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Shefer A, Tutanov O, Belenikin M, Tsentalovich YP, Tamkovich S. Blood Plasma Circulating DNA-Protein Complexes: Involvement in Carcinogenesis and Prospects for Liquid Biopsy of Breast Cancer. J Pers Med 2023; 13:1691. [PMID: 38138918 PMCID: PMC10744380 DOI: 10.3390/jpm13121691] [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: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 12/24/2023] Open
Abstract
Circulating DNA (cirDNA) is a promising tool in translational medicine. However, studies of cirDNA have neglected its association with proteins, despite ample evidence that this interaction may affect the fate of DNA in the bloodstream and its molecular functions. The goal of the current study is to shed light on the differences between the proteomic cargos of histone-containing nucleoprotein complexes (NPCs) from healthy female (HFs) and breast cancer patients (BCPs), and to reveal the proteins involved in carcinogenesis. NPCs were isolated from the blood samples of HFs and BCPs using affinity chromatography. A total of 177 and 169 proteins were identified in NPCs from HFs and BCPs using MALDI-TOF mass spectrometry. A bioinformatics analysis revealed that catalytically active proteins, as well as proteins that bind nucleic acids and regulate the activity of receptors, are the most represented among the unique proteins of blood NPCs from HFs and BCPs. In addition, the proportion of proteins participating in ion channels and proteins binding proteins increases in the NPCs from BCP blood. However, the involvement in transport and signal transduction was greater in BCP NPCs compared to those from HFs. Gene ontology term (GO) analysis revealed that the NPC protein cargo from HF blood was enriched with proteins involved in the negative regulation of cell proliferation, and in BCP blood, proteins involved in EMT, invasion, and cell migration were observed. The combination of SPG7, ADRB1, SMCO4, PHF1, and PSMG1 NPC proteins differentiates BCPs from HFs with a sensitivity of 100% and a specificity of 80%. The obtained results indirectly indicate that, in tandem with proteins, blood cirDNA is an important part of intercellular communication, playing a regulatory and integrating role in the physiology of the body.
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Affiliation(s)
- Aleksei Shefer
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Oleg Tutanov
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37203, USA;
| | | | - Yuri P. Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
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Tutanov O, Shefer A, Tsentalovich Y, Tamkovich S. Comparative Analysis of Molecular Functions and Biological Role of Proteins from Cell-Free DNA-Protein Complexes Circulating in Plasma of Healthy Females and Breast Cancer Patients. Int J Mol Sci 2023; 24:ijms24087279. [PMID: 37108441 PMCID: PMC10138639 DOI: 10.3390/ijms24087279] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 03/18/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Cell-free DNA (cfDNA) circulates in the bloodstream packed in membrane-coated structures (such as apoptotic bodies) or bound to proteins. To identify proteins involved in the formation of deoxyribonucleoprotein complexes circulating in the blood, native complexes were isolated using affinity chromatography with immobilized polyclonal anti-histone antibodies from plasma of healthy females (HFs) and breast cancer patients (BCPs). It was found that the nucleoprotein complexes (NPCs) from HF plasma samples contained shorter DNA fragments (~180 bp) than BCP NPCs. However, the share of DNA in the NPCs from cfDNA in blood plasma in HFs and BCPs did not differ significantly, as well as the share of NPC protein from blood plasma total protein. Proteins were separated by SDS-PAGE and identified by MALDI-TOF mass spectrometry. Bioinformatic analysis showed that in the presence of a malignant tumor, the proportion of proteins involved in ion channels, protein binding, transport, and signal transduction increased in the composition of blood-circulating NPCs. Moreover, 58 (35%) proteins are differentially expressed in a number of malignant neoplasms in the NPCs of BCPs. Identified NPC proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or as being useful in developing gene-targeted therapy approaches.
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Affiliation(s)
- Oleg Tutanov
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksei Shefer
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
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Tutanov O, Tamkovich S. The Influence of Proteins on Fate and Biological Role of Circulating DNA. Int J Mol Sci 2022; 23:ijms23137224. [PMID: 35806228 PMCID: PMC9266439 DOI: 10.3390/ijms23137224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/31/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Circulating DNA has already proven itself as a valuable tool in translational medicine. However, one of the overlooked areas of circulating DNA research is its association with different proteins, despite considerable evidence that this association might impact DNA’s fate in circulation and its biological role. In this review, we attempt to shed light on current ideas about circulating DNA origins and forms of circulation, known biological effects, and the clinical potential of circulating tumor deoxyribonucleoprotein complexes.
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Tutanov O, Shtam T, Grigor’eva A, Tupikin A, Tsentalovich Y, Tamkovich S. Blood Plasma Exosomes Contain Circulating DNA in Their Crown. Diagnostics (Basel) 2022; 12:diagnostics12040854. [PMID: 35453902 PMCID: PMC9027845 DOI: 10.3390/diagnostics12040854] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/21/2022] [Accepted: 03/28/2022] [Indexed: 01/13/2023] Open
Abstract
It is known that circulating DNA (cirDNA) is protected from nuclease activity by proteins that form macromolecular complexes with DNA. In addition, it was previously shown that cirDNA can bind to the outer surface of exosomes. NTA analysis and real-time PCR show that exosomes from healthy females (HF) or breast cancer patients (BCP) plasma contain less than 1.4 × 10−8 pg of DNA. Thus, only a minor part of cirDNA is attached to the outer side of the exosome as part of the vesicle crown: the share of exosomal DNA does not exceed 0.025% HF plasma DNA and 0.004% BCP plasma DNA. Treatment of plasma exosomes with DNase I with subsequent dot immunoassay reveals that H2a, H2b, and H3 histones are not part of the exosomal membrane, but are part of the cirDNA–protein macromolecular complex associated with the surface of the exosome either through interaction with DNA-binding proteins or with histone-binding proteins. Using bioinformatics approaches after identification by MALDI-TOF mass spectrometry, 16 exosomal DNA-binding proteins were identified. It was shown that four proteins—AIFM1, IGHM, CHD5, and KCNIP3—are candidates for DNA binding on the outer membrane of exosomes; the crown of exosomes may include five DNA-binding proteins: H2a, H2b, H3, IGHM, and ALB. Of note, AIFM1, IGHM, and CHD5 proteins are found only in HF plasma exosomes; KCNIP3 protein is identified only in BCP plasma exosomes; and H2a, H2b, H3, and ALB are revealed in all samples of plasma exosomes. Two histone-binding proteins, CHD5 and KDM6B, have been found in exosomes from HF plasma. The data obtained indicate that cirDNA preferentially binds to the outer membrane of exosomes by association with DNA-binding proteins.
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Affiliation(s)
- Oleg Tutanov
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Tatiana Shtam
- Petersburg Nuclear Physics Institute Named by B.P. Konstantinov of National Research Center “Kurchatov Institute”, 188300 Gatchina, Russia;
| | - Alina Grigor’eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.G.); (A.T.)
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (A.G.); (A.T.)
| | - Yuri Tsentalovich
- International Tomography Center, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
| | - Svetlana Tamkovich
- V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia;
- Correspondence:
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Tutanov O, Proskura K, Kamyshinsky R, Shtam T, Tsentalovich Y, Tamkovich S. Proteomic Profiling of Plasma and Total Blood Exosomes in Breast Cancer: A Potential Role in Tumor Progression, Diagnosis, and Prognosis. Front Oncol 2020. [DOI: 10.3389/fonc.2020.580891] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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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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Tutanov O, Orlova E, Proskura K, Grigor’eva A, Yunusova N, Tsentalovich Y, Alexandrova A, Tamkovich S. Proteomic Analysis of Blood Exosomes from Healthy Females and Breast Cancer Patients Reveals an Association between Different Exosomal Bioactivity on Non-tumorigenic Epithelial Cell and Breast Cancer Cell Migration in Vitro. Biomolecules 2020; 10:biom10040495. [PMID: 32218180 PMCID: PMC7226042 DOI: 10.3390/biom10040495] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 02/06/2023] Open
Abstract
Exosomes are important intercellular communication vehicles, secreted into body fluids by multiple cell types, including tumor cells. They contribute to the metastatic progression of tumor cells through paracrine signalling. It has been recently discovered that blood circulating exosomes contain distinguishable fractions of free and cell-surface-associated vesicles. We evaluated the influence of protein cargoes from exosomes from plasma, and exosomes from the total blood of healthy females (HFs) and breast cancer patients (BCPs), on cell motility. We conducted a mass spectrometric analysis of exosomal contents isolated from samples using ultrafiltration and ultracentrifugation approaches and verified their nature using transmission electron microscopy, nanoparticle tracking analysis and flow cytometry. We observed that malignant neoplasm-associated proteins in exosomes from BCP total blood were detected more often than in plasma (66% vs. 59%). FunRich analysis to assess Gene Ontology (GO) enrichment revealed that proteins with catalytic activities, transporter functions and protein metabolism activities were increased in exosomes from BCP blood. Finally, GO analysis revealed that proteomic profiles of exosomes from HF total blood were enriched with proteins inhibiting cell migration and invasion, which explains the low stimulating activity of exosomes from HF total blood on SKBR-3 cancer cell migration velocity. This allows exosomes to act as intermediaries providing intercellular communications through horizontal transfer of RNA and functionally active proteins, potentially affecting the development of both primary neoplasms and distant metastases.
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Affiliation(s)
- Oleg Tutanov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.T.); (K.P.); (A.G.)
| | - Evgeniya Orlova
- Laboratory of Carcinogenesis Mechanisms, “N.N. Blokhin Cancer Research Center” of the Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (E.O.); (A.A.)
| | - Ksenia Proskura
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.T.); (K.P.); (A.G.)
- Department of Mammology, Novosibirsk Regional Clinical Oncological Dispensary, 630108 Novosibirsk, Russia
| | - Alina Grigor’eva
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.T.); (K.P.); (A.G.)
| | - Natalia Yunusova
- Laboratory of Tumor Biochemistry, Cancer Research Institute, Тomsk National Research Medical Center, Russian Academy of Science, 634028 Tomsk, Russia;
- Department of Biochemistry and Molecular Biology, Siberian State Medical University, 634050 Tomsk, Russia
| | - Yuri Tsentalovich
- Laboratory of Proteomics and Metabolomics, International Tomography Center SB RAS, 630090 Novosibirsk, Russia;
| | - Antonina Alexandrova
- Laboratory of Carcinogenesis Mechanisms, “N.N. Blokhin Cancer Research Center” of the Ministry of Health of the Russian Federation, 115478 Moscow, Russia; (E.O.); (A.A.)
| | - Svetlana Tamkovich
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia; (O.T.); (K.P.); (A.G.)
- Department of Molecular Biology and Biotechnology, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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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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