Reactome pathway. Using the STRING website, we assessed interactions between the target proteins and built networks. Our analysis revealed that the JAK-STAT and Hippo signaling pathways, cytokine pathways, the VEGFA-VEGFR2 pathway, mechanisms of cell cycle regulation, and neovascularization are the most relevant to the effect of lncRNA on NSCLC.
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Affiliation(s)
- Eleonora A. Braga
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Alexey M. Burdennyy
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
| | - Sergey G. Morozov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (A.M.B.); (V.I.L.); (I.V.P.); (S.G.M.)
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Safonova TN, Zaitseva GV, Loginov VI, Burdennyy AM. [Predictive significance of genetic analysis of the development of dry eye disease of different origin]. Vestn Oftalmol 2023; 139:13-18. [PMID: 38235625 DOI: 10.17116/oftalma202313906113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
One of the etiological causes of dry eye disease (DED) is systemic autoimmune diseases (AID): primary Sjögren's syndrome (PSS), rheumatoid arthritis (RA); their manifestation may begin with ophthalmic symptoms. The relationship of PSS and RA with genetic factors is proven. The contribution of polymorphic markers of the genes THBS1, MUC1, TRIM21, STAT4, PTPN22 in the development of these diseases is established, as well as their connection with the development of DED. A panel of genetic markers for evaluating the risk of developing DED in PSS and RA is developed, and its sensitivity and specificity is determined. PURPOSE The aim of the study was to determine the prognostic significance of a panel of polymorphic gene markers in the development of dry eye syndrome in patients with primary Sjögren's syndrome and rheumatoid arthritis over a five-year follow-up period. MATERIAL AND METHODS Patients with a verified diagnosis of PSS and RA without signs of DED were examined (n=35 and n=42, respectively). The control group included 82 volunteers without AID and DED. The observation period was 5 years. Every year all study subjects underwent an ophthalmological clinical and functional examination. RESULTS Dry eye disease had developed in groups of patients with AID with predisposing genotypes of polymorphic markers of the genes THBS1, MUC1, TRIM21, STAT4, PTPN22. The peak of DED development in these patients was in the third year of the follow-up. As a result of ROC analysis, it was found that the sensitivity and specificity of determining the predisposing genotypes of polymorphic markers of the THBS1, MUC1, TRIM21, STAT4, PTPN22 genes was 68 and 87%, respectively (p<0.0001). CONCLUSION Genetic research methods are essential for minimally invasive early diagnosis of dry eye disease, and can subsequently become the basis for a personalized approach to its treatment.
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Affiliation(s)
- T N Safonova
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - G V Zaitseva
- Krasnov Research Institute of Eye Diseases, Moscow, Russia
| | - V I Loginov
- Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, Moscow, Russia
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Gubenko MS, Loginov VI, Burdennyy AM, Pronina IV, Kazubskaya TP, Pertsov SS. Changes in the Level of Methylation of a Group of microRNA Genes as a Factor in the Development and Progression of Non-Small Cell Lung Cancer. Bull Exp Biol Med 2022; 174:254-258. [PMID: 36598670 DOI: 10.1007/s10517-023-05684-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Indexed: 01/05/2023]
Abstract
We studied changes in the level of methylation of a number of microRNA genes hypermethylated in non-small cell lung cancer and its histological subtypes as well as the relationship of methylation of a group of microRNA genes with clinical and morphological features of the tumor with smoking status. A significantly high level of methylation of 7 genes (MIR124-1/3, MIR125B-1, MIR129-2, MIR137, MIR1258, and MIR339) was revealed in adenocarcinoma and squamous cell lung cancer in comparison with samples of adjacent histologically unchanged lung tissue. In squamous cell lung cancer, a significantly high level of methylation of the MIR124-2 gene in the tumor was also shown. In addition, differences in the methylation profile of adenocarcinoma and squamous cell carcinoma at stages III-IV of the oncological process were revealed. A high level of methylation of the MIR137 and MIR1258 genes was shown for adenocarcinoma and MIR339, MIR129-2, and MIR124-2 for squamous cell carcinoma. Significant differences in the level of methylation of MIR124-2 and MIR375 genes were revealed for smoking patients with squamous cell lung cancer.
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Affiliation(s)
- M S Gubenko
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - V I Loginov
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - A M Burdennyy
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.
| | - I V Pronina
- 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
| | - S S Pertsov
- P. K. Anokhin Research Institute of Normal Physiology, Moscow, Russia
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Braga EA, Fridman MV, Burdennyy AM, Filippova EA, Loginov VI, Pronina IV, Dmitriev AA, Kushlinskii NE. Regulation of the Key Epithelial Cancer Suppressor miR-124 Function by Competing Endogenous RNAs. Int J Mol Sci 2022; 23:13620. [PMID: 36362406 PMCID: PMC9655303 DOI: 10.3390/ijms232113620] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/31/2022] [Accepted: 11/02/2022] [Indexed: 12/01/2023] Open
Abstract
A decrease in the miR-124 expression was observed in various epithelial cancers. Like a classical suppressor, miR-124 can inhibit the translation of multiple oncogenic proteins. Epigenetic mechanisms play a significant role in the regulation of miR-124 expression and involve hypermethylation of the MIR-124-1/-2/-3 genes and the effects of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) according to the model of competing endogenous RNAs (ceRNAs). More than 40 interactomes (lncRNA/miR-124/mRNA) based on competition between lncRNAs and mRNAs for miR-124 binding have been identified in various epithelial cancers. LncRNAs MALAT1, NEAT1, HOXA11-AS, and XIST are the most represented in these axes. Fourteen axes (e.g., SND1-IT1/miR-124/COL4A1) are involved in EMT and/or metastasis. Moreover, eight axes (e.g., OIP5-AS1/miR-124-5p/IDH2) are involved in key pathways, such as Wnt/b-catenin, E2F1, TGF-β, SMAD, ERK/MAPK, HIF-1α, Notch, PI3K/Akt signaling, and cancer cell stemness. Additionally, 15 axes impaired patient survival and three axes reduced chemo- or radiosensitivity. To date, 14 cases of miR-124 regulation by circRNAs have been identified. Half of them involve circHIPK3, which belongs to the exonic ecircRNAs and stimulates cell proliferation, EMT, autophagy, angiogenesis, and multidrug resistance. Thus, miR-124 and its interacting partners may be considered promising targets for cancer therapy.
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Affiliation(s)
- Eleonora A. Braga
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Elena A. Filippova
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Research Centre for Medical Genetics, 115522 Moscow, Russia
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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Pronina IV, Uroshlev LA, Moskovtsev AA, Zaichenko DM, Filippova EA, Fridman MV, Burdennyy AM, Loginov VI, Kazubskaya TP, Kushlinskii NE, Dmitriev AA, Braga EA, Brovkina OI. Dysregulation of lncRNA–miRNA–mRNA Interactome as a Marker of Metastatic Process in Ovarian Cancer. Biomedicines 2022; 10:biomedicines10040824. [PMID: 35453574 PMCID: PMC9031843 DOI: 10.3390/biomedicines10040824] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer (OC) is one of the most common types of cancer among malignancies of the female reproductive system. This pathology is asymptomatic until advanced stages and has a poor prognosis. Our study aimed to search for lncRNA–miRNA–mRNA competing triplets that promote ovarian tumorigenesis. For this purpose, we analyzed tumor samples from the TCGA database and verified the results experimentally in a set of 46 paired samples of tumor and matched histologically unchanged ovarian tissues from OC patients. The list of RNAs selected in silico for experimental studies included 13 mRNAs, 10 lncRNAs, and 5 miRNAs related to epithelial–mesenchymal transition and angiogenesis. We evaluated the expression of these RNAs by qRT-PCR and assessed the correlation between levels of miRNAs, mRNAs, and lncRNAs. Sixteen significant triplets were revealed, in some of which, e.g., OIP5-AS1–miR-203a–c-MET and OIP5-AS1–miR-203a–ZEB2, both lncRNA and mRNA had sites for miR-203a direct binding. Transfection of the OVCAR-3 and SKOV-3 cell lines with the miR-203a mimic was used to confirm the novel links of miR-203a with ZEB2 and c-MET in OC. These connections suggest that the interactomes have the potential for diagnostics of metastasis at early onset.
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Affiliation(s)
- Irina V. Pronina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
| | - Leonid A. Uroshlev
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Alexey A. Moskovtsev
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Danila M. Zaichenko
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
| | - Elena A. Filippova
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Alexey M. Burdennyy
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
| | - Tatiana P. Kazubskaya
- N. N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (T.P.K.); (N.E.K.)
| | - Nikolay E. Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, 115478 Moscow, Russia; (T.P.K.); (N.E.K.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Eleonora A. Braga
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
- Correspondence:
| | - Olga I. Brovkina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (I.V.P.); (L.A.U.); (A.A.M.); (D.M.Z.); (E.A.F.); (A.M.B.); (V.I.L.); (O.I.B.)
- Federal Research and Clinical Center of Federal Medical-Biological Agency of Russia, 115682 Moscow, Russia
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Loginov VI, Burdennyy AM, Filippova EA, Pronina IV, Lukina SS, Kazubskaya TP, Karpukhin AV, Khodyrev DS, Braga EA. Aberrant Methylation of 21 MicroRNA Genes in Breast Cancer: Sets of Genes Associated with Progression and a System of Markers for Predicting Metastasis. Bull Exp Biol Med 2021; 172:67-71. [PMID: 34792716 DOI: 10.1007/s10517-021-05333-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Indexed: 12/19/2022]
Abstract
Systemic analysis of the relationship between the levels of methylation of 21 microRNA genes and the parameters of breast cancer progression was performed on a representative sample of 91 paired specimens of breast cancer and histologically normal tissues and a system of markers for prediction of metastasis was proposed. A significant association of hypermethylation of 11 genes with late (III-IV) clinical stages was found, and for 6 genes (MIR124-1, MIR127, MIR34B/C, MIR9-3, MIR1258, and MIR339) this association was highly significant (p≤0.001, FDR=0.01). For MIR9-3 and MIR339, an association with tumor size was demonstrated (p<0.001, FDR=0.01). No association of the levels of methylation of the analyzed microRNA genes with the degree of differentiation were found. An association with lymph node metastasis was established for 9 microRNA genes; the most significant association was shown for 6 genes MIR125B-1, MIR127, MIR9-3, MIR339, MIR124-3, and MIR1258 (p<0.005, FDR=0.05). Based on these 6 genes, a marker system for predicting breast cancer metastasis was developed by ROC analysis. This system is characterized by 87% sensitivity and 77% specificity (AUC=0.894). The proposed system may have clinical application in the personalized treatment of breast cancer patients.
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Affiliation(s)
- V I Loginov
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - A M Burdennyy
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.
| | - E A Filippova
- Research Institute of General Pathology and Pathophysiology, 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
| | - T P Kazubskaya
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - A V Karpukhin
- N. P. Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - D S Khodyrev
- Federal Research Clinical Center of Specialized Types of Medical Care and Medical Technologies, Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - E A Braga
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Safonova TN, Zaitseva GV, Burdennyy AM, Loginov VI. [Association of polymorphic markers rs7947461 of the TRIM21 gene and rs33996649 of the PTPN22 gene with the risk of developing exogenous dry eye syndrome]. Vestn Oftalmol 2021; 137:217-223. [PMID: 34669330 DOI: 10.17116/oftalma2021137052217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this age of technological advancement, an increasing number of people is being exposed to external risk factors of damaging their ocular surface (wearing contact lenses, electromagnetic radiation from computers, mobile devices, etc.). However, the presence of external factors does not lead to a 100% risk of developing the dry eye disease (DED). The trigger mechanism in the development of autoimmune lesions of the ocular environment in some systemic diseases is known to be associated with molecular genetic factors. The search for molecular genetic disorders is based on the analysis of polymorphic markers of a number of genes responsible for the state of the eye surface. PURPOSE To study the relationship of polymorphic markers rs7947461 of the TRIM21 gene and rs33996649 of the PTPN22 gene with the risk of developing dry eye syndrome of exogenous etiology. MATERIAL AND METHODS The study included 57 people with exogenous risk factors for DED development. The control group included volunteers without a history of ophthalmic pathologies (n=75). Genotyping was done by real-time polymerase chain reaction followed by melting curve analysis. Statistical processing of data was done using the Statistica 6.1 RUS software for statistical analysis. RESULTS In the course of the study, 31 patients of the main group were diagnosed with DED and separated into the 1st subgroup; DED diagnosis was not confirmed in 26 patients, who were put into the 2nd subgroup. The 1st subgroup showed a significant increase in the frequency of predisposing genotypes of the TRIM21 and PTPN22 genes. The relative risk of developing DED turned out to be 2.5 and 4.86 times higher, respectively. In the 2nd subgroup, no statistically significant data was found on the presence of predisposing genotypes of polymorphic markers of the TRIM21 and PTPN22 genes (p=0.3). CONCLUSION The revealed association of polymorphic markers rs7947461 of the TRIM21 gene and rs33996649 of the PTPN22 gene with the risk of developing DED of exogenous etiology puts these loci as possible markers for diagnosing this pathology.
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Affiliation(s)
- T N Safonova
- Research Institute of Eye Disease, Moscow, Russia
| | - G V Zaitseva
- Research Institute of Eye Disease, Moscow, Russia
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - V I Loginov
- Institute of General Pathology and Pathophysiology, Moscow, Russia
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Burdennyy AM, Filippova EA, Ivanova NA, Lukina SS, Pronina IV, Loginov VI, Fridman MV, Kazubskaya TP, Utkin DO, Braga EA, Kushlinskii NE. Hypermethylation of Genes in New Long Noncoding RNA in Ovarian Tumors and Metastases: A Dual Effect. Bull Exp Biol Med 2021; 171:370-374. [PMID: 34292442 DOI: 10.1007/s10517-021-05230-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/21/2022]
Abstract
The role of methylation in the regulation of genes of long noncoding RNA (lncRNA) is still poorly understood. We revealed new hypermethylated lncRNA genes in ovarian tumors and their effect on metastasis of ovarian cancer. A multiple and significant (p<0.001) increase in methylation of a group of lncRNA genes (MEG3, SEMA3B-AS1, ZNF667-AS1, and TINCR) was shown by quantitative methylation-specific PCR using the non-parametric Mann-Whitney test. Moreover, methylation of SEMA3B-AS1, ZNF667-AS1, and TINCR genes in ovarian cancer tumors was detected for the first time. Comparative analysis of 19 samples of peritoneal metastases and paired primary tumors showed a significant decrease in the methylation level of the same 4 genes: MEG3 (p=0.004), SEMA3B-AS1 (p=0.002), TINCR (p=0.002), and ZNF667-AS1 (p<0.001). Reduced methylation of suppressor lncRNA genes in peritoneal metastases is probably associated with the involvement of these lncRNA in the regulation of plastic reversion of the epithelial-mesenchymal transition to the mesenchymal-epithelial transition. Thus, the effect of lncRNA and their methylation on the development of tumors and metastases of ovarian cancer was demonstrated, which is important for understanding of the pathogenesis and mechanisms of metastasis of ovarian cancer. New properties of lncRNA can find application in the development of new approaches in the therapy of ovarian 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
| | - N A Ivanova
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - S S Lukina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - I V Pronina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - V I Loginov
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - M V Fridman
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - T P Kazubskaya
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - D O Utkin
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - E A Braga
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.
| | - N E Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
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11
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Filippova EA, Fridman MV, Burdennyy AM, Loginov VI, Pronina IV, Lukina SS, Dmitriev AA, Braga EA. Long Noncoding RNA GAS5 in Breast Cancer: Epigenetic Mechanisms and Biological Functions. Int J Mol Sci 2021; 22:ijms22136810. [PMID: 34202777 PMCID: PMC8267719 DOI: 10.3390/ijms22136810] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/15/2021] [Accepted: 06/18/2021] [Indexed: 12/12/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been identified as contributors to the development and progression of cancer through various functions and mechanisms. LncRNA GAS5 is downregulated in multiple cancers and acts as a tumor suppressor in breast cancer. GAS5 interacts with various proteins (e.g., E2F1, EZH2, and YAP), DNA (e.g., the insulin receptor promoter), and various microRNAs (miRNAs). In breast cancer, GAS5 binds with miR-21, miR-222, miR-221-3p, miR-196a-5p, and miR-378a-5p that indicates the presence of several elements for miRNA binding (MREs) in GAS5. Mediated by the listed miRNAs, GAS5 is involved in the upregulation of a number of mRNAs of suppressor proteins such as PTEN, PDCD4, DKK2, FOXO1, and SUFU. Furthermore, the aberrant promoter methylation is involved in the regulation of GAS5 gene expression in triple-negative breast cancer and some other carcinomas. GAS5 can stimulate apoptosis in breast cancer via diverse pathways, including cell death receptors and mitochondrial signaling pathways. GAS5 is also a key player in the regulation of some crucial signal pathways in breast cancer, such as PI3K/AKT/mTOR, Wnt/β-catenin, and NF-κB signaling. Through epigenetic and other mechanisms, GAS5 can increase sensitivity to multiple drugs and improve prognosis. GAS5 is thus a promising target in the treatment of breast cancer patients.
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Affiliation(s)
- Elena A. Filippova
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (E.A.F.); (A.M.B.); (V.I.L.); (I.V.P.); (S.S.L.)
| | - Marina V. Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Alexey M. Burdennyy
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (E.A.F.); (A.M.B.); (V.I.L.); (I.V.P.); (S.S.L.)
| | - Vitaly I. Loginov
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (E.A.F.); (A.M.B.); (V.I.L.); (I.V.P.); (S.S.L.)
| | - Irina V. Pronina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (E.A.F.); (A.M.B.); (V.I.L.); (I.V.P.); (S.S.L.)
| | - Svetlana S. Lukina
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (E.A.F.); (A.M.B.); (V.I.L.); (I.V.P.); (S.S.L.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia;
| | - Eleonora A. Braga
- Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia; (E.A.F.); (A.M.B.); (V.I.L.); (I.V.P.); (S.S.L.)
- Correspondence:
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12
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Kushlinskii NE, Loginov VI, Utkin DO, Filippova EA, Burdennyy AM, Korotkova EA, Pronina IV, Lukina SS, Smirnova AV, Gershtein ES, Braga EA. [Novel miRNAs as Potential Regulators of PD-1/PD-L1 Immune Checkpoint, and Prognostic Value of MIR9-1 and MIR124-2 Methylation in Ovarian Cancer]. Mol Biol (Mosk) 2020; 54:990-996. [PMID: 33276362 DOI: 10.31857/s0026898420060075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/05/2020] [Indexed: 11/24/2022]
Abstract
Ovarian cancer (OC) is mostly detected at late stages weighed down with metastasis, and the five-year survival rate of patients is only 30%, which dictates the necessity to develop gentler and more selectively targeted drugs that current chemotherapeutic agents. The search for factors that can influence on the activity of the PD-1/PD-L1 immune checkpoint signaling pathway in tumors is relevant, and micro RNAs (miRNAs) play an important role in it. Over the past 5 years, only a few miRNAs (miR-34a, miR-145, and miR-424), which have a regulatory effect on the PD-1/PD-L1 system in OC patients, have been discovered. In present work, the methylation levels of 13 miRNA genes in 26 primary tumors and 19 peritoneal metastases of OC patients were determined and compared with the level of the soluble form of PD-L1 (sPD-L1) in the blood plasma of the same patients. It was shown that the methylation levels of five miRNA genes (MIR124-2, MIR34B/C, MIR9-1, MIR9-3, and MIR339) in tumors are in direct correlation with the sPD-L1 level in the blood plasma. In addition, when analyzing these five genes, a significant association of the methylation level of the MIR9-1 gene with a decrease in the three-year relapse-free survival, and a trend for decrease in the three-year survival rate with the methylation level of the MIR124-2 gene of OC patients were determined. Thus, the first data suggesting the role of inhibitors of the sPD-L1 immune checkpoint for five miRNAs (miR-124, miR-34b, miR-34c, miR-9, miR-339) and the possibility of using hypermethylated MIR9-1 and, presumably, MIR124-2 genes as independent prognostic markers of poor disease-free survival in OC patients were obtained.
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Affiliation(s)
- N E Kushlinskii
- Blokhin Russian Cancer Research Center, Ministry of Healthcare of the Russian Federation, Moscow, 115478 Russia
| | - V I Loginov
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,Research Centre for Medical Genetics, Moscow, 115478 Russia
| | - D O Utkin
- Sechenov First Moscow State Medical University, Ministry of Healthcare of the Russian Federation, Moscow, 119435 Russia
| | - E A Filippova
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - E A Korotkova
- Blokhin Russian Cancer Research Center, Ministry of Healthcare of the Russian Federation, Moscow, 115478 Russia
| | - I V Pronina
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - S S Lukina
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - A V Smirnova
- Sechenov First Moscow State Medical University, Ministry of Healthcare of the Russian Federation, Moscow, 119435 Russia
| | - E S Gershtein
- Blokhin Russian Cancer Research Center, Ministry of Healthcare of the Russian Federation, Moscow, 115478 Russia
| | - E A Braga
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,Research Centre for Medical Genetics, Moscow, 115478 Russia.,
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13
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Kushlinskii NE, Utkin DO, Loginov VI, Filippova EA, Burdennyy AM, Kushlinsky DN, Pronina IV, Braga EA. [Clinical significance of methylation of a group of miRNA genes in patients with ovarian cancer.]. Klin Lab Diagn 2020; 65:321-327. [PMID: 32298550 DOI: 10.18821/0869-2084-2020-65-5-321-327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/18/2020] [Indexed: 02/05/2023]
Abstract
It was found that the proportion of microRNA genes inactivated by methylation of regulatory CpG islands is several times higher than the genes encoding proteins, which increases their attractiveness as promising markers of cancer. The aim of this work is to evaluate the clinical significance of methylation of 13 tumor-associated microRNA genes (MIR-124a-2, MIR-124a-3, MIR-125-B1, MIR-127, MIR-129-2, MIR-132, MIR-137, MIR-203a, MIR-34b/c, MIR-375, MIR-9-1, MIR-9-3, MIR-339) in 26 patients with ovarian cancer. Methylation level was evaluated by the method of methylation-specific PCR in real time. The data obtained in primary tumors (26), histologically unchanged ovarian tissues (15) and peritoneal metastases (19) were compared using a number of statistical programs. For all 13 genes, an increase in the level of methylation was revealed during the transition from unchanged tissue to primary tumors and further from primary tumors to peritoneal metastases; moreover, in the genes MIR-203a, MIR-375 and MIR-339, the level of methylation in metastases increased most significantly (in 2 and more times). A correlation was observed for the first time, showing a consistency between the increase in methylation level in some miRNA pairs, for example, MIR-129-2/MIR-132 (rs> 0,7; p<0,0001), both in primary tumors and in metastases. An analysis of microRNA gene methylation in clinical samples of ovarian cancer showed a correlation between the observed molecular changes both with the initial stages of tumor formation and with the progression and dissemination of ovarian cancer, with the presence of metastases in a large omentum and with the appearance of ascites. The revealed dependencies deepen the understanding of the mechanism of peritoneal metastasis and can be used to select new diagnostic and prognostic markers of ovarian cancer.
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Affiliation(s)
- N E Kushlinskii
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russian Federation
| | - D O Utkin
- N.N. Blokhin National Medical Research Center of Oncology, Moscow, 115478, Russian Federation
| | - V I Loginov
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - E A Filippova
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - A M Burdennyy
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - D N Kushlinsky
- A.F. Tsyb Medical Radiological Scientific Center - branch of the Federal State Budgetary Institution «National Medical Research Center of Radiology» of the Ministry of Health of the Russian Federation, Obninsk, 249036, Russian Federation
| | - I V Pronina
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
| | - E A Braga
- The Institute of General Pathology and Pathophysiology of the Ministry of Science and Higher Education of the Russian Federation, Moscow, 125315, Russian Federation
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14
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Braga EA, Burdennyy AM, Pronina IV, Filippova EA, Kazubskaya TP, Fridman MV, Khodyrev DS, Karpukhin AV, Loginov VI, Kushlinskii NE. System of Markers Based on the Methylation of a Group of Proapoptotic Genes in Combination with MicroRNA in the Diagnosis of Breast Cancer. Bull Exp Biol Med 2020; 168:366-370. [PMID: 31938917 DOI: 10.1007/s10517-020-04710-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Indexed: 01/18/2023]
Abstract
Systems of markers for the diagnosis of breast cancer based on DNA methylation of a group of suppressor protein-coding genes, hypermethylated microRNA genes, and their combinations were compiled. On a representative sample of 70 paired breast cancer specimens (tumor/normal), MS-PCR analysis revealed a significant increase in the methylation frequency of 5 protein-coding genes: RASSF1A suppressor and apoptosis genes APAF1, BAX, BIM/BCL2L11, and DAPK1 (34-61% vs. 4-24%) and 6 microRNA genes: MIRG124G1, MIRG125bG1, MIRG129G2, MIRG148a, MIRG34b/c, and MIRG9G3 (36-76% vs. 6-27%). ROC-analysis showed that a combination of 4 genes (APAF1, BAX, BIM/BCL2L11, and DAPK1) and MIRG125bG1 gene constitute a highly efficient 5-marker system with 100% specificity and sensitivity of 94-96% at AUC=0.98-0.97, suitable also for patients with stage I and II breast cancer. Detection of methylation of at least one gene in this system in biopsy or postoperative material is sufficient to refer the sample to breast cancer.
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Affiliation(s)
- E A Braga
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia. .,N. P. Bochkov Research Center of Medical Genetics, Moscow, Russia.
| | - A M Burdennyy
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.,N. M. Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - I V Pronina
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia
| | - E A Filippova
- 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
| | - M V Fridman
- N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - D S Khodyrev
- Federal Research Clinical Center of Specialized Types of Medical Care and Medical Technologies of Federal Medical-Biological Agency of Russia, Moscow, Russia
| | - A V Karpukhin
- N. P. Bochkov Research Center of Medical Genetics, Moscow, Russia
| | - V I Loginov
- Research Institute of General Pathology and Pathophysiology, Moscow, Russia.,N. P. Bochkov Research Center of Medical Genetics, Moscow, Russia
| | - N E Kushlinskii
- N. N. Blokhin National Medical Research Center of Oncology, Ministry of Health of the Russian Federation, Moscow, Russia
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15
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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 (Mosk) 2019; 52:801-809. [PMID: 30363055 DOI: 10.1134/s0026898418050105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 09/14/2017] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- V I Loginov
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,Research Center of Medical Genetics, Moscow, 115478 Russia.,
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - E A Filippova
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - I V Pronina
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - T P Kazubskaya
- Blokhin Russian Cancer Research Center, Moscow, 115478 Russia
| | - D N Kushlinsky
- Blokhin Russian Cancer Research Center, Moscow, 115478 Russia
| | - V D Ermilova
- Blokhin Russian Cancer Research Center, Moscow, 115478 Russia
| | - S V Rykov
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Kurchatov Institute National Research Center, Moscow, 117545 Russia
| | - D S Khodyrev
- State Research Institute for Genetics and Selection of Industrial Microorganisms, Kurchatov Institute National Research Center, Moscow, 117545 Russia.,Federal Research Clinical Center of Specialized Types of Medical Care and Medical Technologies, Federal Biomedical Agency of Russia, Moscow, 115682 Russia
| | - E A Braga
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,Research Center of Medical Genetics, Moscow, 115478 Russia.,
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16
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Petunina NA, Martirosian NS, Trukhina LV, Saakyan SV, Panteleeva OG, Burdennyy AM, Nosikov VV. Association between polymorphic markers in candidate genes and the risk of manifestationof endocrine ophthalmopathy in patients with Graves' disease. TERAPEVT ARKH 2019; 90:35-39. [PMID: 30701793 DOI: 10.26442/terarkh2018901035-39] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
AIM To analyze the association between the polymorphic markers in CTLA4, TNF, IL10 and IL16 genes and the risk of manifestation of endocrine ophthalmopathy (EO) in patients with Graves' disease (GD). MATERIALS AND METHODS Case-control study included 248 patients with GD. Using polymerase chain reaction we studied the distribution of alleles and genotypes of polymorphic markers such as A60G (rs3087243) in CTLA4 gene, G(-308)A (rs1800629) in TNF gene, G(-1082)A (rs1800896) in IL10 gene, T3249C (rs4778641) in IL16 gene among 141 patients with Graves' disease and EO and 107 patients with GD without EO. RESULTS The frequencies of A alleles and the AA genotypes were significantly increased and the frequencies of G alleles and the GG genotype polymorphic markers rs3087243 of CTLA4 gene and rs1800896 of IL10 gene, as well as the GG genotype polymorphic marker rs1800629 of TNF gene were reduced in patients with GD and EO. The polymorphism in CTLA4 gene was also associated with the activity and the severity of EO. The comparative analysis of the allele and genotype frequency distribution of polymorphic markers of IL16 gene did not show the significant difference. CONCLUSION The risk of manifestation and the development of EO in patients with Graves' disease can be caused by not only environmental, but also genetic risk factors.
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Affiliation(s)
- N A Petunina
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - N S Martirosian
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - L V Trukhina
- I.M. Sechenov First Moscow State Medical University, Ministry of Health of Russia (Sechenov University), Moscow, Russia
| | - S V Saakyan
- Moscow Helmholtz Research Institute of Eye Diseases, Moscow, Russia
| | - O G Panteleeva
- Moscow Helmholtz Research Institute of Eye Diseases, Moscow, Russia
| | - A M Burdennyy
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - V V Nosikov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
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17
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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 (Mosk) 2019; 51:73-84. [PMID: 28251969 DOI: 10.7868/s0026898416060161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/23/2015] [Indexed: 11/23/2022]
Abstract
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 rs 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 (rs 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.
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Affiliation(s)
- I V Pronina
- Research Centre of Medical Genetics, Moscow, 115478 Russia.,Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,
| | - E A Klimov
- Biological Faculty, Moscow State University, Moscow, 119234 Russia
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334 Russia
| | - E V Beresneva
- State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, 117545 Russia
| | - M V Fridman
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 117971 Russia
| | - V D Ermilova
- Blokhin Cancer Research Center, Moscow, 115478 Russia
| | | | - A V Karpukhin
- Research Centre of Medical Genetics, Moscow, 115478 Russia
| | - E A Braga
- Research Centre of Medical Genetics, Moscow, 115478 Russia.,Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - V I Loginov
- Research Centre of Medical Genetics, Moscow, 115478 Russia.,Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,
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18
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Saakyan SV, Parmon YV, Tsygankov AY, Amiryan AG, Burdennyy AM. [Unilateral multifocal uveal melanoma (a clinical and genetic study)]. Vestn Oftalmol 2018; 134:78-85. [PMID: 30499543 DOI: 10.17116/oftalma201813405178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study presents clinical and genetic analysis of a case of unilateral multifocal uveal choroidal melanoma in a patient of 67 years. Results of ophthalmoscopy, echography, fluorescent angiography, optical coherence tomography are described. Molecular genetic testing of peripheral blood samples was performed, including detection of the occurrences of CC genotype in C3435T polymorphism of the gene ABCB1/MDR1 associated with unfavorable vital prognosis. Analysis of the genes GNAQ and GNA11 revealed two mutually exclusive mutations in the genes GNAQG183A and GNAQA209C showing genetic heterogeneity of the two tumor lesions. Organ preservation treatment of unilateral multifocal uveal melanoma was proven possible with brachytherapy method. Uveal melanoma with multicentric growth is of interest to ophthalmologists because it requires differential diagnostics from a variety of diseases including metastases in the choroid, such as metastases of uveal melanoma and skin melanoma, as well as other intraocular neoplasms.
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Affiliation(s)
- S V Saakyan
- Helmholtz Moscow Research Institute of Eye Diseases, 14/19 Sadovaya-Chernogryazskaya St., Moscow, Russian Federation, 105062; A.I. Yevdokimov Moscow State University of Medicine and Dentristy, 20/1 Delegatskaya St., Moscow, Russian Federation, 127473
| | - Ya V Parmon
- Helmholtz Moscow Research Institute of Eye Diseases, 14/19 Sadovaya-Chernogryazskaya St., Moscow, Russian Federation, 105062
| | - A Yu Tsygankov
- Helmholtz Moscow Research Institute of Eye Diseases, 14/19 Sadovaya-Chernogryazskaya St., Moscow, Russian Federation, 105062; A.I. Yevdokimov Moscow State University of Medicine and Dentristy, 20/1 Delegatskaya St., Moscow, Russian Federation, 127473
| | - A G Amiryan
- Helmholtz Moscow Research Institute of Eye Diseases, 14/19 Sadovaya-Chernogryazskaya St., Moscow, Russian Federation, 105062
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, 8 Baltiiskaya St., Moscow, Russian Federation, 125315
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Petunina NA, Martirosian NS, Trukhina LV, Saakyan SV, Panteleeva OG, Burdennyy AM, Nosikov VV. Association between polymorphic markers in candidate genes and the risk of manifestationof endocrine ophthalmopathy in patients with Graves’ disease. TERAPEVT ARKH 2018. [DOI: 10.26442/terarkh201890104-39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aim. To analyze the association between the polymorphic markers in CTLA4, TNF, IL10 and IL16 genes and the risk of manifestation of endocrine ophthalmopathy (EO) in patients with Graves’ disease (GD). Materials and methods. Case-control study included 248 patients with GD. Using polymerase chain reaction we studied the distribution of alleles and genotypes of polymorphic markers such as A60G (rs3087243) in CTLA4 gene, G(-308)A (rs1800629) in TNF gene, G(-1082)A (rs1800896) in IL10 gene, T3249C (rs4778641) in IL16 gene among 141 patients with Graves’ disease and EO and 107 patients with GD without EO. Results and discussion. The frequencies of A alleles and the AA genotypes were significantly increased and the frequencies of G alleles and the GG genotype polymorphic markers rs3087243 of CTLA4 gene and rs1800896 of IL10 gene, as well as the GG genotype polymorphic marker rs1800629 of TNF gene were reduced in patients with GD and EO. The polymorphism in CTLA4 gene was also associated with the activity and the severity of EO. The comparative analysis of the allele and genotype frequency distribution of polymorphic markers of IL16 gene did not show the significant difference. Conclusion. The risk of manifestation and the development of EO in patients with Graves’ disease can be caused by not only environmental, but also genetic risk factors.
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Loginov VI, Burdennyy AM, Pronina IV, Khokonova VV, Kurevljov SV, Kazubskaya TP, Kushlinskii NE, Braga EA. [Novel miRNA genes hypermethylated in breast cancer]. Mol Biol (Mosk) 2017; 50:797-802. [PMID: 27830681 DOI: 10.7868/s0026898416050104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 12/09/2015] [Indexed: 11/23/2022]
Abstract
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.
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Affiliation(s)
- V I Loginov
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,
| | - A M Burdennyy
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - I V Pronina
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - V V Khokonova
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - S V Kurevljov
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia
| | - T P Kazubskaya
- Blokhin Russian Cancer Research Center, Moscow, 115478 Russia
| | - N E Kushlinskii
- Blokhin Russian Cancer Research Center, Moscow, 115478 Russia
| | - E A Braga
- Institute of General Pathology and Pathophysiology, Moscow, 125315 Russia.,
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Pronina IV, Loginov VI, Burdennyy AM, Fridman MV, Senchenko VN, Kazubskaya TP, Kushlinskii NE, Dmitriev AA, Braga EA. DNA methylation contributes to deregulation of 12 cancer-associated microRNAs and breast cancer progression. Gene 2017; 604:1-8. [DOI: 10.1016/j.gene.2016.12.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/11/2016] [Accepted: 12/16/2016] [Indexed: 12/01/2022]
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