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Article ; Online: Concentration of cell-free DNA in different tumor types.

Bryzgunova, O E / Konoshenko, M Yu / Laktionov, P P

2020 Volume 21, Issue 1, Page(s) 63–75

Abstract: ... ...

Abstract	Introduction
MeSH term(s)	Cell-Free Nucleic Acids/blood ; Cell-Free Nucleic Acids/genetics ; DNA/blood ; DNA/genetics ; Humans ; Neoplasms/blood ; Neoplasms/classification ; Neoplasms/diagnosis ; Neoplasms/genetics
Chemical Substances	Cell-Free Nucleic Acids ; DNA (9007-49-2)
Language	English
Publishing date	2020-12-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2112530-2
ISSN	1744-8352 ; 1473-7159
ISSN (online)	1744-8352
ISSN	1473-7159
DOI	10.1080/14737159.2020.1860021
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Article: [Current methods of extracellular DNA methylation analysis].

Bryzgunova, O E / Laktionov, P P

Molekuliarnaia biologiia

2017 Volume 51, Issue 2, Page(s) 195–214

Abstract: The discovery of the enormous role methylated cytosine plays in regulating gene expression has led to the development of a variety of techniques for detecting cytosine modification. A majority of these techniques are geared towards analyzing genomic DNA, ...

Abstract	The discovery of the enormous role methylated cytosine plays in regulating gene expression has led to the development of a variety of techniques for detecting cytosine modification. A majority of these techniques are geared towards analyzing genomic DNA, which is typically available in large quantities. The concentration of cell-free DNAs (cfDNA) extracted from biological fluids including plasma, saliva, tears, or urine is relatively low and their degree of the fragmentation is high. Moreover, for noninvasive diagnostics of cancer, methylation patterns must be studied in minor cancer-specific fractions of DNA molecules substantially diluted by excess unmethylated molecules. The above limitations complicate the application of traditional techniques for cfDNA methylation analysis. In this manuscript, we review the state-of-art analysis of cfDNA methylation, hydroxymethylation, and noncanonical methylation (outside of CpG islands). The review covers methodological approaches to studying individual CpGs and genomic loci, as well as techniques for the large-scale analysis of methylation.
MeSH term(s)	Animals ; DNA Methylation ; Humans ; Oligonucleotide Array Sequence Analysis/instrumentation ; Oligonucleotide Array Sequence Analysis/methods ; Polymerase Chain Reaction/instrumentation ; Polymerase Chain Reaction/methods ; Sequence Analysis, DNA/instrumentation ; Sequence Analysis, DNA/methods
Language	Russian
Publishing date	2017-03
Publishing country	Russia (Federation)
Document type	Journal Article ; Review
ZDB-ID	213542-5
ISSN	0026-8984
ISSN	0026-8984
DOI	10.7868/S0026898417010074
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Article: Extracellular Nucleic Acids in Urine: Sources, Structure, Diagnostic Potential.

Bryzgunova, O E / Laktionov, P P

Acta naturae

2015 Volume 7, Issue 3, Page(s) 48–54

Abstract: Cell-free nucleic acids (cfNA) may reach the urine through cell necrosis or apoptosis, active secretion of nucleic acids by healthy and tumor cells of the urinary tract, and transport of circulating nucleic acids (cir- NA) from the blood into primary ... ...

Abstract	Cell-free nucleic acids (cfNA) may reach the urine through cell necrosis or apoptosis, active secretion of nucleic acids by healthy and tumor cells of the urinary tract, and transport of circulating nucleic acids (cir- NA) from the blood into primary urine. Even though urinary DNA and RNA are fragmented, they can be used to detect marker sequences. MicroRNAs are also of interest as diagnostic probes. The stability of cfNA in the urine is determined by their structure and packaging into supramolecular complexes and by nuclease activity in the urine. This review summarizes current data on the sources of urinary cfNA, their structural features, diagnostic potential and factors affecting their stability.
Language	English
Publishing date	2015-10-20
Publishing country	Russia (Federation)
Document type	Journal Article
ISSN	2075-8251
ISSN	2075-8251
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Article: [Generation of blood circulating DNA: the sources, peculiarities of circulation and structure].

Bryzgunova, O E / Laktionov, P P

Biomeditsinskaia khimiia

2015 Volume 61, Issue 4, Page(s) 409–426

Abstract: Extracellular nucleic acids (exNA) were described in blood of both healthy and illness people as early as in 1948, but staied overlooked until middle 60th. Starting from the beginning of new millennium and mainly in the last 5 years exNA are intensively ... ...

Abstract	Extracellular nucleic acids (exNA) were described in blood of both healthy and illness people as early as in 1948, but staied overlooked until middle 60th. Starting from the beginning of new millennium and mainly in the last 5 years exNA are intensively studied. Main attention is directed to investigation of exNA as the source of diagnostic material whereas the mechanisms of their generation, as well as mechanisms to providing long-term circulation of exNA in the bloodstream are not established unambiguously. According to some authors, the main source of circulating nucleic acids in blood are the processes of apoptosis and necrosis, while others refer to the possible nucleic acid secretion by healthy and tumor cells. Circulating DNA were found to be stable in the blood for a long time, escaping from the action of DNA hydrolyzing enzymes and are apparently packed in different supramolecular complexes. This review presents the opinions of various authors and evidence in favor of all the theories describingappearance of extracellular DNA, the features of the circulation and structure of the extracellular DNA and factors affecting the time of DNA circulation in blood.
MeSH term(s)	Adsorption ; Animals ; Apoptosis ; DNA/blood ; DNA, Neoplasm/blood ; Erythrocytes/chemistry ; Erythrocytes/pathology ; Exosomes/chemistry ; Extracellular Vesicles/chemistry ; Half-Life ; Humans ; Necrosis/blood ; Necrosis/pathology ; Neoplasms/blood ; Neoplasms/pathology ; Neoplastic Cells, Circulating/chemistry ; Neoplastic Cells, Circulating/pathology ; Nucleoproteins/chemistry ; Nucleosomes/chemistry
Chemical Substances	DNA, Neoplasm ; Nucleoproteins ; Nucleosomes ; DNA (9007-49-2)
Language	Russian
Publishing date	2015-07
Publishing country	Russia (Federation)
Document type	English Abstract ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2130758-1
ISSN	2310-6905 ; 2310-6972 ; 0042-8809
ISSN (online)	2310-6905
ISSN	2310-6972 ; 0042-8809
DOI	10.18097/PBMC20156104409
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Article ; Online: Data analysis algorithm for the development of extracellular miRNA-based diagnostic systems for prostate cancer.

Bryzgunova, O E / Zaporozhchenko, I A / Lekchnov, E A / Amelina, E V / Konoshenko, M Yu / Yarmoschuk, S V / Pashkovskaya, O A / Zheravin, A A / Pak, S V / Rykova, E Yu / Laktionov, P P

PloS one

2019 Volume 14, Issue 4, Page(s) e0215003

Abstract: Urine of prostate cancer (PCa) carries miRNAs originated from prostate cancer cells as a part of both nucleoprotein complexes and cell-secreted extracellular vesicles. The analysis of such miRNA-markers in urine can be a convenient option for PCa ... ...

Abstract	Urine of prostate cancer (PCa) carries miRNAs originated from prostate cancer cells as a part of both nucleoprotein complexes and cell-secreted extracellular vesicles. The analysis of such miRNA-markers in urine can be a convenient option for PCa screening. The aims of this study were to reveal miRNA-markers of PCa in urine and design a robust and precise diagnostic test, based on miRNA expression analysis. The expression analysis of the 84 miRNAs in paired urine extracellular vesicles (EVs) and cell free urine supernatant samples from healthy donors, patients with benign and malignant prostate tumours was done using miRCURY LNA miRNA qPCR Panels (Exiqon, Denmark). Sets of miRNAs differentially expressed between the donor groups were found in urine EVs and urine supernatant. Diagnostically significant miRNAs were selected and algorithm of data analysis, based on expression data on 24-miRNA in urine and obtained using 17 analytical systems, was designed. The developed algorithm of data analysis describes a series of steps necessary to define cut-off values and sequentially analyze miRNA expression data according to the cut-offs to facilitate classification of subjects in case/control groups and allows to detect PCa patients with 97.5% accuracy.
MeSH term(s)	Aged ; Aged, 80 and over ; Algorithms ; Biomarkers, Tumor/genetics ; Biomarkers, Tumor/urine ; Case-Control Studies ; Data Interpretation, Statistical ; Extracellular Vesicles/genetics ; Gene Regulatory Networks ; Humans ; Male ; MicroRNAs/genetics ; MicroRNAs/urine ; Middle Aged ; Prostatic Hyperplasia/diagnosis ; Prostatic Hyperplasia/genetics ; Prostatic Hyperplasia/urine ; Prostatic Neoplasms/diagnosis ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/urine
Chemical Substances	Biomarkers, Tumor ; MicroRNAs
Language	English
Publishing date	2019-04-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0215003
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Article: Kontaminatsiia preparatov ékzosom, vydelennykh iz biologicheskikh zhidkosteĭ.

Grigor'eva, A E / Dyrkheeva, N S / Bryzgunova, O E / Tamkovich, S N / Chelobanov, B P / Ryabchikova, E I

Biomeditsinskaia khimiia

2017 Volume 63, Issue 1, Page(s) 91–96

Abstract: The aim of our study was to attract the attention of researchers at the problem of contamination of exosome preparations. Using a transmission electron microscope JEM-1400 ("JEOL", Japan) we have examined exosome preparations, isolated according to the ... ...

Title translation	Contamination of exosome preparations, isolated from biological fluids.
Abstract	The aim of our study was to attract the attention of researchers at the problem of contamination of exosome preparations. Using a transmission electron microscope JEM-1400 ("JEOL", Japan) we have examined exosome preparations, isolated according to the conventional scheme of sequential centrifugation from different biological fluids: plasma and urine of healthy persons and patients with oncologic diseases, bovine serum, and culture fluid (MDCK, MDA-MB и MCF-7 cells). All exosome preparations (over 200) contained exosomes, which were identified by immuno-electron microscopy using antibodies to tetraspanins CD63 or CD9. Besides exosomes, all the studied preparations contained contaminating structures: distinct particles of low electron density without limiting membrane ("non-vesicles"). Two main kinds of the "non-vesicles" species were found in exosome preparations: 20-40 nm in size, representing 10-40% of all structures in the preparations; and 40-100 nm in size (identical to exosomes by size). Morphology of the "non-vesicles" allowed to identify them as lipoproteins of intermediate and low density (20-40 nm), and very low density (40-100 nm). The highest level of the contamination was detected in exosome preparations, isolated from blood samples. The results of our study indicate the need to control the composition of exosome preparation by electron microscopy and take into account the presence of contaminating structures in analysis of experimental data.
MeSH term(s)	Adenocarcinoma/blood ; Adenocarcinoma/chemistry ; Animals ; Artifacts ; Biomarkers/metabolism ; Breast Neoplasms/blood ; Breast Neoplasms/chemistry ; Cell Fractionation ; Cell-Derived Microparticles/metabolism ; Cell-Derived Microparticles/ultrastructure ; Dogs ; Exosomes/metabolism ; Exosomes/ultrastructure ; Female ; Gene Expression ; Humans ; Lipoproteins/chemistry ; Lipoproteins/ultrastructure ; MCF-7 Cells ; Madin Darby Canine Kidney Cells ; Male ; Microscopy, Electron, Transmission ; Particle Size ; Prostatic Neoplasms/chemistry ; Prostatic Neoplasms/urine ; Tetraspanin 30/genetics ; Tetraspanin 30/metabolism ; Tetraspanin-29/genetics ; Tetraspanin-29/metabolism ; Ultracentrifugation
Chemical Substances	Biomarkers ; CD63 protein, human ; CD9 protein, human ; Lipoproteins ; Tetraspanin 30 ; Tetraspanin-29
Language	Russian
Publishing date	2017-01
Publishing country	Russia (Federation)
Document type	Journal Article
ZDB-ID	2130758-1
ISSN	2310-6905 ; 2310-6972 ; 0042-8809
ISSN (online)	2310-6905
ISSN	2310-6972 ; 0042-8809
DOI	10.18097/PBMC2017630191
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Article: Analiz predstavlennosti mikroRNK v mikrovezikulakh mochi i beskletochnoĭ moche pri zabolevaniiakh predstatel'noĭ zhelezy.

Zaporozhchenko, I A / Bryzgunova, O E / Lekchnov, E A / Osipov, I D / Zaripov, M M / Yurchenko, Yu B / Yarmoschuk, S V / Pashkovskaya, O A / Rykova, E Yu / Zheravin, A A / Laktionov, P P

Biomeditsinskaia khimiia

2018 Volume 64, Issue 1, Page(s) 38–45

Abstract: Urine of prostate cancer patients contains tumor-specific biopolymers, including protein- and microvesiclesassociated miRNAs that can potentially be used as oncomarkers. Previously we have characterized urine extracellular vesicles and demonstrated ... ...

Title translation	Representation analysis of miRNA from clarified urine and urine microvesicles in prostate malignancies and non-malignant neoplasms.
Abstract	Urine of prostate cancer patients contains tumor-specific biopolymers, including protein- and microvesiclesassociated miRNAs that can potentially be used as oncomarkers. Previously we have characterized urine extracellular vesicles and demonstrated diagnostic potential of their miRNA cargo. In this study, we have performed a comparative analysis of the expression of 84 miRNA in paired samples of urine microvesicles and clarified urine from healthy men, patients with benign hyperplasia and cancer of the prostate using miRCURY LNA miRNA qPCR Panels. Subsets of miRNAs with differences in expression between the fractions of the urine were found in all three groups. Two groups of miRNA were identified based on the patterns of their differential expression. They regulate several key signaling pathways associated with prostate cancer development.
MeSH term(s)	Body Fluids ; Cell-Derived Microparticles ; Extracellular Vesicles ; Humans ; Male ; MicroRNAs ; Prostatic Neoplasms
Chemical Substances	MicroRNAs
Language	Russian
Publishing date	2018-03-12
Publishing country	Russia (Federation)
Document type	Journal Article
ZDB-ID	2130758-1
ISSN	2310-6905 ; 2310-6972 ; 0042-8809
ISSN (online)	2310-6905
ISSN	2310-6972 ; 0042-8809
DOI	10.18097/PBMC20186401038
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Article: Redistribution of Free- and Cell-Surface-Bound DNA in Blood of Benign and Malignant Prostate Tumor Patients.

Bryzgunova, O E / Tamkovich, S N / Cherepanova, A V / Yarmoshchuk, S V / Permyakova, V I / Anykeeva, O Y / Laktionov, P P

Acta naturae

2015 Volume 7, Issue 2, Page(s) 115–118

Abstract: A direct correlation between the concentration of cell-free and cell-surface-bound circulating DNA (cfDNA and csbDNA, respectively) was demonstrated. Based on an inverse correlation between blood plasma DNase activity and the cfDNA concentration, blood ... ...

Abstract	A direct correlation between the concentration of cell-free and cell-surface-bound circulating DNA (cfDNA and csbDNA, respectively) was demonstrated. Based on an inverse correlation between blood plasma DNase activity and the cfDNA concentration, blood DNases are supposed to regulate the cfDNA concentration. However, no correlation was found between the DNase activity in blood plasma and the csbDNA concentration, indicating that blood DNases are not involved in csbDNA dissociation from the cell surface. The possibility of DNA redistribution between cfDNA and csbDNA indicates that the total pool of circulating DNA (cfDNA + csbDNA) should be used for a correct analysis of marker DNA concentrations and data standardization.
Language	English
Publishing date	2015-05-22
Publishing country	Russia (Federation)
Document type	Journal Article
ISSN	2075-8251
ISSN	2075-8251
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Article: [Modern methods of prostate cancer diagnostics].

Bryzgunova, O E / Vlasov, V V / Laktiononv, P P

Biomeditsinskaia khimiia

2007 Volume 53, Issue 2, Page(s) 128–139

Abstract: The review highlights analytics capacities of immunochemical and molecular-genetic methods used in the non-invasive test for prostate cancer and monitoring of efficacy of anticancer therapy. The perspectives of their applications in clinical practice ... ...

Abstract	The review highlights analytics capacities of immunochemical and molecular-genetic methods used in the non-invasive test for prostate cancer and monitoring of efficacy of anticancer therapy. The perspectives of their applications in clinical practice also have been evaluated.
MeSH term(s)	Diagnosis, Differential ; Humans ; Male ; Monitoring, Physiologic ; Prostatic Neoplasms/diagnosis ; Prostatic Neoplasms/genetics ; Prostatic Neoplasms/therapy
Language	Russian
Publishing date	2007-03
Publishing country	Russia (Federation)
Document type	English Abstract ; Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2130758-1
ISSN	2310-6905 ; 2310-6972 ; 0042-8809
ISSN (online)	2310-6905
ISSN	2310-6972 ; 0042-8809
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Article ; Online: Data analysis algorithm for the development of extracellular miRNA-based diagnostic systems for prostate cancer.

O E Bryzgunova / I A Zaporozhchenko / E A Lekchnov / E V Amelina / M Yu Konoshenko / S V Yarmoschuk / O A Pashkovskaya / A A Zheravin / S V Pak / E Yu Rykova / P P Laktionov

PLoS ONE, Vol 14, Iss 4, p e

2019 Volume 0215003

Abstract	Urine of prostate cancer (PCa) carries miRNAs originated from prostate cancer cells as a part of both nucleoprotein complexes and cell-secreted extracellular vesicles. The analysis of such miRNA-markers in urine can be a convenient option for PCa screening. The aims of this study were to reveal miRNA-markers of PCa in urine and design a robust and precise diagnostic test, based on miRNA expression analysis. The expression analysis of the 84 miRNAs in paired urine extracellular vesicles (EVs) and cell free urine supernatant samples from healthy donors, patients with benign and malignant prostate tumours was done using miRCURY LNA miRNA qPCR Panels (Exiqon, Denmark). Sets of miRNAs differentially expressed between the donor groups were found in urine EVs and urine supernatant. Diagnostically significant miRNAs were selected and algorithm of data analysis, based on expression data on 24-miRNA in urine and obtained using 17 analytical systems, was designed. The developed algorithm of data analysis describes a series of steps necessary to define cut-off values and sequentially analyze miRNA expression data according to the cut-offs to facilitate classification of subjects in case/control groups and allows to detect PCa patients with 97.5% accuracy.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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