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Konoshenko M, Laktionov P, Bryzgunova O. Prostate cancer therapy outcome prediction: are miRNAs a suitable guide for therapeutic decisions? Andrology 2024; 12:705-718. [PMID: 37750354 DOI: 10.1111/andr.13535] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/04/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Radical prostatectomy, radiotherapy, chemotherapy, and androgen-deprivation therapy are among the most common treatment options for different forms of prostate cancer (PCa). However, making therapeutic decisions is difficult due to the lack of reliable prediction markers indicating therapy outcomes in clinical practice. The involvement of miRNAs in all mechanisms of the PCa development and their easy detection characterize them as attractive PCa biomarkers. Although there are extensive data on the role of miRNAs in PCa therapy resistance and sensitivity development, the issues of whether they could be used as a guide for therapy choice and, if so, how we can progress toward this goal, remain unclear. Thus, generalizable reviews and studies which summarize, compare, and analyze data on miRNA involvement in responses to different types of PCa therapies are required. OBJECTIVES Data on the involvement of miRNAs in therapy responses, on the role of cross-miRNA expression in different therapies, and on miRNA targets were analyzed in order to determine the miRNA-related factors which can lend perspective to the future development of personalized predictors of PCa sensitivity/resistance to therapies. MATERIALS AND METHODS The data available on the miRNAs associated with different PCa therapies (resistance and sensitivity therapies) are summarized and analyzed in this study, including analyses using bioinformatics resources. Special attention was dedicated to the mechanisms of the development of therapy resistance. RESULTS AND DISCUSSION A comprehensive combined analysis of the current data revealed a panel of miRNAs that were shown to be most closely associated with the PCa therapy response and were found to regulate the genes involved in PCa development via cell proliferation regulation, epithelial-mesenchymal transition (EMT), apoptosis, cell-cycle progression, angiogenesis, metastasis and invasion regulation, androgen-independent development, and colony formation. CONCLUSION The selected miRNA-based panel has the potential to be a guide for therapeutic decision making in the effective treatment of PCa.
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Affiliation(s)
- MariaYu Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Chernonosova V, Khlebnikova M, Popova V, Starostina E, Kiseleva E, Chelobanov B, Kvon R, Dmitrienko E, Laktionov P. Electrospun Scaffolds Enriched with Nanoparticle-Associated DNA: General Properties, DNA Release and Cell Transfection. Polymers (Basel) 2023; 15:3202. [PMID: 37571096 PMCID: PMC10421399 DOI: 10.3390/polym15153202] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Biomaterial-mediated, spatially localized gene delivery is important for the development of cell-populated scaffolds used in tissue engineering. Cells adhering to or penetrating into such a scaffold are to be transfected with a preloaded gene that induces the production of secreted proteins or cell reprogramming. In the present study, we produced silica nanoparticles-associated pDNA and electrospun scaffolds loaded with such nanoparticles, and studied the release of pDNA from scaffolds and cell-to-scaffold interactions in terms of cell viability and pDNA transfection efficacy. The pDNA-coated nanoparticles were characterized with dynamic light scattering and transmission electron microscopy. Particle sizes ranging from 56 to 78 nm were indicative of their potential for cell transfection. The scaffolds were characterized using scanning electron microscopy, X-ray photoelectron spectroscopy, stress-loading tests and interaction with HEK293T cells. It was found that the properties of materials and the pDNA released vary, depending on the scaffold's composition. The scaffolds loaded with pDNA-nanoparticles do not have a pronounced cytotoxic effect, and can be recommended for cell transfection. It was found that (pDNA-NPs) + PEI9-loaded scaffold demonstrates good potential for cell transfection. Thus, electrospun scaffolds suitable for the transfection of inhabiting cells are eligible for use in tissue engineering.
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Affiliation(s)
- Vera Chernonosova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (V.P.); (B.C.); (E.D.)
| | - Marianna Khlebnikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (V.P.); (B.C.); (E.D.)
| | - Victoriya Popova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (V.P.); (B.C.); (E.D.)
| | - Ekaterina Starostina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia;
| | - Elena Kiseleva
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Boris Chelobanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (V.P.); (B.C.); (E.D.)
| | - Ren Kvon
- Boreskov Institute of Catalysis, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Elena Dmitrienko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (V.P.); (B.C.); (E.D.)
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (V.P.); (B.C.); (E.D.)
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Bryzgunova O, Bondar A, Ruzankin P, Tarasenko A, Zaripov M, Kabilov M, Laktionov P. Locus-Specific Bisulfate NGS Sequencing of GSTP1, RNF219, and KIAA1539 Genes in the Total Pool of Cell-Free and Cell-Surface-Bound DNA in Prostate Cancer: A Novel Approach for Prostate Cancer Diagnostics. Cancers (Basel) 2023; 15:cancers15020431. [PMID: 36672380 PMCID: PMC9856824 DOI: 10.3390/cancers15020431] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539, also known as FAM214B) in the total pool of blood cell-free DNA, including cell-free DNA from plasma and cell-surface-bound DNA, of patients with prostate cancer and healthy donors was studied on the MiSeq platform. Our study found a higher methylation index of loci for total cell-free DNA compared with cell-free DNA. For total cell-free DNA, the methylation of GSTP1 in each of the 11 positions provided a complete separation of cancer patients from healthy donors, whereas for cell-free DNA, there were no positions in the three genes allowing for such separation. Among the prostate cancer patients, the minimum proportion of GSTP1 genes methylated in any of the 17 positions was 12.1% of the total circulated DNA fragments, and the minimum proportion of GSTP1 genes methylated in any of the 11 diagnostically specific positions was 8.4%. Total cell-free DNA was shown to be more convenient and informative as a source of methylated DNA molecules circulating in the blood than cell-free DNA.
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Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-51-44; Fax: +7-383-363-51-53
| | - Anna Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Ruzankin
- Sobolev Institute of Mathematics, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton Tarasenko
- Sobolev Institute of Mathematics, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marat Zaripov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Tamkovich S, Tupikin A, Kozyakov A, Laktionov P. Size and Methylation Index of Cell-Free and Cell-Surface-Bound DNA in Blood of Breast Cancer Patients in the Contest of Liquid Biopsy. Int J Mol Sci 2022; 23:ijms23168919. [PMID: 36012175 PMCID: PMC9408721 DOI: 10.3390/ijms23168919] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/15/2022] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
Aberrantly methylated circulating DNA (cirDNA) has proven to be a good cancer marker, but its detection is limited by low concentrations, fragmentation, and insufficiency. Since the methylated cirDNA was shown to be more stable in circulation than the unmethylated one and was shown to bind with the blood cell surface, we studied the concentration, representation, and fragmentation of tumor-derived methylated DNA in cell-free and cell-surface-associated DNA. We found that long DNA fragments (more than 10 kb) are mainly associated with the surface of blood cells. However, in plasma short DNA fragments (100–1000 bp) were also found along with long DNA fragments. Isolation of short fragments after separation of cirDNA in 6% PAGE followed by quantitative PCR (L1 element) has shown that short DNA fragments in healthy females represent 22% versus 0.5–4.4% in breast cancer patients. The methylated form of the RARβ2 gene was detected only in long DNA fragments by Real-time TaqMan PCR of bisulfite-converted DNA. The methylation index of cirDNA from healthy women was estimated at 0%, 9%, and 7% in plasma, PBS-EDTA, and trypsin eluates from the surface of blood cells, respectively. The methylation index of breast cancer patients’ DNA was found to be 33%, 15%, and 61% in the same fractions confirming the overrepresentation of methylated DNA in csbDNA.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
- Department of Clinical Biochemistry, V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, Novosibirsk 630090, Russia
- Correspondence:
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Anton Kozyakov
- Department of Mammology, Novosibirsk Regional Clinical Oncological Dispensary, Novosibirsk 630108, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
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Konoshenko M, Lansukhay Y, Krasilnikov S, Laktionov P. MicroRNAs as Predictors of Lung-Cancer Resistance and Sensitivity to Cisplatin. Int J Mol Sci 2022; 23:ijms23147594. [PMID: 35886942 PMCID: PMC9321818 DOI: 10.3390/ijms23147594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Platinum-based chemotherapy, cisplatin (DDP) specifically, is the main strategy for treating lung cancer (LC). However, currently, there is a lack of predictive drug-resistance markers, and there is increased interest in the development of a reliable and sensitive panels of markers for DDP chemotherapy-effectiveness prediction. MicroRNAs represent a perspective pool of markers for chemotherapy effectiveness. Objectives: Data on miRNAs associated with LC DDP chemotherapy response are summarized and analyzed. Materials and methods: A comprehensive review of the data in the literature and an analysis of bioinformatics resources were performed. The gene targets of miRNAs, as well as their reciprocal relationships with miRNAs, were studied using several databases. Results and Discussion: The complex analysis of bioinformatics resources and the literature indicated that the expressions of 12 miRNAs have a high predictive potential for LC DDP chemotherapy responses. The obtained information was discussed from the point of view of the main mechanisms of LC chemoresistance. Conclusions: An overview of the published data and bioinformatics resources, with respect to the predictive microRNA markers of chemotherapy response, is presented in this review. The selected microRNAs and gene panel have a high potential for predicting LC DDP sensitiveness or DDP resistance as well as for the development of a DDP co-therapy.
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Affiliation(s)
- Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia; (Y.L.); (S.K.)
- Correspondence:
| | - Yuriy Lansukhay
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia; (Y.L.); (S.K.)
| | - Sergey Krasilnikov
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia; (Y.L.); (S.K.)
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia;
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia; (Y.L.); (S.K.)
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Zakharova I, Saaya S, Shevchenko A, Stupnikova A, Zhiven' M, Laktionov P, Stepanova A, Romashchenko A, Yanshole L, Chernonosov A, Volkov A, Kizilova E, Zavjalov E, Chernyavsky A, Romanov A, Karpenko A, Zakian S. Mitomycin-Treated Endothelial and Smooth Muscle Cells Suitable for Safe Tissue Engineering Approaches. Front Bioeng Biotechnol 2022; 10:772981. [PMID: 35360387 PMCID: PMC8963790 DOI: 10.3389/fbioe.2022.772981] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/04/2022] [Indexed: 11/13/2022] Open
Abstract
In our previous study, we showed that discarded cardiac tissue from the right atrial appendage and right ventricular myocardium is an available source of functional endothelial and smooth muscle cells for regenerative medicine and tissue engineering. In the study, we aimed to find out what benefits are given by vascular cells from cardiac explants used for seeding on vascular patches engrafted to repair vascular defects in vivo. Additionally, to make the application of these cells safer in regenerative medicine we tested an in vitro approach that arrested mitotic division to avoid the potential tumorigenic effect of dividing cells. A tissue-engineered construction in the form of a patch based on a polycaprolactone-gelatin scaffold and seeded with endothelial and smooth muscle cells was implanted into the abdominal aorta of immunodeficient SCID mice. Aortic patency was assessed using ultrasound, MRI, immunohistochemical and histological staining. Endothelial and smooth muscle cells were treated with mitomycin C at a therapeutic concentration of 10 μg/ml for 2 h with subsequent analysis of cell proliferation and function. The absence of the tumorigenic effect of mitomycin C-treated cells, as well as their angiogenic potential, was examined by injecting them into immunodeficient mice. Cell-containing patches engrafted in the abdominal aorta of immunodeficient mice form the vessel wall loaded with the appropriate cells and extracellular matrix, and do not interfere with normal patency. Endothelial and smooth muscle cells treated with mitomycin C show no tumorigenic effect in the SCID immunodeficient mouse model. During in vitro experiments, we have shown that treatment with mitomycin C does not lead to a decrease in cell viability. Despite the absence of proliferation, mitomycin C-treated vascular cells retain specific cell markers, produce specific extracellular matrix, and demonstrate the ability to stimulate angiogenesis in vivo. We pioneered an approach to arresting cell division with mitomycin C in endothelial and smooth muscle cells from cardiac explant, which prevents the risk of malignancy from dividing cells in vascular surgery. We believe that this approach to the fabrication of tissue-engineered constructs based on mitotically inactivated cells from waste postoperative material may be valuable to bring closer the development of safe cell products for regenerative medicine.
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Affiliation(s)
- Irina Zakharova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- *Correspondence: Irina Zakharova,
| | - Shoraan Saaya
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Alexander Shevchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alena Stupnikova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Deparment of Natural Science, Novosibirsk State University, Novosibirsk, Russia
| | - Maria Zhiven'
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel Laktionov
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alena Stepanova
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Romashchenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lyudmila Yanshole
- International Tomography Center,The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Volkov
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Elena Kizilova
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Deparment of Natural Science, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii Zavjalov
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Chernyavsky
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Alexander Romanov
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Andrey Karpenko
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
| | - Suren Zakian
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- E.N. Meshalkin National Medical Research Center, Ministry of Health of the Russian Federation, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Konoshenko M, Laktionov P. The miRNAs involved in prostate cancer chemotherapy response as chemoresistance and chemosensitivity predictors. Andrology 2021; 10:51-71. [PMID: 34333834 DOI: 10.1111/andr.13086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/09/2021] [Accepted: 07/30/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Reliable molecular markers that allow the rational prescription of an effective chemotherapy type for each prostate cancer patient are still needed. Since microRNAs expression is associated with the response to different types of prostate cancer therapy, microRNAs represent a pool of perspective markers of therapy effectiveness comprising chemotherapy. OBJECTIVES The available data on microRNAs associated with chemotherapy response (resistance and sensitivity) are summarized and analyzed in the article. MATERIALS AND METHODS A review of the published data, as well as their analysis by current bioinformatics resources, was conducted. The molecular targets of microRNAs, as well as the reciprocal relationships between the microRNAs and their targets, were studied using the DIANA, STRING, and TransmiR databases. Special attention was dedicated to the mechanisms of prostate cancer chemoresistance development. RESULTS AND DISCUSSION The combined analysis of bioinformatics resources and the available literature indicated that the expression of eight microRNAs that are associated with different responses to chemotherapy have a high potential for the prediction of the prostate cancer chemotherapy response, as found in the experiments and confirmed by the functions of regulated genes. CONCLUSION An overview on the published data and bioinformatics resources, with respect to predictive microRNA markers of chemotherapy response, is presented in this review. The selected microRNA and gene panel has a high potential for predicting the chemosensitivity or chemoresistance of prostate cancer and could represent a set of markers for subsequent study using samples of cell-free microRNAs from different patient groups.
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Affiliation(s)
- Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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Bryzgunova O, Konoshenko M, Zaporozhchenko I, Yakovlev A, Laktionov P. Isolation of Cell-Free miRNA from Biological Fluids: Influencing Factors and Methods. Diagnostics (Basel) 2021; 11:865. [PMID: 34064927 PMCID: PMC8151063 DOI: 10.3390/diagnostics11050865] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/29/2021] [Accepted: 05/04/2021] [Indexed: 12/11/2022] Open
Abstract
A vast wealth of recent research has seen attempts of using microRNA (miRNA) found in biological fluids in clinical research and medicine. One of the reasons behind this trend is the apparent their high stability of cell-free miRNA conferred by small size and packaging in supramolecular complexes. However, researchers in both basic and clinical settings often face the problem of selecting adequate methods to extract appropriate quality miRNA preparations for use in specific downstream analysis pipelines. This review outlines the variety of different methods of miRNA isolation from biofluids and examines the key determinants of their efficiency, including, but not limited to, the structural properties of miRNA and factors defining their stability in the extracellular environment.
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Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Maria Konoshenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Ivan Zaporozhchenko
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark;
| | - Alexey Yakovlev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.K.); (A.Y.); (P.L.)
- Meshalkin Siberian Federal Biomedical Research Center, Ministry of Public Health of the Russian Federation, 630055 Novosibirsk, Russia
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Tamkovich S, Tutanov O, Efimenko A, Grigor'eva A, Ryabchikova E, Kirushina N, Vlassov V, Tkachuk V, Laktionov P. Blood Circulating Exosomes Contain Distinguishable Fractions of Free and Cell-Surface-Associated Vesicles. Curr Mol Med 2020; 19:273-285. [PMID: 30868953 DOI: 10.2174/1566524019666190314120532] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [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: 12/03/2018] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Considering exosomes as intercellular transporters, inevitably interacting with the plasma membrane and the large available surface of blood cells, we wonder if a fraction of circulating exosomes is associated with the surface of blood cells. OBJECTIVE The aim of this study was to develop an efficient protocol for isolating exosomes associated with the surface of blood cells and to further investigate the characteristics of this fraction in a healthy state and during the development of breast cancer, as well as its possible implication for use in diagnostic applications. METHODS Blood samples were collected from Healthy Females (HFs) and breast cancer patients (BCPs). Exosomes extracted from blood plasma and eluted from the surface of blood cells were isolated by ultrafiltration with subsequent ultracentrifugation. RESULTS Transmission Electron Microscopy (TEM), along with immunogold labeling, demonstrated the presence of exosomes among membrane-wrapped extracellular vesicles (EVs) isolated from both plasma and blood cell eluates. TEM, nanoparticle tracking analysis, and NanoOrange protein quantitation data showed that cell-associated exosomes constituted no less than 2/3 of total blood exosome number. Exosomes, ranging from 50-70 nm in size, prevailed in the blood of breast cancer patients, whereas smaller exosomes (30-50 nm) were mostly observed in the blood of healthy women. Analysis of specific proteins and RNAs in exosomes circulating in blood demonstrated the significant differences in the packing density of the polymers in exosomes of HFs and BCPs. Preliminary data indicated that detection of cancer-specific miRNA (miR-103, miR-191, miR-195) in exosomes associated with the fraction of red blood cells allowed to discriminate HFs and BCPs more precisely compared to cell-free exosomes circulating in plasma. CONCLUSION Our data provide the basis for using blood cell-associated exosomes for diagnostic applications.
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Affiliation(s)
- Svetlana Tamkovich
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation.,Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Oleg Tutanov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation
| | - Anastasia Efimenko
- Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alina Grigor'eva
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation
| | - Elena Ryabchikova
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Natalia Kirushina
- Department of Mammology, National Novosibirsk Regional Oncologic Dispensary, Novosibirsk, Russian Federation
| | - Valentin Vlassov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Vsevolod Tkachuk
- Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Pavel Laktionov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Novosibirsk Research Institute of Circulation Pathology of Academician E.N. Meshalkin, Novosibirsk, Russian Federation
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10
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Novikova O, Cherepanova A, Nazarkina Z, Laktionov P, Karpenko A, Laktionov P. Isolation And Culture Of Carotid Atherosclerotic Plaque Inner Mass Cells. Atherosclerosis 2019. [DOI: 10.1016/j.atherosclerosis.2019.06.833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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11
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Tamkovich S, Laktionov P. Cell-surface-bound circulating DNA in the blood: Biology and clinical application. IUBMB Life 2019; 71:1201-1210. [PMID: 31091350 DOI: 10.1002/iub.2070] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 01/22/2019] [Accepted: 04/17/2019] [Indexed: 01/04/2023]
Abstract
Cell-surface-bound extracellular DNA (csbDNA) is present on the outer membrane of blood cells, including both red blood cells and leukocytes. Although less well characterized than cell-free DNA (cfDNA) in plasma and serum, leukocyte and red blood cell csbDNA form a considerable fraction of the blood extracellular nucleic acids pool, with typically at least comparable amount of DNA occurring bound to the outer surface of cells as compared with circulating free DNA in plasma. The cellular origin of csbDNA is not clear; however, as with cfDNA, in patients with cancer a proportion is derived from the tumor, thus making it potentially a useful source of DNA for cancer diagnosis, prognosis, and monitoring. © 2019 IUBMB Life, 71(9):1201-1210, 2019.
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Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk National Research State University, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia.,Meshalkin Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
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12
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Zaporozhchenko I, Morozkin E, Ponomaryova A, Rykova E, Cherdyntseva N, Vlassov V, Laktionov P. Two-step microarray analysis of cell-free miRNA in plasma of lung cancer patients. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx361.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Rykova E, Sizikov A, Roggenbuck D, Antonenko O, Bryzgalov L, Morozkin E, Skvortsova K, Vlassov V, Laktionov P, Kozlov V. Circulating DNA in rheumatoid arthritis: pathological changes and association with clinically used serological markers. Arthritis Res Ther 2017; 19:85. [PMID: 28464939 PMCID: PMC5414163 DOI: 10.1186/s13075-017-1295-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 04/07/2017] [Indexed: 12/15/2022] Open
Abstract
Background Early diagnosis of rheumatoid arthritis (RA) is crucial to providing effective therapy and often hampered by unspecific clinical manifestations. Elevated levels of extracellular circulating DNA (cirDNA) in patients with autoimmune disease were found to be associated with etiopathogenesis. To our knowledge, this is the first study to investigate the putative diagnostic use of cirDNA in RA and its association with disease activity. Methods Blood samples were taken from 63 healthy subjects (HS) and 74 patients with RA. cirDNA was extracted from plasma and cell surface-bound cirDNA fractions (csbDNA). cirDNA concentration was measured by quantitative real-time polymerase chain reaction. Rheumatoid factor was analyzed by immunonephelometry, whereas C-reactive protein and anticitrullinated protein/peptide antibodies (ACPA) were detected by enzyme-linked immunosorbent assay. Results Plasma cirDNA was significantly elevated in patients with RA compared with HS (12.0 versus 8.4 ng/ml, p < 0.01). In contrast, nuclear csbDNA (n-csbDNA) was significantly decreased (24.0 versus 50.8 ng/ml, p < 0.01), whereas mitochondrial csbDNA (m-csbDNA) was elevated (1.44 × 106 copies/ml versus 0.58 × 106 copies/ml, p < 0.05) in RA. The combination of csbDNA (mitochondrial + nuclear) with ACPA reveals the best positive/negative likelihood ratios (LRs) for the discrimination RA from HS (LR+ 61.00, LR− 0.03) in contrast to ACPA (LR+ 9.00, LR− 0.19) or csbDNA (LR+ 8.00, LR− 0.18) alone. Conclusions Nuclear and mitochondrial cirDNA levels in plasma and on the surface of blood cells are modulated in RA. Combination of cirDNA values with ACPA can improve the serological diagnosis of RA. Electronic supplementary material The online version of this article (doi:10.1186/s13075-017-1295-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Rykova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Novosibirsk State Technical University, Novosibirsk, Russia
| | - Aleksey Sizikov
- Federal State Budgetary Scientific Institution "Research Institute of Fundamental and Clinical Immunology", Novosibirsk, Russia
| | - Dirk Roggenbuck
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Oksana Antonenko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.
| | | | - Evgeniy Morozkin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Academician E. N. Meshalkin, Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
| | - Kseniya Skvortsova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.,Academician E. N. Meshalkin, Novosibirsk Research Institute of Circulation Pathology, Novosibirsk, Russia
| | - Vladimir Kozlov
- Federal State Budgetary Scientific Institution "Research Institute of Fundamental and Clinical Immunology", Novosibirsk, Russia
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14
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Tutanov O, Tamkovich S, Grigoryeva A, Ryabchikova E, Duzhak T, Tsentalovich Y, Laktionov P, Vlassov V. 1PD Breast cancer blood-derived exosomes: Characterisation of protein composition in search for new biomarkers. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Tutanov O, Tamkovich S, Duzhak T, Tsentalovich Y, Laktionov P. Blood-circulating nucleoprotein complexes: DNA and protein content in healthy donors and breast cancer patients. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61542-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Bryzgunova O, Lekhnov E, Skvortsova T, Morozkin E, Zaporozhchenko I, Grigorieva A, Zaripov M, Ryabchikova E, Vlassov V, Laktionov P. P67. European Journal of Cancer Supplements 2015. [DOI: 10.1016/j.ejcsup.2015.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Cherepanova A, Vlassov V, Laktionov P. P133. EJC Suppl 2015. [DOI: 10.1016/j.ejcsup.2015.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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18
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Ponomaryova A, Rykova E, Cherdyntseva N, Morozkin E, Zaporozhchenko I, Skvortsova T, Dobrodeev A, Zav’yalov A, Tuzikov S, Vlassov V, Laktionov P. P90. EJC Suppl 2015. [DOI: 10.1016/j.ejcsup.2015.08.077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Zaporozhchenko I, Morozkin E, Skvortsova T, Rykova E, Ponomareva A, Cherdyntseva N, Polovnikov E, Anikeeva O, Pashkovskaya O, Vlassov V, Laktionov P. P34. European Journal of Cancer Supplements 2015. [DOI: 10.1016/j.ejcsup.2015.08.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Morozkin E, Rykova E, Bondar A, Skvortsova T, Zaporozhchenko I, Kurilshikov A, Anikeeva O, Krasnova N, Polovnikov E, Ponomaryova A, Laktionov P. P124. European Journal of Cancer Supplements 2015. [DOI: 10.1016/j.ejcsup.2015.08.067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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21
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Tamkovich S, Bondar A, Morozov I, Kirushina N, Permyakova V, Voitsitskiy V, Laktionov P. P39a. EJC Suppl 2015. [DOI: 10.1016/j.ejcsup.2015.08.107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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22
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Bondar A, Kurilshikov A, Morozkin E, Zaripov M, Kabilov M, Voytsitskiy V, Vlassov V, Laktionov P. P124. EJC Suppl 2015. [DOI: 10.1016/j.ejcsup.2015.08.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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23
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Zaporozhchenko I, Morozkin E, Skvortsova T, Rykova E, Ponomareva A, Cherdyntseva N, Vlassov V, Laktionov P. 429 Plasma microRNAs as noninvasive biomarkers for lung cancer. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)30263-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Bondar A, Kurilshikov A, Morozkin E, Zaripov M, Kabilov M, Voytsitskiy V, Vlassov V, Laktionov P. 430 Epigenetic cell-free DNA biomarkers of prostate cancer: The search by massively parallel sequencing. Eur J Cancer 2015. [DOI: 10.1016/s0959-8049(16)30264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Rykova E, Sizikov A, Antonenko O, Skvortsova K, Morozkin E, Vlassov V, Laktionov P, Kozlov V. FRI0491 Circulating dna changes in rheumatoid arthritis patients blood. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.1618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Ponomaryova A, Rykova E, Cherdyntseva N, Dobrodeev A, Skvortsova T, Zav'yalov A, Tuzikov S, Vlassov V, Laktionov P. 14 CIRCULATING DNA IN LUNG CANCER: EPIGENETIC MARKERS FOR DIAGNOSTICS AND POST-TREATMENT FOLLOW-UP. Lung Cancer 2013. [DOI: 10.1016/s0169-5002(13)70235-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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27
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Cortese R, Kwan A, Lalonde E, Bryzgunova O, Bondar A, Wu Y, Gordevicius J, Park M, Oh G, Kaminsky Z, Tverkuviene J, Laurinavicius A, Jankevicius F, Sendorek DHS, Haider S, Wang SC, Jarmalaite S, Laktionov P, Boutros PC, Petronis A. Epigenetic markers of prostate cancer in plasma circulating DNA. Hum Mol Genet 2012; 21:3619-31. [PMID: 22619380 DOI: 10.1093/hmg/dds192] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Epigenetic differences are a common feature of many diseases, including cancer, and disease-associated changes have even been detected in bodily fluids. DNA modification studies in circulating DNA (cirDNA) may lead to the development of specific non-invasive biomarkers. To test this hypothesis, we investigated cirDNA modifications in prostate cancer patients with locally confined disease (n = 19), in patients with benign prostate hyperplasias (n = 20) and in men without any known prostate disease (n = 20). This initial discovery screen identified 39 disease-associated changes in cirDNA modification, and seven of these were validated using the sodium bisulfite-based mapping of modified cytosines in both the discovery cohort and an independent 38-patient validation cohort. In particular, we showed that the DNA modification of regions adjacent to the gene encoding ring finger protein 219 distinguished prostate cancer from benign hyperplasias with good sensitivity (61%) and specificity (71%). We also showed that repetitive sequences detected in this study were meaningful, as they indicated a highly statistically significant loss of DNA at the pericentromeric region of chromosome 10 in prostate cancer patients (p = 1.8 × 10(-6)). Based on these strong univariate results, we applied machine-learning techniques to develop a multi-locus biomarker that correctly distinguished prostate cancer samples from unaffected controls with 72% accuracy. Lastly, we used systems biology techniques to integrate our data with publicly available DNA modification and transcriptomic data from primary prostate tumors, thereby prioritizing genes for further studies. These data suggest that cirDNA epigenomics are promising source for non-invasive biomarkers.
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Affiliation(s)
- Rene Cortese
- The Krembil Family Epigenetics Laboratory, Centre for Addiction and Mental Health, Toronto, ON, Canada M5T 1R8
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28
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Baranov K, Volkova O, Chikaev N, Mechetina L, Laktionov P, Najakshin A, Taranin A. A direct antigen-binding assay for detection of antibodies against native epitopes using alkaline phosphatase-tagged proteins. J Immunol Methods 2008; 332:73-81. [DOI: 10.1016/j.jim.2007.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 12/13/2007] [Accepted: 12/19/2007] [Indexed: 11/15/2022]
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29
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Cherepanova A, Tamkovich S, Pyshnyi D, Kharkova M, Vlassov V, Laktionov P. Immunochemical assay for deoxyribonuclease activity in body fluids. J Immunol Methods 2007; 325:96-103. [PMID: 17618645 DOI: 10.1016/j.jim.2007.06.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 05/17/2007] [Accepted: 06/10/2007] [Indexed: 10/23/2022]
Abstract
We have developed two microtiter plate assays to quantify the deoxyribonuclease activity in biological fluids. Both assays are based on hydrolysis of biotinylated and fluorescein-labeled DNA substrates, with subsequent immunochemical detection of non-digested DNA. The assay based on hydrolysis of 974 bp PCR product labeled with biotinylated forward and fluorescein-labeled reverse primers is more sensitive (0.05 U/ml) and convenient for quantifying the DNase activity in biological fluids than the assay based on hydrolysis of double-labeled 20 bp oligonucleotide. The DNase activity in urine and blood plasma of healthy donors was measured using the PCR product-based assay. Urine samples revealed greater activity, 1.49+/-1.41 U/ml; blood plasma DNase I-like activity was 0.36+/-0.20 U/ml. DNase II-like activity was not detected in the plasma samples. The data obtained confirm that DNase I-like enzymes are responsible for the majority of deoxyribonuclease activity in blood plasma.
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Affiliation(s)
- Anna Cherepanova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, 8, Lavrentiev Ave., Novosibirsk, 630090, Russia
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30
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Laktionov P, Rykova E, Toni M, Spisni E, Griffoni C, Bryksin A, Volodko N, Vlassov V, Tomasi V. Knock down of cytosolic phospholipase A2: an antisense oligonucleotide having a nuclear localization binds a C-terminal motif of glyceraldehyde-3-phosphate dehydrogenase. Biochim Biophys Acta Mol Cell Biol Lipids 2004; 1636:129-35. [PMID: 15164760 DOI: 10.1016/j.bbalip.2003.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2003] [Revised: 07/16/2003] [Accepted: 10/21/2003] [Indexed: 11/28/2022]
Abstract
We have previously shown that an antisense, effective in the knock down of cytosolic phospholipase A2 (cPLA2), localizes mainly in the nucleus of human endothelial cells and monocytes and that glyceraldehyde-3-phosphate dehydrogenase (GAPDH) is involved in its nuclear localization. In this study, we clarify how GAPDH participates in the nuclear localization of this antisense oligodeoxynucleotide (ODN) directed against cPLA2 mRNA. A central TAAAT motif providing specificity and high affinity binding was assumed to interact with the enzyme Rossmann fold region on the basis of competition to this site by NAD+. To asses whether the TAAAT motif interacts directly with the enzyme Rossmann fold region, we evaluated the binding to GAPDH of different oligonucleotides and the effect of competitors such as NAD+, NADH, mononucleotides, DNA, polyribonucleic acids and polyanions. We found that the dissociation constant for TAAAT containing oligonucleotides was three--to fivefold higher with respect to oligo not containing this motif. By covalently linking 32P-labeled cPLA2p(N)16 to GAPDH and after executing hydrolysis with hydroxylamine, the labeling was exclusively found in the C-terminal domain (aa 286-334). These results indicate that the antisense oligonucleotide interacts with a site not having a defined function but which can be negatively allosterically regulated when NAD+ or polynucleotides are bound to Rossmann fold.
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Affiliation(s)
- Pavel Laktionov
- Institute of Bioorganic Chemistry, Academy of Sciences Siberian Division, Novosibirsk, Russia
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31
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Laktionov P, Chelobanov B, Rykova E, Vlassov V. Interaction of oligonucleotides with cellular proteins. Nucleosides Nucleotides Nucleic Acids 2001; 20:859-62. [PMID: 11563132 DOI: 10.1081/ncn-100002446] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Oligonucleotides (ODNs) conjugated to 4-[(N-2-chloroethyl-N-methyl)amino] benzylamine were used to investigate ODN-binding proteins in cells of different origin. The data obtained demonstrate that 68, 46, 38 and 28 kDa ODN-binding proteins are universal for tested cell lines.
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Affiliation(s)
- P Laktionov
- Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, pr. Lavrentieva 8, Novosibirsk 630090, Russia
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32
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Tosquellas G, Bryksin A, Alvarez K, Morvan F, Vasseur JJ, Rayner B, Rykova E, Laktionov P, Vlassov V, Imbach JL. Prooligonucleotides exhibit less serum-protein binding than phosphodiester and phosphorothioate oligonucleotides. Nucleosides Nucleotides Nucleic Acids 2000; 19:995-1003. [PMID: 10893717 DOI: 10.1080/15257770008033038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The protein-binding properties of dodecathymidine derivatives (prooligos) bearing either methyl- or tert-butyl-S-acylthioethyl (Me- or tBuSATE) protecting groups were evaluated. The dissociation constants (Kd) were estimated for complexes of prooligos with serum blood proteins and lactoferrin using prooligos to compete the binding of the radiolabeled, alkylating probe oligonucleotide CIRp(T)12 with the proteins. tBuSATE and MeSATE prooligos have decreased affinity of binding with serum proteins and lactoferrin compared with their parent oligos. These data suggest that prooligos should cause less side effects which combined with their stability to nucleases and enhanced permeability into cells make them potentially useful for design of therapeutics.
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Affiliation(s)
- G Tosquellas
- Laboratoire de Chimie Organique Biomoléculaire de Synthèse, Université de Montpellier II, France
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Abstract
Oligonucleotides (ODNs) conjugated to rhodamin (Rh) and 4-[(N-2-chloroethyl-N-methyl)amino] benzylamine were used to investigate ODNs transport into keratinocytes. Affinity labeling of two proteins, 63 and 35 kDa, and the inhibition of the affinity labeling and ODNs uptake by the cells in the presence of nucleic acids, polyanions and trypsin suggest, that the proteins are involved in transport of nucleic acids in keratinocytes.
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Affiliation(s)
- P Laktionov
- Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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34
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Abstract
It was shown that plasmid pUC19 DNA stimulates in vitro proliferation of CBA mouse splenocytes in a dose-dependent manner. Stimulation effect of the plasmid DNA is additive with COn A or LPS, synergistic with PMA and is inhibited by nonimmunogenic phosphodiester oligonucleotides and Fab fragments of antimouse Ig antibodies. These data and the data of affinity labelling of ODN-binding proteins indicate that immunoglobulin receptors are involved in DNA-induced lymphocyte activation.
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Affiliation(s)
- E Rykova
- Institute of Bioorganic Chemistry, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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35
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Vlassov V, Yakubov L, Nechaeva M, Pautova L, Rykova E, Laktionov P, Vlassova I, Balakireva L. Molecular Interactions of Oligonucleotides in Organism - A Source of Broad Spectrum of Biological Activities. PHOSPHORUS SULFUR 1996. [DOI: 10.1080/10426509608054707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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