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Navals P, Rangaswamy AMM, Kasyanchyk P, Berezovski MV, Keillor JW. Conformational Modulation of Tissue Transglutaminase via Active Site Thiol Alkylating Agents: Size Does Not Matter. Biomolecules 2024; 14:496. [PMID: 38672511 PMCID: PMC11048362 DOI: 10.3390/biom14040496] [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: 03/03/2024] [Revised: 04/02/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
TG2 is a unique member of the transglutaminase family as it undergoes a dramatic conformational change, allowing its mutually exclusive function as either a cross-linking enzyme or a G-protein. The enzyme's dysregulated activity has been implicated in a variety of pathologies (e.g., celiac disease, fibrosis, cancer), leading to the development of a wide range of inhibitors. Our group has primarily focused on the development of peptidomimetic targeted covalent inhibitors, the nature and size of which were thought to be important features to abolish TG2's conformational dynamism and ultimately inhibit both its activities. However, we recently demonstrated that the enzyme was unable to bind guanosine triphosphate (GTP) when catalytically inactivated by small molecule inhibitors. In this study, we designed a library of models targeting covalent inhibitors of progressively smaller sizes (15 to 4 atoms in length). We evaluated their ability to inactivate TG2 by measuring their respective kinetic parameters kinact and KI. Their impact on the enzyme's ability to bind GTP was then evaluated and subsequently correlated to the conformational state of the enzyme, as determined via native PAGE and capillary electrophoresis. All irreversible inhibitors evaluated herein locked TG2 in its open conformation and precluded GTP binding. Therefore, we conclude that steric bulk and structural complexity are not necessary factors to consider when designing TG2 inhibitors to abolish G-protein activity.
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Affiliation(s)
| | | | | | | | - Jeffrey W. Keillor
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (P.N.); (A.M.M.R.); (P.K.); (M.V.B.)
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2
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Affinito A, Quintavalle C, Chianese RV, Roscigno G, Fiore D, D'Argenio V, Thomas G, Savarese A, Ingenito F, Cocca L, Nuzzo S, Berezovski MV, Stoppelli MP, Condorelli G. MCT4-driven CAF-mediated metabolic reprogramming in breast cancer microenvironment is a vulnerability targetable by miR-425-5p. Cell Death Discov 2024; 10:140. [PMID: 38485929 PMCID: PMC10940713 DOI: 10.1038/s41420-024-01910-x] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 02/26/2024] [Accepted: 03/06/2024] [Indexed: 03/18/2024] Open
Abstract
Multiple oncogenic alterations contribute to breast cancer development. Metabolic reprogramming, deeply contributing to tumor microenvironment (TME) education, is now widely recognized as a hallmark of cancer. The reverse Warburg effect induces cancer-associated fibroblasts (CAFs) to produce and secrete L-lactate, enhancing malignant characteristics such as neoangiogenesis, metastatic dissemination, and treatment resistance. Monocarboxylate transporter (MCT) 4 is involved in lactate efflux from CAFs into stromal and epithelial cells. Here, we first assess the expression of miR-425-5p and its target MCT4 in breast cancer CAFs and normal fibroblasts. We analyzed the metabolic changes induced by miR-425-5p in CAFs and its role in the education of breast cancer epithelial cells. We show that miR-425-5p-induced MCT4 knockdown decreased lactate extrusion from CAFs and its availability in the TME. miR-425-5p overexpression induced profound metabolic transformation in CAFs, ultimately influencing breast cancer metabolism. Furthermore, miR-425-5p impaired the capacity of CAFs to sustain vessel formation and breast cancer cell migration, viability, and proliferation. These findings emphasize the key role of miR-425-5p in breast cancer metabolism and aggressiveness, and its possible importance for breast cancer therapy and monitoring.
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Affiliation(s)
- Alessandra Affinito
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
- AKA Biotech, Naples, Italy
| | - Cristina Quintavalle
- Institute Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), CNR, Naples, Italy
| | - Rosario Vincenzo Chianese
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Giuseppina Roscigno
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Danilo Fiore
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
- Institute Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), CNR, Naples, Italy
| | - Valeria D'Argenio
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Roma, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
| | | | - Alessia Savarese
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Francesco Ingenito
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Lorenza Cocca
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | | | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences and John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, ON, Canada
| | | | - Gerolama Condorelli
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy.
- Institute Experimental Endocrinology and Oncology "Gaetano Salvatore" (IEOS), CNR, Naples, Italy.
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Uppal GK, Poolsup S, Zaripov E, Gu Y, Berezovski MV. Comparative analysis of aptamers binding to SARS-CoV-2 N protein using capillary electrophoresis and bio-layer interferometry. Anal Bioanal Chem 2024; 416:1697-1705. [PMID: 38305861 DOI: 10.1007/s00216-024-05174-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/12/2024] [Accepted: 01/24/2024] [Indexed: 02/03/2024]
Abstract
Aptamers are increasingly employed in SARS-CoV-2 theragnostics in recent years. Characterization of aptamers, testing affinity and kinetic parameters (e.g., equilibrium dissociation constant (KD), kon, and koff), can be done by several methods and influenced by many factors. This study aims to characterize the binding of aptamers to SARS-CoV-2 nucleocapsid (N) protein using capillary electrophoresis (CE) and bio-layer interferometry (BLI). These two analytical methods differ by how the aptamer binds to its target protein once the aptamer, as a capture ligand, is partitioned in solution (CE) or immobilized on the biosensor (BLI). With CE, the KD values of the N-binding aptamers (tNSP1, tNSP2, and tNSP3) were determined to be 18 ± 4 nM, 45 ± 11 nM, and 32 ± 7 nM, respectively, while the KD measurements by BLI yielded 4.8 ± 0.6, 4.5 ± 0.5, and 2.9 ± 0.3 nM, respectively. CE results showed a higher KD across all aptamers tested. The differences in the steric hindrance and confirmational structures of the aptamers immobilized on the BLI biosensors versus those suspended in the CE sample solution affect the molecular interactions between aptamers and the target proteins. Moreover, the buffer composition including pH and ionic strength can influence the stability of aptamer structures, or aptamer-protein complexes. All these variables affect the binding and calculated KD. In this sense, a KD value alone is not sufficient to make comparisons between aptamers; instead, the entire experimental setup should also be considered. This is particularly important when implementing aptamers in different bioanalytical systems.
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Affiliation(s)
- Gurcharan K Uppal
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Yuxuan Gu
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.
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Muratov K, Zaripov E, Berezovski MV, Gagosz F. DFT-Enabled Development of Hemilabile (P ∧N) Ligands for Gold(I/III) RedOx Catalysis: Application to the Thiotosylation of Aryl Iodides. J Am Chem Soc 2024; 146:3660-3674. [PMID: 38315643 DOI: 10.1021/jacs.3c08943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Ligand-enabled oxidative addition of Csp2-X bonds to Au(I) centers has recently appeared as a valuable strategy for the development of catalytic RedOx processes. Several cross-coupling reactions that were previously considered difficult to achieve were reported lately, thus expanding the synthetic potential of gold(I) complexes beyond the traditional nucleophilic functionalization of π-systems. MeDalPhos has played an important role in this development and, despite several studies on alternative structures, remains, so far, the only general ligand for such process. We report herein the discovery and DFT-enabled structural optimization of a new family of hemilabile (P∧N) ligands that can promote the oxidative addition of aryl iodides to gold(I). These flexible ligands, which possess a common 2-methylamino heteroaromatic N-donor motif, are structurally and electronically tunable, beyond being easily accessible and affordable. The corresponding Au(I) complexes were shown to outperform the reactivity of (MeDalPhos)Au(I) in a series of alkoxy- and amidoarylations of alkenes. Their synthetic potential and comparatively higher reactivity were further highlighted in the thiotosylation of aryl iodides, a challenging unreported C-S cross-coupling reaction that could not be achieved under classical Pd(0/II) catalysis and that allows for general and divergent access to aryl sulfur derivatives.
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Affiliation(s)
- Karim Muratov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Fabien Gagosz
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1N 6N5, Canada
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Hüttmann N, Li Y, Poolsup S, Zaripov E, D’Mello R, Susevski V, Minic Z, Berezovski MV. Surface Proteome of Extracellular Vesicles and Correlation Analysis Reveal Breast Cancer Biomarkers. Cancers (Basel) 2024; 16:520. [PMID: 38339272 PMCID: PMC10854524 DOI: 10.3390/cancers16030520] [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: 12/23/2023] [Revised: 01/13/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Breast cancer (BC) is the second most frequently diagnosed cancer and accounts for approximately 25% of new cancer cases in Canadian women. Using biomarkers as a less-invasive BC diagnostic method is currently under investigation but is not ready for practical application in clinical settings. During the last decade, extracellular vesicles (EVs) have emerged as a promising source of biomarkers because they contain cancer-derived proteins, RNAs, and metabolites. In this study, EV proteins from small EVs (sEVs) and medium EVs (mEVs) were isolated from BC MDA-MB-231 and MCF7 and non-cancerous breast epithelial MCF10A cell lines and then analyzed by two approaches: global proteomic analysis and enrichment of EV surface proteins by Sulfo-NHS-SS-Biotin labeling. From the first approach, proteomic profiling identified 2459 proteins, which were subjected to comparative analysis and correlation network analysis. Twelve potential biomarker proteins were identified based on cell line-specific expression and filtered by their predicted co-localization with known EV marker proteins, CD63, CD9, and CD81. This approach resulted in the identification of 11 proteins, four of which were further investigated by Western blot analysis. The presence of transmembrane serine protease matriptase (ST14), claudin-3 (CLDN3), and integrin alpha-7 (ITGA7) in each cell line was validated by Western blot, revealing that ST14 and CLDN3 may be further explored as potential EV biomarkers for BC. The surface labeling approach enriched proteins that were not identified using the first approach. Ten potential BC biomarkers (Glutathione S-transferase P1 (GSTP1), Elongation factor 2 (EEF2), DEAD/H box RNA helicase (DDX10), progesterone receptor (PGR), Ras-related C3 botulinum toxin substrate 2 (RAC2), Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), Aconitase 2 (ACO2), UTP20 small subunit processome component (UTP20), NEDD4 binding protein 2 (N4BP2), Programmed cell death 6 (PDCD6)) were selected from surface proteins commonly identified from MDA-MB-231 and MCF7, but not identified in MCF10A EVs. In total, 846 surface proteins were identified from the second approach, of which 11 were already known as BC markers. This study supports the proposition that Evs are a rich source of known and novel biomarkers that may be used for non-invasive detection of BC. Furthermore, the presented datasets could be further explored for the identification of potential biomarkers in BC.
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Affiliation(s)
- Nico Hüttmann
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Yingxi Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Rochelle D’Mello
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Vanessa Susevski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (N.H.); (Y.L.); (S.P.); (E.Z.); (R.D.); (V.S.)
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada;
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Kolovskaya OS, Zyuzyukina AV, Dassie JP, Zamay GS, Zamay TN, Boyakova NV, Khorzhevskii VA, Kirichenko DA, Lapin IN, Shchugoreva IA, Artyushenko PV, Tomilin FN, Veprintsev DV, Glazyrin YE, Minic Z, Bozhenko VK, Kudinova EA, Kiseleva YY, Krat AV, Slepov EV, Bukatin AS, Zukov RA, Shesternya PA, Berezovski MV, Giangrande PH, Kichkailo AS. Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples. Front Mol Biosci 2023; 10:1184285. [PMID: 37363395 PMCID: PMC10285395 DOI: 10.3389/fmolb.2023.1184285] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction: Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch® is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood. The MDA231 aptamer was originally selected against triple-negative breast cancer cell line MDA-MB-231 using cell-SELEX. Methods: The aptamer structure in solution was predicted using mFold program and molecular dynamic simulations. The affinity and specificity of the evolved aptamers were evaluated by flow cytometry and laser scanning microscopy on clinical tissues from breast cancer patients. CTCs were isolated form the patients' blood using the developed method of aptamer-based magnetic separation. Breast cancer origin of CTCs was confirmed by cytological, RT-qPCR and Immunocytochemical analyses. Results: MDA231 can specifically recognize breast cancer cells in surgically resected tissues from patients with different molecular subtypes: triple-negative, Luminal A, and Luminal B, but not in benign tumors, lung cancer, glial tumor and healthy epithelial from lungs and breast. This RNA aptamer can identify cancer cells in complex cellular environments, including tumor biopsies (e.g., tumor tissues vs. margins) and clinical blood samples (e.g., circulating tumor cells). Breast cancer origin of the aptamer-based magnetically separated CTCs has been proved by immunocytochemistry and mammaglobin mRNA expression. Discussion: We suggest a simple, minimally-invasive breast cancer diagnostic method based on non-epithelial MDA231 aptamer-specific magnetic isolation of circulating tumor cells. Isolated cells are intact and can be utilized for molecular diagnostics purposes.
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Affiliation(s)
- Olga S. Kolovskaya
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Alena V. Zyuzyukina
- Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Justin P. Dassie
- Department of Internal Medicine, University of Iowa, Iowa, IA, United States
| | - Galina S. Zamay
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Tatiana N. Zamay
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Nina V. Boyakova
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
- Department of General Surgery, Named After Prof. M.I. Gulman, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Vladimir A. Khorzhevskii
- Department of Pathological Anatomy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Daria A. Kirichenko
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Ivan N. Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk, Russia
| | - Irina A. Shchugoreva
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Polina V. Artyushenko
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, Russia
| | - Felix N. Tomilin
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, Russia
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, Russia
| | - Dmitry V. Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Yury E. Glazyrin
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
| | - Zoran Minic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | | | | | | | - Alexey V. Krat
- Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Eugene V. Slepov
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Anton S. Bukatin
- Alferov Federal State Budgetary Institution of Higher Education and Science, Saint Petersburg National Research Academic University of the Russian Academy of Sciences, Saint Petersburg, Russia
- Institute for Analytical Instrumentation of the Russian Academy of Sciences, Saint Petersburg, Russia
| | - Ruslan A. Zukov
- Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia
| | - Pavel A. Shesternya
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Paloma H. Giangrande
- Department of Internal Medicine, University of Iowa, Iowa, IA, United States
- Platform Discovery Sciences, Biology, Wave Life Sciences, Cambridge, MA, United States
| | - Anna S. Kichkailo
- Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, Krasnoyarsk, Russia
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Minic Z, Li Y, Hüttmann N, Uppal GK, D’Mello R, Berezovski MV. Lysine Acetylome of Breast Cancer-Derived Small Extracellular Vesicles Reveals Specific Acetylation Patterns for Metabolic Enzymes. Biomedicines 2023; 11:biomedicines11041076. [PMID: 37189694 DOI: 10.3390/biomedicines11041076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/20/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Cancer-derived small extracellular vesicles have been proposed as promising potential biomarkers for diagnosis and prognosis of breast cancer (BC). We performed a proteomic study of lysine acetylation of breast cancer-derived small extracellular vesicles (sEVs) to understand the potential role of the aberrant acetylated proteins in the biology of invasive ductal carcinoma and triple-negative BC. Three cell lines were used as models for this study: MCF10A (non-metastatic), MCF7 (estrogen and progesterone receptor-positive, metastatic) and MDA-MB-231 (triple-negative, highly metastatic). For a comprehensive protein acetylation analysis of the sEVs derived from each cell line, acetylated peptides were enriched using the anti-acetyl-lysine antibody, followed by LC-MS/MS analysis. In total, there were 118 lysine-acetylated peptides, of which 22, 58 and 82 have been identified in MCF10A, MCF7 and MDA-MB-231 cell lines, respectively. These acetylated peptides were mapped to 60 distinct proteins and mainly identified proteins involved in metabolic pathways. Among the acetylated proteins identified in cancer-derived sEVs from MCF7 and MDA-MB-231 cell lines are proteins associated with the glycolysis pathway, annexins and histones. Five acetylated enzymes from the glycolytic pathway, present only in cancer-derived sEVs, were validated. These include aldolase (ALDOA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK1), enolase (ENO) and pyruvate kinase M1/2 (PKM). For three of these enzymes (ALDOA, PGK1 and ENO) the specific enzymatic activity was significantly higher in MDA-MB-231 when compared with MCF10A-derived sEVs. This study reveals that sEVs contain acetylated glycolytic metabolic enzymes that could be interesting potential candidates for early BC diagnostics.
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Affiliation(s)
- Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Yingxi Li
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Gurcharan K. Uppal
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Rochelle D’Mello
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Maxim V. Berezovski
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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8
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Poolsup S, Zaripov E, Hüttmann N, Minic Z, Artyushenko PV, Shchugoreva IA, Tomilin FN, Kichkailo AS, Berezovski MV. Discovery of DNA aptamers targeting SARS-CoV-2 nucleocapsid protein and protein-binding epitopes for label-free COVID-19 diagnostics. Mol Ther Nucleic Acids 2023; 31:731-743. [PMID: 36816615 PMCID: PMC9927813 DOI: 10.1016/j.omtn.2023.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 02/10/2023] [Indexed: 02/16/2023]
Abstract
The spread of COVID-19 has affected billions of people across the globe, and the diagnosis of viral infection still needs improvement. Because of high immunogenicity and abundant expression during viral infection, SARS-CoV-2 nucleocapsid (N) protein could be an important diagnostic marker. This study aimed to develop a label-free optical aptasensor fabricated with a novel single-stranded DNA aptamer to detect the N protein. The N-binding aptamers selected using asymmetric-emulsion PCR-SELEX and their binding affinity and cross-reactivity were characterized by biolayer interferometry. The tNSP3 aptamer (44 nt) was identified to bind the N protein of wild type and Delta and Omicron variants with high affinity (KD in the range of 0.6-3.5 nM). Utilizing tNSP3 to detect the N protein spiked in human saliva evinced the potential of this aptamer with a limit of detection of 4.5 nM. Mass spectrometry analysis was performed along with molecular dynamics simulation to obtain an insight into how tNSP3 binds to the N protein. The identified epitope peptides are localized within the RNA-binding domain and C terminus of the N protein. Hence, we confirmed the performance of this aptamer as an analytical tool for COVID-19 diagnosis.
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Affiliation(s)
- Suttinee Poolsup
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Emil Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Polina V Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Irina A Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Felix N Tomilin
- Department of Chemistry, Siberian Federal University, Krasnoyarsk 660041, Russia.,Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk 660036, Russia
| | - Anna S Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk 660036, Russia.,Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.,John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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9
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Izrael Živković L, Hüttmann N, Susevski V, Medić A, Beškoski V, Berezovski MV, Minić Z, Živković L, Karadžić I. A comprehensive proteomics analysis of the response of Pseudomonas aeruginosa to nanoceria cytotoxicity. Nanotoxicology 2023; 17:20-41. [PMID: 36861958 DOI: 10.1080/17435390.2023.2180451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The increased commercial use and spread of nanoceria raises concerns about the risks associated with its effects on living organisms. Although Pseudomonas aeruginosa may be ubiquitous in nature, it is largely found in locations closely linked with human activity. P. aeruginosa san ai was used as a model organism for a deeper understanding of the interaction between biomolecules of the bacteria with this intriguing nanomaterial. A comprehensive proteomics approach along with analysis of altered respiration and production of targeted/specific secondary metabolites was conducted to study the response of P. aeruginosa san ai to nanoceria. Quantitative proteomics found that proteins associated with redox homeostasis, biosynthesis of amino acids, and lipid catabolism were upregulated. Proteins from outer cellular structures were downregulated, including transporters responsible for peptides, sugars, amino acids and polyamines, and the crucial TolB protein of the Tol-Pal system, required for the structural formation of the outer membrane layer. In accordance with the altered redox homeostasis proteins, an increased amount of pyocyanin, a key redox shuttle, and the upregulation of the siderophore, pyoverdine, responsible for iron homeostasis, were found. Production of extracellular molecules, e.g. pyocyanin, pyoverdine, exopolysaccharides, lipase, and alkaline protease, was significantly increased in P. aeruginosa san ai exposed to nanoceria. Overall, nanoceria at sublethal concentrations induces profound metabolic changes in P. aeruginosa san ai and provokes increased secretion of extracellular virulence factors, revealing the powerful influence this nanomaterial has on the vital functions of the microorganism.
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Affiliation(s)
| | - Nico Hüttmann
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Vanessa Susevski
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Ana Medić
- Department of Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Vladimir Beškoski
- Department of Biochemistry, Faculty of Chemistry, University of Belgrade, Belgrade, Serbia
| | - Maxim V Berezovski
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Zoran Minić
- John L. Holmes Mass Spectrometry Facility, University of Ottawa, Ottawa, Ontario, Canada
| | - Ljiljana Živković
- The Vinča Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Ivanka Karadžić
- Department of Chemistry, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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10
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Kichkailo AS, Narodov AA, Komarova MA, Zamay TN, Zamay GS, Kolovskaya OS, Erakhtin EE, Glazyrin YE, Veprintsev DV, Moryachkov RV, Zabluda VV, Shchugoreva I, Artyushenko P, Mironov VA, Morozov DI, Khorzhevskii VA, Gorbushin AV, Koshmanova AA, Nikolaeva ED, Grinev IP, Voronkovskii II, Grek DS, Belugin KV, Volzhentsev AA, Badmaev ON, Luzan NA, Lukyanenko KA, Peters G, Lapin IN, Kirichenko AK, Konarev PV, Morozov EV, Mironov GG, Gargaun A, Muharemagic D, Zamay SS, Kochkina EV, Dymova MA, Smolyarova TE, Sokolov AE, Modestov AA, Tokarev NA, Shepelevich NV, Ozerskaya AV, Chanchikova NG, Krat AV, Zukov RA, Bakhtina VI, Shnyakin PG, Shesternya PA, Svetlichnyi VA, Petrova MM, Artyukhov IP, Tomilin FN, Berezovski MV. Development of DNA Aptamers for Visualization of Glial Brain Tumors and Detection of Circulating Tumor Cells. Molecular Therapy - Nucleic Acids 2023; 32:267-288. [PMID: 37090419 PMCID: PMC10119962 DOI: 10.1016/j.omtn.2023.03.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/21/2023] [Indexed: 03/30/2023]
Abstract
Here, we present DNA aptamers capable of specific binding to glial tumor cells in vitro, ex vivo, and in vivo for visualization diagnostics of central nervous system tumors. We selected the aptamers binding specifically to the postoperative human glial primary tumors and not to the healthy brain cells and meningioma, using a modified process of systematic evolution of ligands by exponential enrichment to cells; sequenced and analyzed ssDNA pools using bioinformatic tools and identified the best aptamers by their binding abilities; determined three-dimensional structures of lead aptamers (Gli-55 and Gli-233) with small-angle X-ray scattering and molecular modeling; isolated and identified molecular target proteins of the aptamers by mass spectrometry; the potential binding sites of Gli-233 to the target protein and the role of post-translational modifications were verified by molecular dynamics simulations. The anti-glioma aptamers Gli-233 and Gli-55 were used to detect circulating tumor cells in liquid biopsies. These aptamers were used for in situ, ex vivo tissue staining, histopathological analyses, and fluorescence-guided tumor and PET/CT tumor visualization in mice with xenotransplanted human astrocytoma. The aptamers did not show in vivo toxicity in the preclinical animal study. This study demonstrates the potential applications of aptamers for precise diagnostics and fluorescence-guided surgery of brain tumors.
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Affiliation(s)
- Anna S. Kichkailo
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Corresponding author: Anna S. Kichkailo, Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia.
| | - Andrey A. Narodov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Maria A. Komarova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Galina S. Zamay
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Olga S. Kolovskaya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Evgeniy E. Erakhtin
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Yury E. Glazyrin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Roman V. Moryachkov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Vladimir V. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina Shchugoreva
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina Artyushenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Vladimir A. Mironov
- Department of Chemistry, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu 702-701, South Korea
| | - Dmitry I. Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, Jyväskylä 40014, Finland
| | - Vladimir A. Khorzhevskii
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, 3d Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Anton V. Gorbushin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Anastasia A. Koshmanova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Elena D. Nikolaeva
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Igor P. Grinev
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Ivan I. Voronkovskii
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Inter-District Ambulance Hospital named after N.S. Karpovich, 17 Kurchatova, Krasnoyarsk 660062, Russia
| | - Daniil S. Grek
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Kirill V. Belugin
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexander A. Volzhentsev
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Oleg N. Badmaev
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia A. Luzan
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Kirill A. Lukyanenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Georgy Peters
- National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
| | - Ivan N. Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
| | - Andrey K. Kirichenko
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Petr V. Konarev
- National Research Center Kurchatov Institute, 1 Akademika Kurchatova, Moscow 123182, Russia
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre “Crystallography and Photonics” RAS, 59 Leninsky pr., Moscow 119333, Russia
| | - Evgeny V. Morozov
- Institute of Chemistry and Chemical Technology SB RAS – The Branch of Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, Krasnoyarsk 660036, Russia
| | - Gleb G. Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Ana Gargaun
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Darija Muharemagic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
| | - Sergey S. Zamay
- Department of Molecular Electronics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences”, 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Elena V. Kochkina
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Maya A. Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 8 Lavrentyev Avenue, Novosibirsk 630090, Russia
| | - Tatiana E. Smolyarova
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Alexey E. Sokolov
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Andrey A. Modestov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Nikolay A. Tokarev
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Nikolay V. Shepelevich
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anastasia V. Ozerskaya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia G. Chanchikova
- Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexey V. Krat
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
| | - Ruslan A. Zukov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Krasnoyarsk Regional Clinical Cancer Center, 16 1-ya Smolenskaya, Krasnoyarsk 660133, Russia
| | - Varvara I. Bakhtina
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Pavel G. Shnyakin
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Pavel A. Shesternya
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Valery A. Svetlichnyi
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, 36 Lenina, Tomsk 634050, Russia
| | - Marina M. Petrova
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Ivan P. Artyukhov
- Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N6N5, Canada
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11
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Zamay TN, Starkov AK, Kolovskaya OS, Zamay GS, Veprintsev DV, Luzan N, Nikolaeva ED, Lukyanenko KA, Artyushenko PV, Shchugoreva IA, Glazyrin YE, Koshmanova AA, Krat AV, Tereshina DS, Zamay SS, Pats YS, Zukov RA, Tomilin FN, Berezovski MV, Kichkailo AS. Nucleic Acid Aptamers Increase the Anticancer Efficiency and Reduce the Toxicity of Cisplatin-Arabinogalactan Conjugates In Vivo. Nucleic Acid Ther 2022; 32:497-506. [PMID: 35921069 DOI: 10.1089/nat.2022.0024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cisplatin is an effective drug for treating various cancer types. However, it is highly toxic for both healthy and tumor cells. Therefore, there is a need to reduce its therapeutic dose and increase targeted bioavailability. One of the ways to achieve this could be the coating of cisplatin with polysaccharides and specific carriers for targeted delivery. Nucleic acid aptamers could be used as carriers for the specific delivery of medicine to cancer cells. Cisplatin-arabinogalactan-aptamer (Cis-AG-Ap) conjugate was synthesized based on Cis-dichlorodiammineplatinum, Siberian larch arabinogalactan, and aptamer AS-42 specific to heat-shock proteins (HSP) 71 kDa (Hspa8) and HSP 90-beta (Hsp90ab1). The antitumor effect was estimated using ascites and metastatic Ehrlich tumor models. Cis-AG-Ap toxicity was assessed by blood biochemistry on healthy mice. Here, we demonstrated enhanced anticancer activity of Cis-AG-Ap and its specific accumulation in tumor foci. It was shown that targeted delivery allowed a 15-fold reduction in the therapeutic dose of cisplatin and its toxicity. Cis-AG-Ap sufficiently suppressed the growth of Ehrlich's ascites carcinoma, the mass and extent of tumor metastasis in vivo. Arabinogalactan and the aptamers promoted cisplatin efficiency by enhancing its bioavailability. The described strategy could be very promising for targeted anticancer therapy.
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Affiliation(s)
- Tatiana N Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Alexander K Starkov
- Institute of Chemistry and Chemical Technology SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS," Krasnoyarsk, 660036, Russia
| | - Olga S Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Galina S Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Dmitry V Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia
| | - Natalia Luzan
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Elena D Nikolaeva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Kirill A Lukyanenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia
| | - Polina V Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia
| | - Irina A Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia.,Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia
| | - Yury E Glazyrin
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Anastasia A Koshmanova
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Alexey V Krat
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Dariya S Tereshina
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Sergey S Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia
| | - Yuriy S Pats
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Ruslan A Zukov
- Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
| | - Felix N Tomilin
- Department of Chemistry, Siberian Federal University, Krasnoyarsk, Russia.,Laboratory for Physics of Magnetic Phenomena, Kirensky Institute of Physics, Federal Research Center Krasnoyarsk Science Center SB RAS, Krasnoyarsk, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Anna S Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Research Center" of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk, Russia.,Laboratory For Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenecky, Krasnoyarsk, Russia
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12
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Pane K, Quintavalle C, Nuzzo S, Ingenito F, Roscigno G, Affinito A, Scognamiglio I, Pattanayak B, Gallo E, Accardo A, Thomas G, Minic Z, Berezovski MV, Franzese M, Condorelli G. Comparative Proteomic Profiling of Secreted Extracellular Vesicles from Breast Fibroadenoma and Malignant Lesions: A Pilot Study. Int J Mol Sci 2022; 23:ijms23073989. [PMID: 35409352 PMCID: PMC8999736 DOI: 10.3390/ijms23073989] [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: 02/04/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 02/01/2023] Open
Abstract
Extracellular vesicles (EVs) shuttle proteins, RNA, DNA, and lipids crucial for cell-to-cell communication. Recent findings have highlighted that EVs, by virtue of their cargo, may also contribute to breast cancer (BC) growth and metastatic dissemination. Indeed, EVs are gaining great interest as non-invasive cancer biomarkers. However, little is known about the biological and physical properties of EVs from malignant BC lesions, and even less is understood about EVs from non-malignant lesions, such as breast fibroadenoma (FAD), which are clinically managed using conservative approaches. Thus, for this pilot study, we attempted to purify and explore the proteomic profiles of EVs from benign breast lesions, HER2+ BCs, triple–negative BCs (TNBCs), and continuous BC cell lines (i.e., BT-549, MCF–10A, and MDA-MB-231), combining experimental and semi-quantitative approaches. Of note, proteome-wide analyses showed 49 common proteins across EVs harvested from FAD, HER2+ BCs, TNBCs, and model BC lines. This is the first feasibility study evaluating the physicochemical composition and proteome of EVs from benign breast cells and primary and immortalized BC cells. Our preliminary results hold promise for possible implications in precision medicine for BC.
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Affiliation(s)
- Katia Pane
- IRCCS SYNLAB SDN, Via E. Gianturco 113, 80143 Naples, Italy; (K.P.); (S.N.); (E.G.)
| | - Cristina Quintavalle
- Institute for Experimental Endocrinology and Oncology (IEOS), National Research Council (CNR), Via Pansini 5, 80131 Naples, Italy;
| | - Silvia Nuzzo
- IRCCS SYNLAB SDN, Via E. Gianturco 113, 80143 Naples, Italy; (K.P.); (S.N.); (E.G.)
| | - Francesco Ingenito
- Percuros BV, Eerbeeklaan 42, 2573 HT Den Haag, The Netherlands; (F.I.); (G.R.); (A.A.)
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini 15, 80131 Naples, Italy; (I.S.); (B.P.)
| | - Giuseppina Roscigno
- Percuros BV, Eerbeeklaan 42, 2573 HT Den Haag, The Netherlands; (F.I.); (G.R.); (A.A.)
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini 15, 80131 Naples, Italy; (I.S.); (B.P.)
| | - Alessandra Affinito
- Percuros BV, Eerbeeklaan 42, 2573 HT Den Haag, The Netherlands; (F.I.); (G.R.); (A.A.)
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini 15, 80131 Naples, Italy; (I.S.); (B.P.)
| | - Iolanda Scognamiglio
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini 15, 80131 Naples, Italy; (I.S.); (B.P.)
| | - Birlipta Pattanayak
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini 15, 80131 Naples, Italy; (I.S.); (B.P.)
| | - Enrico Gallo
- IRCCS SYNLAB SDN, Via E. Gianturco 113, 80143 Naples, Italy; (K.P.); (S.N.); (E.G.)
| | - Antonella Accardo
- Department of Pharmacy and Research Centre on Bioactive Peptides (CIRPeB), University of Naples “Federico II”, Via Mezzocannone 16, 80134 Naples, Italy;
| | - Guglielmo Thomas
- Breast Unit Clinica Mediterranea, Mediterranea Cardiocentro, Via Orazio 2, 80122 Naples, Italy;
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (Z.M.); (M.V.B.)
| | - Maxim V. Berezovski
- John L. Holmes Mass Spectrometry Facility, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (Z.M.); (M.V.B.)
| | - Monica Franzese
- IRCCS SYNLAB SDN, Via E. Gianturco 113, 80143 Naples, Italy; (K.P.); (S.N.); (E.G.)
- Correspondence: (M.F.); (G.C.)
| | - Gerolama Condorelli
- Department of Molecular Medicine and Medical Biotechnology, Federico II University of Naples, Via Pansini 15, 80131 Naples, Italy; (I.S.); (B.P.)
- IRCCS Istituto Neurologico Mediterraneo (INM) Neuromed, Via Atinense 18, 86077 Pozzilli, Italy
- Correspondence: (M.F.); (G.C.)
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13
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Medić A, Hüttmann N, Lješević M, Risha Y, Berezovski MV, Minić Z, Karadžić I. A study of the flexibility of the carbon catabolic pathways of extremophilic P. aeruginosa san ai exposed to benzoate versus glucose as sole carbon sources by multi omics analytical platform. Microbiol Res 2022; 259:126998. [PMID: 35276454 DOI: 10.1016/j.micres.2022.126998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/17/2022] [Accepted: 02/26/2022] [Indexed: 10/19/2022]
Abstract
Polyextremophilic, hydrocarbonoclastic Pseudomonas aeruginosa san ai can survive under extreme environmental challenges in the presence of a variety of pollutants such as organic solvents and hydrocarbons, particularly aromatics, heavy metals, and high pH. To date, the metabolic plasticity of the extremophilic P. aeruginosa, has not been sufficiently studied in regard to the effect of changing carbon sources. Therefore, the present study explores the carbon metabolic pathways of polyextremophilic P. aeruginosa san ai grown on sodium benzoate versus glucose and its potential for aromatic degradation. P. aeruginosa san ai removed/metabolised nearly 430 mg/L of benzoate for 48 h, demonstrating a high capacity for aromatic degradation. Comparative functional proteomics, targeted metabolomics and genomics analytical approaches were employed to study the carbon metabolism of the P. aeruginosa san ai. Functional proteomic study of selected enzymes participating in the β-ketoadipate and the Entner-Doudoroff pathways revealed a metabolic reconfiguration induced by benzoate compared to glucose. Metabolome analysis implied the existence of both catechol and protocatechuate branches of the β-ketoadipate pathway. Enzymatic study of benzoate grown cultures confirmed the activity of the ortho- catechol branch of the β-ketoadipate pathway. Even high concentrations of benzoate did not show increased stress protein synthesis, testifying to its extremophilic nature capable of surviving in harsh conditions. This ability of Pseudomonas aeruginosa san ai to efficiently degrade benzoate can provide a wide range of use of this strain in environmental and agricultural application.
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Affiliation(s)
- Ana Medić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia
| | - Nico Hüttmann
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Marija Lješević
- University of Belgrade, Institute of Chemistry, Technology and Metallurgy, Department of Chemistry, Njegoševa 12, 11000 Belgrade, Serbia
| | - Yousef Risha
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Maxim V Berezovski
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Zoran Minić
- University of Ottawa, John L. Holmes Mass Spectrometry Facility, 10 Marie-Curie, Marion Hall, K1N 6N5 Ottawa, ON, Canada
| | - Ivanka Karadžić
- University of Belgrade, Faculty of Medicine, Department of Chemistry, Belgrade, Serbia.
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14
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Mironov V, Shchugoreva IA, Artyushenko PV, Morozov D, Borbone N, Oliviero G, Zamay TN, Moryachkov RV, Kolovskaya OS, Lukyanenko KA, Song Y, Merkuleva IA, Zabluda VN, Peters G, Koroleva LS, Veprintsev DV, Glazyrin YE, Volosnikova EA, Belenkaya SV, Esina TI, Isaeva AA, Nesmeyanova VS, Shanshin DV, Berlina AN, Komova NS, Svetlichnyi VA, Silnikov VN, Shcherbakov DN, Zamay GS, Zamay SS, Smolyarova T, Tikhonova EP, Chen KH, Jeng U, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, Kichkailo AS. Cover Feature: Structure‐ and Interaction‐Based Design of Anti‐SARS‐CoV‐2 Aptamers (Chem. Eur. J. 12/2022). Chemistry 2022. [PMCID: PMC9086947 DOI: 10.1002/chem.202200378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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15
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Mironov V, Shchugoreva IA, Artyushenko PV, Morozov D, Borbone N, Oliviero G, Zamay TN, Moryachkov RV, Kolovskaya OS, Lukyanenko KA, Song Y, Merkuleva IA, Zabluda VN, Peters G, Koroleva LS, Veprintsev DV, Glazyrin YE, Volosnikova EA, Belenkaya SV, Esina TI, Isaeva AA, Nesmeyanova VS, Shanshin DV, Berlina AN, Komova NS, Svetlichnyi VA, Silnikov VN, Shcherbakov DN, Zamay GS, Zamay SS, Smolyarova T, Tikhonova EP, Chen KH, Jeng U, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, Kichkailo AS. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers. Chemistry 2022; 28:e202104481. [PMID: 35025110 PMCID: PMC9015568 DOI: 10.1002/chem.202104481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/16/2021] [Indexed: 11/10/2022]
Abstract
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.
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16
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Ozerskaya AV, Zamay TN, Kolovskaya OS, Tokarev NA, Belugin KV, Chanchikova NG, Badmaev ON, Zamay GS, Shchugoreva IA, Moryachkov RV, Zabluda VN, Khorzhevskii VA, Shepelevich N, Gappoev SV, Karlova EA, Saveleva AS, Volzhentsev AA, Blagodatova AN, Lukyanenko KA, Veprintsev DV, Smolyarova TE, Tomilin FN, Zamay SS, Silnikov VN, Berezovski MV, Kichkailo AS. 11C-radiolabeled aptamer for imaging of tumors and metastases using positron emission tomography- computed tomography. Mol Ther Nucleic Acids 2021; 26:1159-1172. [PMID: 34853715 PMCID: PMC8601970 DOI: 10.1016/j.omtn.2021.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/30/2021] [Accepted: 10/19/2021] [Indexed: 11/25/2022]
Abstract
Identification of primary tumors and metastasis sites is an essential step in cancer diagnostics and the following treatment. Positron emission tomography-computed tomography (PET/CT) is one of the most reliable methods for scanning the whole organism for malignancies. In this work, we synthesized an 11C-labeled oligonucleotide primer and hybridized it to an anti-cancer DNA aptamer. The 11C-aptamer was applied for in vivo imaging of Ehrlich ascites carcinoma and its metastases in mice using PET/CT. The imaging experiments with the 11C-aptamer determined very small primary and secondary tumors of 3 mm2 and less. We also compared 11C imaging with the standard radiotracer, 2-deoxy-2-[fluorine-18]fluoro-D-glucose (18F-FDG), and found better selectivity of the 11C-aptamer to metastatic lesions in the metabolically active organs than 18F-FDG. 11C radionuclide with an ultra-short (20.38 min) half-life is considered safest for PET/CT imaging and does not cause false-positive results in heart imaging. Its combination with aptamers gives us high-specificity and high-contrast imaging of cancer cells and can be applied for PET/CT-guided drug delivery in cancer therapies.
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Affiliation(s)
- Anastasia V. Ozerskaya
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Olga S. Kolovskaya
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Nikolay A. Tokarev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Kirill V. Belugin
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Natalia G. Chanchikova
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Oleg N. Badmaev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Galina S. Zamay
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | | | - Roman V. Moryachkov
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
- Kirensky Institute of Physics, Krasnoyarsk, Russia
| | | | - Vladimir A. Khorzhevskii
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Nikolay Shepelevich
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Stanislav V. Gappoev
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia
| | - Elena A. Karlova
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anastasia S. Saveleva
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Alexander A. Volzhentsev
- Federal Siberian Research Clinical Centre Under the Federal Medical Biological Agency, Krasnoyarsk, Russia
| | - Anna N. Blagodatova
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
| | - Kirill A. Lukyanenko
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | | | - Tatyana E. Smolyarova
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
- Kirensky Institute of Physics, Krasnoyarsk, Russia
| | | | - Sergey S. Zamay
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
| | - Vladimir N. Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Anna S. Kichkailo
- Krasnoyarsk State Medical University named after Prof. V.F. Voino-Yasenetsky, Krasnoyarsk, Russia
- Federal Research Center Krasnoyarsk Science- Center SB RAS, Krasnoyarsk, Russia
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17
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Shabalina AV, Sharko DO, Glazyrin YE, Bolshevich EA, Dubinina OV, Kim AM, Veprintsev DV, Lapin IN, Zamay GS, Krat AV, Zamay SS, Svetlichnyi VA, Kichkailo AS, Berezovski MV. Development of Electrochemical Aptasensor for Lung Cancer Diagnostics in Human Blood. Sensors (Basel) 2021; 21:s21237851. [PMID: 34883850 PMCID: PMC8659852 DOI: 10.3390/s21237851] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 02/04/2023]
Abstract
We describe the preparation and characterization of an aptamer-based electrochemical sensor to lung cancer tumor markers in human blood. The highly reproducible aptamer sensing layer with a high density (up to 70% coverage) on the gold electrode was made. Electrochemical methods and confocal laser scanning microscopy were used to study the stability of the aptamer layer structure and binding ability. A new blocking agent, a thiolated oligonucleotide with an unrelated sequence, was applied to fill the aptamer layer’s defects. Electrochemical aptasensor signal processing was enhanced using deep learning and computer simulation of the experimental data array. It was found that the combinations (coupled and tripled) of cyclic voltammogram features allowed for distinguishing between the samples from lung cancer patients and healthy candidates with a mean accuracy of 0.73. The capacitive component from the non-Faradic electrochemical impedance spectroscopy data indicated the tumor marker’s presence in a sample. These findings allowed for the creation of highly informative aptasensors for early lung cancer diagnostics.
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Affiliation(s)
- Anastasiia V. Shabalina
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Darya O. Sharko
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Yury E. Glazyrin
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Elena A. Bolshevich
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Oksana V. Dubinina
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Anastasiia M. Kim
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Dmitry V. Veprintsev
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
| | - Ivan N. Lapin
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Galina S. Zamay
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Alexey V. Krat
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
- Krasnoyarsk Regional Clinical Cancer Center Named after A.I. Kryzhanovsky, 660133 Krasnoyarsk, Russia
| | - Sergey S. Zamay
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Valery A. Svetlichnyi
- Siberian Physical-Technical Institute, Tomsk State University, 634050 Tomsk, Russia; (A.V.S.); (D.O.S.); (E.A.B.); (O.V.D.); (A.M.K.); (I.N.L.); (V.A.S.)
| | - Anna S. Kichkailo
- Federal Research Center, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science, 660036 Krasnoyarsk, Russia; (Y.E.G.); (D.V.V.); (G.S.Z.); (S.S.Z.)
- Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
- Correspondence: (A.S.K.); (M.V.B.)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, AB K1N 6N5, Canada
- Correspondence: (A.S.K.); (M.V.B.)
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18
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Morozov D, Mironov V, Moryachkov RV, Shchugoreva IA, Artyushenko PV, Zamay GS, Kolovskaya OS, Zamay TN, Krat AV, Molodenskiy DS, Zabluda VN, Veprintsev DV, Sokolov AE, Zukov RA, Berezovski MV, Tomilin FN, Fedorov DG, Alexeev Y, Kichkailo AS. The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer. Mol Ther Nucleic Acids 2021; 25:316-327. [PMID: 34458013 PMCID: PMC8379633 DOI: 10.1016/j.omtn.2021.07.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/17/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.
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Affiliation(s)
- Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, P.O. Box 35, 40014 Jyväskylä, Finland
| | - Vladimir Mironov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Roman V. Moryachkov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Irina A. Shchugoreva
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Polina V. Artyushenko
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Galina S. Zamay
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Olga S. Kolovskaya
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Tatiana N. Zamay
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey V. Krat
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Dmitry S. Molodenskiy
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Vladimir N. Zabluda
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Dmitry V. Veprintsev
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey E. Sokolov
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
| | - Ruslan A. Zukov
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON K1N 6N5, Canada
| | - Felix N. Tomilin
- Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, 50/38 Akademgorodok, Krasnoyarsk 660036, Russia
- Department of Chemistry, Siberian Federal University, 79 Svobodny pr., Krasnoyarsk 660041, Russia
| | - Dmitri G. Fedorov
- Research Center for Computational Design of Advanced Functional Materials, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8568, Japan
| | - Yuri Alexeev
- Computational Science Division, Argonne National Laboratory, Lemont, IL, USA
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center SB RAS,” 50 Akademgorodok, Krasnoyarsk 660036, Russia
- Krasnoyarsk State Medical University, 1 Partizana Zheleznyaka, Krasnoyarsk 660022, Russia
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19
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Galindo-Luján R, Pont L, Minic Z, Berezovski MV, Sanz-Nebot V, Benavente F. Characterization and differentiation of quinoa seed proteomes by label-free mass spectrometry-based shotgun proteomics. Food Chem 2021; 363:130250. [PMID: 34120052 DOI: 10.1016/j.foodchem.2021.130250] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/19/2022]
Abstract
Quinoa seed proteins are of prime importance in human nutrition and in plant breeding for cultivar identification and improvement. In this study, proteins from seeds of black, red, white quinoa from Peru and white quinoa from Bolivia (also known as royal) were extracted, digested and analyzed by nano-liquid chromatography coupled to Orbitrap tandem mass spectrometry (LC-MS/MS). The raw mass spectra data were processed for identification and label-free quantification (LFQ) using MaxQuant/Andromeda against a specific quinoa database from The National Center for Biotechnology Information (NCBI). In total, 1,211 quinoa proteins (85 were uncharacterized) were identified. Inspection and visualization using Venn diagrams, heat maps and Gene Ontology (GO) graphs revealed proteome similarities and differences between the four varieties. The presented data provides the most comprehensive experimental quinoa seed proteome map existing to date in the literature, as a starting point for more specific characterization and nutritional studies of quinoa and quinoa-containing foodstuff.
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Affiliation(s)
- Rocío Galindo-Luján
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Laura Pont
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Maxim V Berezovski
- John L. Holmes Mass Spectrometry Facility, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB), University of Barcelona, 08028 Barcelona, Spain.
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20
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Bakhtina VI, Veprintsev DV, Zamay TN, Demko IV, Mironov GG, Berezovski MV, Petrova MM, Kichkailo AS, Glazyrin YE. Proteomics-Based Regression Model for Assessing the Development of Chronic Lymphocytic Leukemia. Proteomes 2021; 9:proteomes9010003. [PMID: 33498752 PMCID: PMC7924318 DOI: 10.3390/proteomes9010003] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/09/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022] Open
Abstract
The clinical course of chronic lymphocytic leukemia (CLL) is very ambiguous, showing either an indolent nature of the disease or having latent dangerous progression, which, if diagnosed, will require an urgent therapy. The prognosis of the course of the disease and the estimation of the time of therapy initiation are crucial for the selection of a successful treatment strategy. A reliable estimating index is needed to assign newly diagnosed CLL patients to the prognostic groups. In this work, we evaluated the comparative expressions of proteins in CLL blood cells using a label-free quantification by mass spectrometry and calculated the integrated proteomic indexes for a group of patients who received therapy after the blood sampling over different periods of time. Using a two-factor linear regression analysis based on these data, we propose a new pipeline for evaluating model development for estimation of the moment of therapy initiation for newly diagnosed CLL patients.
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Affiliation(s)
- Varvara I. Bakhtina
- Department of Hematology, Krasnoyarsk Regional Clinical Hospital, 660022 Krasnoyarsk, Russia; (V.I.B.); (I.V.D.)
| | - Dmitry V. Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia; (D.V.V.); (A.S.K.)
| | - Tatiana N. Zamay
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Irina V. Demko
- Department of Hematology, Krasnoyarsk Regional Clinical Hospital, 660022 Krasnoyarsk, Russia; (V.I.B.); (I.V.D.)
- Faculty of Medicine, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Gleb G. Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada; (G.G.M.); (M.V.B.)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada; (G.G.M.); (M.V.B.)
| | - Marina M. Petrova
- Faculty of Medicine, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Anna S. Kichkailo
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia; (D.V.V.); (A.S.K.)
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Yury E. Glazyrin
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia; (D.V.V.); (A.S.K.)
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
- Correspondence:
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21
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Risha Y, Minic Z, Ghobadloo SM, Berezovski MV. The proteomic analysis of breast cell line exosomes reveals disease patterns and potential biomarkers. Sci Rep 2020; 10:13572. [PMID: 32782317 PMCID: PMC7419295 DOI: 10.1038/s41598-020-70393-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 07/21/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer cells release small extracellular vesicles, exosomes, that have been shown to contribute to various aspects of cancer development and progression. Differential analysis of exosomal proteomes from cancerous and non-tumorigenic breast cell lines can provide valuable information related to breast cancer progression and metastasis. Moreover, such a comparison can be explored to find potentially new protein biomarkers for early disease detection. In this study, exosomal proteomes of MDA-MB-231, a metastatic breast cancer cell line, and MCF-10A, a non-cancerous epithelial breast cell line, were identified by nano-liquid chromatography coupled to tandem mass spectrometry. We also tested three exosomes isolation methods (ExoQuick, Ultracentrifugation (UC), and Ultrafiltration–Ultracentrifugation) and detergents (n-dodecyl β-d-maltoside, Triton X-100, and Digitonin) for solubilization of exosomal proteins and enhanced detection by mass spectrometry. A total of 1,107 exosomal proteins were identified in both cell lines, 726 of which were unique to the MDA-MB-231 breast cancer cell line. Among them, 87 proteins were predicted to be relevant to breast cancer and 16 proteins to cancer metastasis. Three exosomal membrane/surface proteins, glucose transporter 1 (GLUT-1), glypican 1 (GPC-1), and disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), were identified as potential breast cancer biomarkers and validated with Western blotting and high-resolution flow cytometry. We demonstrated that exosomes are a rich source of breast cancer-related proteins and surface biomarkers that may be used for disease diagnosis and prognosis.
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Affiliation(s)
- Yousef Risha
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Zoran Minic
- John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, Canada
| | - Shahrokh M Ghobadloo
- Cellular Imaging and Cytometry Facility, Faculty of Science, University of Ottawa, Ottawa, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada. .,John L. Holmes Mass Spectrometry Facility, Faculty of Science, University of Ottawa, Ottawa, Canada. .,Cellular Imaging and Cytometry Facility, Faculty of Science, University of Ottawa, Ottawa, Canada.
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22
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Glazyrin YE, Veprintsev DV, Ler IA, Rossovskaya ML, Varygina SA, Glizer SL, Zamay TN, Petrova MM, Minic Z, Berezovski MV, Kichkailo AS. Proteomics-Based Machine Learning Approach as an Alternative to Conventional Biomarkers for Differential Diagnosis of Chronic Kidney Diseases. Int J Mol Sci 2020; 21:ijms21134802. [PMID: 32645927 PMCID: PMC7369970 DOI: 10.3390/ijms21134802] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022] Open
Abstract
Diabetic nephropathy, hypertension, and glomerulonephritis are the most common causes of chronic kidney diseases (CKD). Since CKD of various origins may not become apparent until kidney function is significantly impaired, a differential diagnosis and an appropriate treatment are needed at the very early stages. Conventional biomarkers may not have sufficient separation capabilities, while a full-proteomic approach may be used for these purposes. In the current study, several machine learning algorithms were examined for the differential diagnosis of CKD of three origins. The tested dataset was based on whole proteomic data obtained after the mass spectrometric analysis of plasma and urine samples of 34 CKD patients and the use of label-free quantification approach. The k-nearest-neighbors algorithm showed the possibility of separation of a healthy group from renal patients in general by proteomics data of plasma with high confidence (97.8%). This algorithm has also be proven to be the best of the three tested for distinguishing the groups of patients with diabetic nephropathy and glomerulonephritis according to proteomics data of plasma (96.3% of correct decisions). The group of hypertensive nephropathy could not be reliably separated according to plasma data, whereas analysis of entire proteomics data of urine did not allow differentiating the three diseases. Nevertheless, the group of hypertensive nephropathy was reliably separated from all other renal patients using the k-nearest-neighbors classifier “one against all” with 100% of accuracy by urine proteome data. The tested algorithms show good abilities to differentiate the various groups across proteomic data sets, which may help to avoid invasive intervention for the verification of the glomerulonephritis subtypes, as well as to differentiate hypertensive and diabetic nephropathy in the early stages based not on individual biomarkers, but on the whole proteomic composition of urine and blood.
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Affiliation(s)
- Yury E. Glazyrin
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia; (T.N.Z.); (A.S.K.)
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia;
- Correspondence:
| | - Dmitry V. Veprintsev
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia;
| | - Irina A. Ler
- Department of Nephrology, Krasnoyarsk Interdistrict Clinical Hospital of Emergency Medical Care Named after N.S. Karpovich, 660062 Krasnoyarsk, Russia; (I.A.L.); (M.L.R.); (S.A.V.); (S.L.G.)
| | - Maria L. Rossovskaya
- Department of Nephrology, Krasnoyarsk Interdistrict Clinical Hospital of Emergency Medical Care Named after N.S. Karpovich, 660062 Krasnoyarsk, Russia; (I.A.L.); (M.L.R.); (S.A.V.); (S.L.G.)
| | - Svetlana A. Varygina
- Department of Nephrology, Krasnoyarsk Interdistrict Clinical Hospital of Emergency Medical Care Named after N.S. Karpovich, 660062 Krasnoyarsk, Russia; (I.A.L.); (M.L.R.); (S.A.V.); (S.L.G.)
| | - Sofia L. Glizer
- Department of Nephrology, Krasnoyarsk Interdistrict Clinical Hospital of Emergency Medical Care Named after N.S. Karpovich, 660062 Krasnoyarsk, Russia; (I.A.L.); (M.L.R.); (S.A.V.); (S.L.G.)
- Faculty of Medicine, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Tatiana N. Zamay
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia; (T.N.Z.); (A.S.K.)
| | - Marina M. Petrova
- Faculty of Medicine, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia;
| | - Zoran Minic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada; (Z.M.); (M.V.B.)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N6N5, Canada; (Z.M.); (M.V.B.)
| | - Anna S. Kichkailo
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University Named after Prof. V.F. Voyno-Yasenetsky, 660022 Krasnoyarsk, Russia; (T.N.Z.); (A.S.K.)
- Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”, 660036 Krasnoyarsk, Russia;
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Lupu L, Wiegand P, Hüttmann N, Rawer S, Kleinekofort W, Shugureva I, Kichkailo AS, Tomilin FN, Lazarev A, Berezovski MV, Przybylski M. Front Cover: Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C‐Met by Proteolytic Affinity‐Mass Spectrometry (ChemMedChem 4/2020). ChemMedChem 2020. [DOI: 10.1002/cmdc.202000050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Loredana Lupu
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| | - Pascal Wiegand
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| | - Nico Hüttmann
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa Ottawa, ON K1N 6N5 Canada
| | - Stephan Rawer
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
| | - Wolfgang Kleinekofort
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
- Dept. of Engineering SciencesRhein Main University 65428 Rüsselsheim am Main Germany
| | - Irina Shugureva
- Siberian Federal University Krasnoyarsk 66041 Russia
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”Laboratory for Digital Controlled Drugs and Theranostics Krasnoyarsk 660036 Russia
| | - Anna S. Kichkailo
- Federal Research Center “Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science”Laboratory for Digital Controlled Drugs and Theranostics Krasnoyarsk 660036 Russia
| | - Felix N. Tomilin
- Kirensky Institute of PhysicsRussian Academy of Sciences Siberian Branch Krasnoyarsk 660036 Russia
- Siberian Federal University Krasnoyarsk 66041 Russia
| | - Alexander Lazarev
- Pressure Biosciences Inc. 14 Norfolk Ave. South Easton, MA 02375 USA
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular SciencesUniversity of Ottawa Ottawa, ON K1N 6N5 Canada
| | - Michael Przybylski
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry Marktstraße 29 65428 Rüsselsheim am Main Germany
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Affinito A, Quintavalle C, Esposito CL, Roscigno G, Giordano C, Nuzzo S, Ricci-Vitiani L, Scognamiglio I, Minic Z, Pallini R, Berezovski MV, de Francisis V, Condorelli G. Targeting Ephrin Receptor Tyrosine Kinase A2 with a Selective Aptamer for Glioblastoma Stem Cells. Mol Ther Nucleic Acids 2020; 20:176-185. [PMID: 32169805 PMCID: PMC7068199 DOI: 10.1016/j.omtn.2020.02.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/21/2020] [Accepted: 02/03/2020] [Indexed: 12/29/2022]
Abstract
Despite the benefits associated with radiotherapy and chemotherapy for glioblastoma (GBM) treatment, most patients experience a relapse following initial therapy. Recurrent or progressive GBM usually does not respond anymore to standard therapy, and this is associated with poor patient outcome. GBM stem cells (GSCs) are a subset of cells resistant to radiotherapy and chemotherapy and play a role in tumor recurrence. The targeting of GSCs and the identification of novel markers are crucial issues in the development of innovative strategies for GBM eradication. By differential cell SELEX (systematic evolution of ligands by exponential enrichment), we have recently described two RNA aptamers, that is, the 40L sequence and its truncated form A40s, able to bind the cell surface of human GSCs. Both aptamers were selective for stem-like growing GBM cells and are rapidly internalized into target cells. In this study, we demonstrate that their binding to cells is mediated by direct recognition of the ephrin type-A receptor 2 (EphA2). Functionally, the two aptamers were able to inhibit cell growth, stemness, and migration of GSCs. Furthermore, A40s was able to cross the blood-brain barrier (BBB) and was stable in serum in in vitro experiments. These results suggest that 40L and A40s represent innovative potential therapeutic tools for GBM.
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Affiliation(s)
- Alessandra Affinito
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Via Tommaso de Amicis 95, 80131 Naples, Italy; Percuros B.V., Enschede, the Netherlands
| | - Cristina Quintavalle
- Percuros B.V., Enschede, the Netherlands; IEOS, CNR, Via Tommaso de Amicis 95, 80131 Naples, Italy.
| | | | - Giuseppina Roscigno
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Via Tommaso de Amicis 95, 80131 Naples, Italy
| | - Catello Giordano
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Via Tommaso de Amicis 95, 80131 Naples, Italy
| | | | - Lucia Ricci-Vitiani
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Iolanda Scognamiglio
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Via Tommaso de Amicis 95, 80131 Naples, Italy
| | - Zoran Minic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; John L. Holmes Mass Spectrometry Facility, Ottawa, ON K1N 6N5, Canada
| | - Roberto Pallini
- Institute of Neurosurgery, Università Cattolica del Sacro Cuore, Largo Agostino Gemelli 8, 00168 Rome, Italy
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; John L. Holmes Mass Spectrometry Facility, Ottawa, ON K1N 6N5, Canada
| | | | - Gerolama Condorelli
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Via Tommaso de Amicis 95, 80131 Naples, Italy; IRCCS Neuromed-Istituto Neurologico Mediterraneo Pozzilli, Pozzilli, Italy.
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25
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Lupu L, Wiegand P, Hüttmann N, Rawer S, Kleinekofort W, Shugureva I, Kichkailo AS, Tomilin FN, Lazarev A, Berezovski MV, Przybylski M. Molecular Epitope Determination of Aptamer Complexes of the Multidomain Protein C-Met by Proteolytic Affinity-Mass Spectrometry. ChemMedChem 2020; 15:363-369. [PMID: 31825565 DOI: 10.1002/cmdc.201900489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/29/2019] [Indexed: 12/21/2022]
Abstract
C-Met protein is a glycosylated receptor tyrosine kinase of the hepatocyte growth factor (HGF), composed of an α and a β chain. Upon ligand binding, C-Met transmits intracellular signals by a unique multi-substrate docking site. C-Met can be aberrantly activated leading to tumorigenesis and other diseases, and has been recognized as a biomarker in cancer diagnosis. C-Met aptamers have been recently considered a useful tool for detection of cancer biomarkers. Herein we report a molecular interaction study of human C-Met expressed in kidney cells with two DNA aptamers of 60 and 64 bases (CLN0003 and CLN0004), obtained using the SELEX (Systematic Evolution of Ligands by Exponential Enrichment) procedure. Epitope peptides of aptamer-C-Met complexes were identified by proteolytic affinity-mass spectrometry in combination with SPR biosensor analysis (PROTEX-SPR-MS), using high-pressure proteolysis for efficient digestion. High affinities (KD , 80-510 nM) were determined for aptamer-C-Met complexes, with two-step binding suggested by kinetic analysis. A linear epitope, C-Met (381-393) was identified for CLN0004, while the CLN0003 aptamer revealed an assembled epitope comprised of two peptide sequences, C-Met (524-543) and C-Met (557-568). Structure modeling of C-Met-aptamers were consistent with the identified epitopes. Specificities and affinities were ascertained by SPR analysis of the synthetic epitope peptides. The high affinities of aptamers to C-Met, and the specific epitopes revealed render them of high interest for cellular diagnostic studies.
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Affiliation(s)
- Loredana Lupu
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| | - Pascal Wiegand
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| | - Nico Hüttmann
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany.,Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Stephan Rawer
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
| | - Wolfgang Kleinekofort
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany.,Dept. of Engineering Sciences, Rhein Main University, 65428, Rüsselsheim am Main, Germany
| | - Irina Shugureva
- Siberian Federal University, Krasnoyarsk, 66041, Russia.,Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Laboratory for Digital Controlled Drugs and Theranostics, Krasnoyarsk, 660036, Russia
| | - Anna S Kichkailo
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Laboratory for Digital Controlled Drugs and Theranostics, Krasnoyarsk, 660036, Russia
| | - Felix N Tomilin
- Kirensky Institute of Physics, Russian Academy of Sciences Siberian Branch, Krasnoyarsk, 660036, Russia.,Siberian Federal University, Krasnoyarsk, 66041, Russia
| | - Alexander Lazarev
- Pressure Biosciences Inc., 14 Norfolk Ave., South Easton, MA, 02375, USA
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Michael Przybylski
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstraße 29, 65428, Rüsselsheim am Main, Germany
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Kolovskaya OS, Zamay TN, Zamay GS, Babkin VA, Medvedeva EN, Neverova NA, Kirichenko AK, Zamay SS, Lapin IN, Morozov EV, Sokolov AE, Narodov AA, Fedorov DG, Tomilin FN, Zabluda VN, Alekhina Y, Lukyanenko KA, Glazyrin YE, Svetlichnyi VA, Berezovski MV, Kichkailo AS. Aptamer-Conjugated Superparamagnetic Ferroarabinogalactan Nanoparticles for Targeted Magnetodynamic Therapy of Cancer. Cancers (Basel) 2020; 12:cancers12010216. [PMID: 31952299 PMCID: PMC7017168 DOI: 10.3390/cancers12010216] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 12/06/2019] [Revised: 01/02/2020] [Accepted: 01/10/2020] [Indexed: 11/16/2022] Open
Abstract
Nanotechnologies involving physical methods of tumor destruction using functional oligonucleotides are promising for targeted cancer therapy. Our study presents magnetodynamic therapy for selective elimination of tumor cells in vivo using DNA aptamer-functionalized magnetic nanoparticles exposed to a low frequency alternating magnetic field. We developed an enhanced targeting approach of cancer cells with aptamers and arabinogalactan. Aptamers to fibronectin (AS-14) and heat shock cognate 71 kDa protein (AS-42) facilitated the delivery of the nanoparticles to Ehrlich carcinoma cells, and arabinogalactan (AG) promoted internalization through asialoglycoprotein receptors. Specific delivery of the aptamer-modified FeAG nanoparticles to the tumor site was confirmed by magnetic resonance imaging (MRI). After the following treatment with a low frequency alternating magnetic field, AS-FeAG caused cancer cell death in vitro and tumor reduction in vivo. Histological analyses showed mechanical disruption of tumor tissues, total necrosis, cell lysis, and disruption of the extracellular matrix. The enhanced targeted magnetic theranostics with the aptamer conjugated superparamagnetic ferroarabinogalactans opens up a new venue for making biocompatible contrasting agents for MRI imaging and performing non-invasive anti-cancer therapies with a deep penetrated magnetic field.
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Affiliation(s)
- Olga S Kolovskaya
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Tatiana N Zamay
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Galina S Zamay
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Vasily A Babkin
- Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Elena N Medvedeva
- Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Nadezhda A Neverova
- Irkutsk Institute of Chemistry named after A.E. Favorsky, the Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Andrey K Kirichenko
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Sergey S Zamay
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- L.V. Kirensky Institute of Physics SB RAS-The Branch of Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia
| | - Ivan N Lapin
- Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
| | - Evgeny V Morozov
- L.V. Kirensky Institute of Physics SB RAS-The Branch of Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia
- Institute of Chemistry and Chemical Technology SB RAS-The Branch of Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia
| | - Alexey E Sokolov
- L.V. Kirensky Institute of Physics SB RAS-The Branch of Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia
- School of Engineering Physics and Radio Electronics, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Andrey A Narodov
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Dmitri G Fedorov
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8568, Japan
| | - Felix N Tomilin
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- L.V. Kirensky Institute of Physics SB RAS-The Branch of Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia
- School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Vladimir N Zabluda
- L.V. Kirensky Institute of Physics SB RAS-The Branch of Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences", 660036 Krasnoyarsk, Russia
| | - Yulia Alekhina
- Faculty of Physics, Department of Magnetism, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kirill A Lukyanenko
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
- School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Yury E Glazyrin
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
| | - Valery A Svetlichnyi
- Laboratory of Advanced Materials and Technology, Tomsk State University, 634050 Tomsk, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Anna S Kichkailo
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", 660036 Krasnoyarsk, Russia
- Laboratory for Biomolecular and Medical Technologies, Faculty of Medicine, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, 660022 Krasnoyarsk, Russia
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Grechkin YA, Grechkina SL, Zaripov EA, Fedorenko SV, Mustafina AR, Berezovski MV. Aptamer-Conjugated Tb(III)-Doped Silica Nanoparticles for Luminescent Detection of Leukemia Cells. Biomedicines 2020; 8:biomedicines8010014. [PMID: 31941078 PMCID: PMC7168109 DOI: 10.3390/biomedicines8010014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 12/12/2019] [Revised: 01/04/2020] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
DNA aptamers have many benefits for cell imaging, such as high affinity and specificity, easiness of chemical functionalization, and low cost of production. Among known aptamers, Sgc8-aptamer was selected against acute lymphoblastic leukemia cells with a dissociation constant in a nanomolar range. The aptamer was previously used for the covalent coupling with fluorescent and magnetic nanoparticles, as well as for the fabrication of aptamer-based biosensors. Among commonly used fluorescent tags, lanthanide nanoparticles offer stable luminescence with narrow, well-resolved emission peaks and the absence of photoblinking. In other words, lanthanide nanoparticles could serve as luminescence reporters and be used in biosensing. In our study, we conjugated amino- and carboxyl-modified silica-coated terbium (III) thiacalix[4]arenesulfonate luminescent nanoparticles with Sgc8-aptamer and showed the ability of the aptamer-conjugated nanoparticles to detect leukemia cells using fluorescence microscopy. In addition, we conducted a cell viability assay and confirmed that the nanoparticles do not induce spontaneous cell apoptosis or necrosis and could be potentially used for bioimaging applications.
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Affiliation(s)
- Yaroslav A. Grechkin
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (Y.A.G.); (E.A.Z.)
| | - Svetlana L. Grechkina
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia; (S.L.G.); (S.V.F.); (A.R.M.)
| | - Emil A. Zaripov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (Y.A.G.); (E.A.Z.)
| | - Svetlana V. Fedorenko
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia; (S.L.G.); (S.V.F.); (A.R.M.)
| | - Asiya R. Mustafina
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center, Russian Academy of Sciences, 420111 Kazan, Russia; (S.L.G.); (S.V.F.); (A.R.M.)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada; (Y.A.G.); (E.A.Z.)
- Correspondence:
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28
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Pero-Gascon R, Benavente F, Minic Z, Berezovski MV, Sanz-Nebot V. On-line Aptamer Affinity Solid-Phase Extraction Capillary Electrophoresis-Mass Spectrometry for the Analysis of Blood α-Synuclein. Anal Chem 2019; 92:1525-1533. [PMID: 31825201 DOI: 10.1021/acs.analchem.9b04802] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this paper, an on-line aptamer affinity solid-phase extraction capillary electrophoresis-mass spectrometry method is described for the purification, preconcentration, separation, and characterization of α-synuclein (α-syn) in blood at the intact protein level. A single-stranded DNA aptamer is used to bind with high affinity and selectivity α-syn, which is a major component of Lewy bodies, the typical aggregated protein deposits found in Parkinson's disease (PD). Under the conditions optimized with recombinant α-syn, repeatability (2.1 and 5.4% percent relative standard deviation for migration times and peak areas, respectively) and microcartridge lifetime (around 20 analyses/microcartridge) were good, the method was linear between 0.5 and 10 μg·mL-1, and limit of detection was 0.2 μg·mL-1 (100 times lower than by CE-MS, 20 μg·mL-1). The method was subsequently applied to the analysis of endogenous α-syn from red blood cells lysate of healthy controls and PD patients.
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Affiliation(s)
- Roger Pero-Gascon
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB) , University of Barcelona , Barcelona 08028 , Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB) , University of Barcelona , Barcelona 08028 , Spain
| | - Zoran Minic
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB) , University of Barcelona , Barcelona 08028 , Spain
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29
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Zamay TN, Zamay GS, Shnayder NA, Dmitrenko DV, Zamay SS, Yushchenko V, Kolovskaya OS, Susevski V, Berezovski MV, Kichkailo AS. Nucleic Acid Aptamers for Molecular Therapy of Epilepsy and Blood-Brain Barrier Damages. Mol Ther Nucleic Acids 2019; 19:157-167. [PMID: 31837605 PMCID: PMC6920299 DOI: 10.1016/j.omtn.2019.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 01/28/2023]
Abstract
Epilepsy is the fourth most prevalent brain disorder affecting millions of people of all ages. Epilepsy is divided into six categories different in etiology and molecular mechanisms; however, their common denominator is the inability to maintain ionic homeostasis. Antiepileptic drugs have a broad spectrum of action and high toxicity to the whole organism. In many cases, they could not penetrate the blood-brain barrier (BBB) and reach corresponding targets. Nucleic acid aptamers are a new and promising class of antiepileptic drugs as they are non-toxic, specific, and able to regulate the permeability of ion channels or inhibit inflammatory proteins. In this review, we summarize the mechanisms of epileptogenesis and its interconnection with the BBB and show the potential of aptamers for antiepileptic treatment.
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Affiliation(s)
- Tatiana N Zamay
- V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Galina S Zamay
- V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia; Federal Research Center, Krasnoyarsk Research Center Siberian Branch of Russian Academy of Science, Krasnoyarsk, Russia
| | - Natalia A Shnayder
- V.M. Bekhterev National Medical Research Center of Psychiatry and Neurology, Saint Petersburg, Russia
| | - Diana V Dmitrenko
- V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Sergey S Zamay
- Federal Research Center, Krasnoyarsk Research Center Siberian Branch of Russian Academy of Science, Krasnoyarsk, Russia
| | - Victoria Yushchenko
- V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia
| | - Olga S Kolovskaya
- V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia; Federal Research Center, Krasnoyarsk Research Center Siberian Branch of Russian Academy of Science, Krasnoyarsk, Russia
| | - Vanessa Susevski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada.
| | - Anna S Kichkailo
- V.F. Voyno-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia; Federal Research Center, Krasnoyarsk Research Center Siberian Branch of Russian Academy of Science, Krasnoyarsk, Russia.
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30
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Burgos-Canul YY, Canto-Canché B, Berezovski MV, Mironov G, Loyola-Vargas VM, Barba de Rosa AP, Tzec-Simá M, Brito-Argáez L, Carrillo-Pech M, Grijalva-Arango R, Muñoz-Pérez G, Islas-Flores I. The cell wall proteome from two strains of Pseudocercospora fijiensis with differences in virulence. World J Microbiol Biotechnol 2019; 35:105. [PMID: 31267317 DOI: 10.1007/s11274-019-2681-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 06/20/2019] [Indexed: 11/25/2022]
Abstract
Pseudocercospora fijiensis causes black Sigatoka disease, the most important threat to banana. The cell wall is crucial for fungal biological processes, including pathogenesis. Here, we performed cell wall proteomics analyses of two P. fijiensis strains, the highly virulent Oz2b, and the less virulent C1233 strains. Strains were starved from nitrogen to mimic the host environment. Interestingly, in vitro cultures of the C1233 strain grew faster than Oz2b in PDB medium, suggesting that C1233 survives outside the host better than the highly virulent Oz2b strain. Both strains were submitted to nitrogen starvation and the cell wall proteins were isolated and subjected to nano-HPLC-MS/MS. A total of 2686 proteins were obtained from which only 240 had a known function and thus, bioinformatics analyses were performed on this group. We found that 90 cell wall proteins were shared by both strains, 21 were unique for Oz2b and 39 for C1233. Shared proteins comprised 24 pathogenicity factors, including Avr4 and Ecp6, two effectors from P. fijiensis, while the unique proteins comprised 16 virulence factors in C1233 and 11 in Oz2b. The P. fijiensis cell wall proteome comprised canonical proteins, but thirty percent were atypical, a feature which in other phytopathogens has been interpreted as contamination. However, a comparison with the identities of atypical proteins in other reports suggests that the P. fijiensis proteins we detected were not contaminants. This is the first proteomics analysis of the P. fijiensis cell wall and our results expands the understanding of the fundamental biology of fungal phytopathogens and will help to decipher the molecular mechanisms of pathogenesis and virulence in P. fijiensis.
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Affiliation(s)
- Yamily Y Burgos-Canul
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON, K1N 6N5, Canada
| | - Gleb Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, ON, K1N 6N5, Canada
| | - Víctor M Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Ana Paulina Barba de Rosa
- IPICYT, Instituto Potosino de Investigación Científica y Tecnológica, San Luis Potosí, S.L.P., Mexico
| | - Miguel Tzec-Simá
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Ligia Brito-Argáez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Mildred Carrillo-Pech
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Rosa Grijalva-Arango
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Gilberto Muñoz-Pérez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, C.P. 97205, Mérida, Yucatán, Mexico.
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31
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Zamay GS, Kolovskaya OS, Ivanchenko TI, Zamay TN, Veprintsev DV, Grigorieva VL, Garanzha II, Krat AV, Glazyrin YE, Gargaun A, Lapin IN, Svetlichnyi VA, Berezovski MV, Kichkailo AS. Development of DNA Aptamers to Native EpCAM for Isolation of Lung Circulating Tumor Cells from Human Blood. Cancers (Basel) 2019; 11:cancers11030351. [PMID: 30871104 PMCID: PMC6468627 DOI: 10.3390/cancers11030351] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 02/06/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 02/05/2023] Open
Abstract
We selected DNA aptamers to the epithelial cell adhesion molecule (EpCAM) expressed on primary lung cancer cells isolated from the tumors of patients with non-small cell lung cancer using competitive displacement of aptamers from EpCAM by a corresponding antibody. The resulting aptamers clones showed good nanomolar affinity to EpCAM-positive lung cancer cells. Confocal microscopy imaging and spectral profiling of lung cancer tissues confirmed the same protein target for the aptamers and anti-EpCAM antibodies. Furthermore, the resulted aptamers were successfully applied for isolation and detection of circulating tumor cells in clinical samples of peripheral blood of lung cancer patients.
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Affiliation(s)
- Galina S Zamay
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
| | - Olga S Kolovskaya
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
| | - Tatiana I Ivanchenko
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
| | - Tatiana N Zamay
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
| | - Dmitry V Veprintsev
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
| | - Valentina L Grigorieva
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
| | - Irina I Garanzha
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
| | - Alexey V Krat
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
- Krasnoyarsk Regional Clinical Cancer Center named after A.I. Kryzhanovsky, Krasnoyarsk 660133, Russia.
| | - Yury E Glazyrin
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
| | - Ana Gargaun
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Ivan N Lapin
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, Tomsk 634050, Russia.
| | - Valery A Svetlichnyi
- Laboratory of Advanced Materials and Technology, Siberian Physical-Technical Institute of Tomsk State University, Tomsk 634050, Russia.
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Anna S Kichkailo
- Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk 660036, Russia.
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Krasnoyarsk 660022, Russia.
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Pero-Gascon R, Sanz-Nebot V, Berezovski MV, Benavente F. Analysis of Circulating microRNAs and Their Post-Transcriptional Modifications in Cancer Serum by On-Line Solid-Phase Extraction-Capillary Electrophoresis-Mass Spectrometry. Anal Chem 2018; 90:6618-6625. [PMID: 29730931 DOI: 10.1021/acs.analchem.8b00405] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this paper, an on-line solid-phase extraction capillary electrophoresis-mass spectrometry (SPE-CE-MS) method is described for the purification, preconcentration, separation, and characterization of endogenous microRNA (miRNA) and their post-transcriptional modifications in serum. First, analysis by CE-MS was optimized using a standard mixture of hsa-miR-21-5p (miR-21-5p) and hsa-let-7g-5p (let-7g-5p). For SPE-CE-MS, a commercial silicon carbide (SiC) resin was used to prepare the microcartridges. Under the optimized conditions with standards, the microcartridge lifetime (>25 analyses) and repeatability (2.8% RSD for the migration times; 4.4 and 6.4% RSD for the miR-21-5p and let-7g-5p peak areas, respectively) were good, the method was linear between 25 and 100 nmol·L-1, and the limit of detection (LOD) was around 10 nmol·L-1 (50 times lower than by CE-MS). In order to analyze human serum samples, an off-line sample pretreatment based on phenol/chloroform/isoamyl alcohol (PCA) extraction was necessary prior to SPE-CE-MS. The potential of the SPE-CE-MS method to screen for B-cell chronic lymphocytic leukemia (CLL) was demonstrated by an analysis of serum samples from healthy controls and patients. MicroRNAs, specifically miR-21-5p and a 23 nucleotide long 5'-phosphorylated miRNA with 3'-uridylation (iso-miR-16-5p), were only detected in the CLL patients.
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Affiliation(s)
- Roger Pero-Gascon
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB) , University of Barcelona , Barcelona 08028 , Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB) , University of Barcelona , Barcelona 08028 , Spain
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, Institute for Research on Nutrition and Food Safety (INSA·UB) , University of Barcelona , Barcelona 08028 , Spain
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Mironov GG, Bouzekri A, Watson J, Loboda O, Ornatsky O, Berezovski MV. Aptamer-facilitated mass cytometry. Anal Bioanal Chem 2018; 410:3047-3051. [PMID: 29556738 DOI: 10.1007/s00216-018-1011-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/08/2018] [Indexed: 11/29/2022]
Abstract
Mass cytometry is a novel cell-by-cell analysis technique, which uses elemental tags instead of fluorophores. Sample cells undergo rapid ionization in inductively coupled plasma and the ionized elemental tags are then analyzed by means of time-of-flight mass spectrometry. Benefits of the mass cytometry approach are in no need for compensation, the high number of detection channels (up to 100) and low background noise. In this work, we applied a biotinylated aptamer against human PTK7 receptor for characterization of positive (human acute lymphoblastic leukemia) and negative (human Burkitt's lymphoma) cells by a mass cytometry instrument. Our proof of principal experiments showed that biotinylated aptamers in conjunction with metal-labeled neutravidin can be successfully utilized for mass cytometry experiments at par with commercially available antibodies. Graphical abstract Biotinylated aptamers in conjunction with metal-labeled neutravidin bind to cell biomarkers, and then injected into the inductively coupled plasma (ICP) source, where cells are vaporized, atomized, and ionized in the plasma for subsequent mass spectrometry (MS) analysis of lanthanide metals.
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Affiliation(s)
- Gleb G Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, K1N 6N5, Canada
| | - Alexandre Bouzekri
- Fluidigm Canada Inc., 1380 Rodick Road, Suite 400, Markham, L3R 4G5, Canada
| | - Jessica Watson
- Fluidigm Canada Inc., 1380 Rodick Road, Suite 400, Markham, L3R 4G5, Canada
| | - Olga Loboda
- Fluidigm Canada Inc., 1380 Rodick Road, Suite 400, Markham, L3R 4G5, Canada
| | - Olga Ornatsky
- Fluidigm Canada Inc., 1380 Rodick Road, Suite 400, Markham, L3R 4G5, Canada
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie-Curie, Ottawa, K1N 6N5, Canada.
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Kolovskaya OS, Zamay TN, Belyanina IV, Karlova E, Garanzha I, Aleksandrovsky AS, Kirichenko A, Dubynina AV, Sokolov AE, Zamay GS, Glazyrin YE, Zamay S, Ivanchenko T, Chanchikova N, Tokarev N, Shepelevich N, Ozerskaya A, Badrin E, Belugin K, Belkin S, Zabluda V, Gargaun A, Berezovski MV, Kichkailo AS. Aptamer-Targeted Plasmonic Photothermal Therapy of Cancer. Mol Ther Nucleic Acids 2017; 9:12-21. [PMID: 29246290 PMCID: PMC5582647 DOI: 10.1016/j.omtn.2017.08.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 08/11/2017] [Accepted: 08/11/2017] [Indexed: 11/30/2022]
Abstract
Novel nanoscale bioconjugates combining unique plasmonic photothermal properties of gold nanoparticles (AuNPs) with targeted delivery using cell-specific DNA aptamers have a tremendous potential for medical diagnostics and therapy of many cell-based diseases. In this study, we demonstrate the high anti-cancer activity of aptamer-conjugated, 37-nm spherical gold nanoparticles toward Ehrlich carcinoma in tumor-bearing mice after photothermal treatment. The synthetic anti-tumor aptamers bring the nanoparticles precisely to the desired cells and selectively eliminate cancer cells after the subsequent laser treatment. To prove tumor eradication, we used positron emission tomography (PET) utilizing radioactive glucose and computer tomography, followed by histological analysis of cancer tissue. Three injections of aptamer-conjugated AuNPs and 5 min of laser irradiations are enough to make the tumor undetectable by PET. Histological analysis proves PET results and shows lower damage of healthy tissue in addition to a higher treatment efficiency and selectivity of the gold nanoparticles functionalized with aptamers in comparison to control experiments using free unconjugated nanoparticles.
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Affiliation(s)
- Olga S Kolovskaya
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Tatiana N Zamay
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Siberian Federal University, Krasnoyarsk, Russia
| | - Irina V Belyanina
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Siberian Federal University, Krasnoyarsk, Russia
| | - Elena Karlova
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Irina Garanzha
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Siberian Federal University, Krasnoyarsk, Russia
| | - Aleksandr S Aleksandrovsky
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia; Siberian Federal University, Krasnoyarsk, Russia
| | - Andrey Kirichenko
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia
| | - Anna V Dubynina
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Alexey E Sokolov
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia; Siberian Federal University, Krasnoyarsk, Russia
| | - Galina S Zamay
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Yury E Glazyrin
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Sergey Zamay
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Tatiana Ivanchenko
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia
| | - Natalia Chanchikova
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Nikolay Tokarev
- The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Nikolay Shepelevich
- The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Anastasia Ozerskaya
- The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Evgeniy Badrin
- The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Kirill Belugin
- The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Simon Belkin
- The Federal State-Financed Institution "Federal Siberian Research Clinical Centre under the Federal Medical Biological Agency", Krasnoyarsk, Russia
| | - Vladimir Zabluda
- Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia
| | - Ana Gargaun
- University of Ottawa, Department of Chemistry and Biomolecular Sciences, Ottawa, ON, Canada
| | - Maxim V Berezovski
- University of Ottawa, Department of Chemistry and Biomolecular Sciences, Ottawa, ON, Canada.
| | - Anna S Kichkailo
- Krasnoyarsk State Medical University named after Professor V.F. Voyno-Yasenetskii, Krasnoyarsk, Russia; Kirensky Institute of Physics, Federal Research Center KSC SB RAS, Krasnoyarsk, Russia.
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Belyanina IV, Zamay TN, Zamay GS, Zamay SS, Kolovskaya OS, Ivanchenko TI, Denisenko VV, Kirichenko AK, Glazyrin YE, Garanzha IV, Grigorieva VV, Shabanov AV, Veprintsev DV, Sokolov AE, Sadovskii VM, Gargaun A, Berezovski MV, Kichkailo AS. In Vivo Cancer Cells Elimination Guided by Aptamer-Functionalized Gold-Coated Magnetic Nanoparticles and Controlled with Low Frequency Alternating Magnetic Field. Am J Cancer Res 2017; 7:3326-3337. [PMID: 28900513 PMCID: PMC5595135 DOI: 10.7150/thno.17089] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 05/29/2017] [Indexed: 12/22/2022] Open
Abstract
Biomedical applications of magnetic nanoparticles under the influence of a magnetic field have been proved useful beyond expectations in cancer therapy. Magnetic nanoparticles are effective heat mediators, drug nanocarriers, and contrast agents; various strategies have been suggested to selectively target tumor cancer cells. Our study presents magnetodynamic nanotherapy using DNA aptamer-functionalized 50 nm gold-coated magnetic nanoparticles exposed to a low frequency alternating magnetic field for selective elimination of tumor cells in vivo. The cell specific DNA aptamer AS-14 binds to the fibronectin protein in Ehrlich carcinoma hence helps deliver the gold-coated magnetic nanoparticles to the mouse tumor. Applying an alternating magnetic field of 50 Hz at the tumor site causes the nanoparticles to oscillate and pull the fibronectin proteins and integrins to the surface of the cell membrane. This results in apoptosis followed by necrosis of tumor cells without heating the tumor, adjacent healthy cells and tissues. The aptamer-guided nanoparticles and the low frequency alternating magnetic field demonstrates a unique non-invasive nanoscalpel technology for precise cancer surgery at the single cell level.
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36
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Zamay GS, Ivanchenko TI, Zamay TN, Grigorieva VL, Glazyrin YE, Kolovskaya OS, Garanzha IV, Barinov AA, Krat AV, Mironov GG, Gargaun A, Veprintsev DV, Bekuzarov SS, Kirichenko AK, Zukov RA, Petrova MM, Modestov AA, Berezovski MV, Zamay AS. DNA Aptamers for the Characterization of Histological Structure of Lung Adenocarcinoma. Mol Ther Nucleic Acids 2017; 6:150-162. [PMID: 28325282 PMCID: PMC5363495 DOI: 10.1016/j.omtn.2016.12.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 12/05/2016] [Accepted: 12/05/2016] [Indexed: 12/31/2022]
Abstract
Nucleic acid aptamers are becoming popular as molecular probes for identification and imaging pathology and, at the same time, as a convenient platform for targeted therapy. Recent studies have shown that aptamers may be effectively used for tumor characterization and as commercially available monoclonal antibodies. Here we present three DNA aptamers binding to whole transformed lung cancer tissues, including tumor cells, connective tissues, and blood vessels. Protein targets have been revealed using affinity purification followed by mass spectrometry analyses, and they have been validated using a panel of correspondent antibodies and 3D imaging of tumor tissues. Each of the proteins targeted by the aptamers is involved in cancer progression and most of them are crucial for lung adenocarcinoma. We propose the use of these aptamers in aptahistochemistry for the characterization of the histological structure of lung adenocarcinoma. The value of the presented aptamers is their application together or separately for indicating the spread of neoplastic transformation, for complex differential diagnostics, and for targeted therapy of the tumor itself as well as all transformed structures of the adjacent tissues. Moreover, it has been demonstrated that these aptamers could be used for intraoperative tumor visualization and margin assessment.
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Affiliation(s)
- Galina S Zamay
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk 660036, Russia
| | - Tatiana I Ivanchenko
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Tatiana N Zamay
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Valentina L Grigorieva
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Yury E Glazyrin
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Olga S Kolovskaya
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk 660036, Russia
| | - Irina V Garanzha
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk 660036, Russia
| | | | - Alexey V Krat
- Krasnoyarsk Regional Clinical Cancer Center, Krasnoyarsk 660022, Russia
| | - Gleb G Mironov
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Ana Gargaun
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Dmitry V Veprintsev
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk 660036, Russia
| | - Sergey S Bekuzarov
- Krasnoyarsk Regional Clinical Pathological Anatomical Bureau, Krasnoyarsk 660022, Russia
| | - Andrey K Kirichenko
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Ruslan A Zukov
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Krasnoyarsk Regional Clinical Cancer Center, Krasnoyarsk 660022, Russia
| | - Marina M Petrova
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia
| | - Andrey A Modestov
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Krasnoyarsk Regional Clinical Cancer Center, Krasnoyarsk 660022, Russia
| | - Maxim V Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
| | - Anna S Zamay
- Laboratory for Biomolecular and Medical Technologies, Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia; Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, Krasnoyarsk 660036, Russia.
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37
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Zamay TN, Zamay GS, Belyanina IV, Zamay SS, Denisenko VV, Kolovskaya OS, Ivanchenko TI, Grigorieva VL, Garanzha IV, Veprintsev DV, Glazyrin YE, Shabanov AV, Prinz VY, Seleznev VA, Sokolov AE, Prokopenko VS, Kim PD, Gargaun A, Berezovski MV, Zamay AS. Noninvasive Microsurgery Using Aptamer-Functionalized Magnetic Microdisks for Tumor Cell Eradication. Nucleic Acid Ther 2016; 27:105-114. [PMID: 27923103 DOI: 10.1089/nat.2016.0634] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Magnetomechanical cell disruption using nano- and microsized structures is a promising biomedical technology used for noninvasive elimination of diseased cells. It applies alternating magnetic field (AMF) for ferromagnetic microdisks making them oscillate and causing cell membrane disruption with cell death followed by apoptosis. In this study, we functionalized the magnetic microdisks with cell-binding DNA aptamers and guided the microdisks to recognize cancerous cells in a mouse tumor in vivo. Only 10 min of the treatment with a 100 Hz AMF was enough to eliminate cancer cells from a malignant tumor. Our results demonstrate a good perspective of using aptamer-modified magnetic microdisks for noninvasive microsurgery for tumors.
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Affiliation(s)
- Tatiana N Zamay
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,2 Siberian Federal University , Krasnoyarsk, Russia
| | - Galina S Zamay
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Irina V Belyanina
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,2 Siberian Federal University , Krasnoyarsk, Russia
| | - Sergey S Zamay
- 3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Valery V Denisenko
- 3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia .,4 Institute of Computational Modeling, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Olga S Kolovskaya
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Tatiana I Ivanchenko
- 3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Valentina L Grigorieva
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,2 Siberian Federal University , Krasnoyarsk, Russia
| | - Irina V Garanzha
- 2 Siberian Federal University , Krasnoyarsk, Russia .,3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Dmitry V Veprintsev
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Yury E Glazyrin
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia
| | - Alexandr V Shabanov
- 3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Viktor Y Prinz
- 5 The Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, Russia
| | - Vladimir A Seleznev
- 5 The Institute of Semiconductor Physics, Siberian Branch of the Russian Academy of Sciences , Novosibirsk, Russia
| | - Alexey E Sokolov
- 6 Institute of Physics, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | | | - Petr D Kim
- 3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
| | - Ana Gargaun
- 8 Department of Chemistry and Biomolecular Sciences, University of Ottawa , Ottawa, Canada
| | - Maxim V Berezovski
- 8 Department of Chemistry and Biomolecular Sciences, University of Ottawa , Ottawa, Canada
| | - Anna S Zamay
- 1 Laboratory of Biomolecular and Medical Technologies, Krasnoyarsk State Medical University , Krasnoyarsk, Russia .,3 Krasnoyarsk Research Center, Siberian Branch of the Russian Academy of Sciences , Krasnoyarsk, Russia
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Zamay GS, Zamay TN, Kolovskii VA, Shabanov AV, Glazyrin YE, Veprintsev DV, Krat AV, Zamay SS, Kolovskaya OS, Gargaun A, Sokolov AE, Modestov AA, Artyukhov IP, Chesnokov NV, Petrova MM, Berezovski MV, Zamay AS. Electrochemical aptasensor for lung cancer-related protein detection in crude blood plasma samples. Sci Rep 2016; 6:34350. [PMID: 27694916 PMCID: PMC5046130 DOI: 10.1038/srep34350] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 09/09/2016] [Indexed: 12/15/2022] Open
Abstract
The development of an aptamer-based electrochemical sensor for lung cancer detection is presented in this work. A highly specific DNA-aptamer, LC-18, selected to postoperative lung cancer tissues was immobilized onto a gold microelectrode and electrochemical measurements were performed in a solution containing the redox marker ferrocyanide/ferricyanide. The aptamer protein targets were harvested from blood plasma of lung cancer patients by using streptavidin paramagnetic beads and square wave voltammetry of the samples was performed at various concentrations. In order to enhance the sensitivity of the aptasensor, silica-coated iron oxide magnetic beads grafted with hydrophobic C8 and C4 alkyl groups were used in a sandwich detection approach. Addition of hydrophobic beads increased the detection limit by 100 times. The detection limit of the LC-18 aptasensor was enhanced by the beads to 0.023 ng/mL. The formation of the aptamer – protein – bead sandwich on the electrode surface was visualized by electron microcopy. As a result, the electrochemical aptasensor was able to detect cancer-related targets in crude blood plasma of lung cancer patients.
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Affiliation(s)
- Galina S Zamay
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia.,Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, 50/24, Akademgorodok, Krasnoyarsk, 660036, Russia
| | - Tatiana N Zamay
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia
| | | | - Alexandr V Shabanov
- Krasnoyarsk Research Center Siberian branch of Russian Academy of Science 50, Akademgorodok, Krasnoyarsk, 660036, Russia
| | - Yury E Glazyrin
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia.,Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, 50/24, Akademgorodok, Krasnoyarsk, 660036, Russia
| | - Dmitry V Veprintsev
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Alexey V Krat
- Krasnoyarsk Regional Clinical Cancer Center named after A.I. Kryzhanovsky 1, Smolenskaya, Krasnoyarsk, 660022, Russia
| | - Sergey S Zamay
- Krasnoyarsk Research Center Siberian branch of Russian Academy of Science 50, Akademgorodok, Krasnoyarsk, 660036, Russia
| | - Olga S Kolovskaya
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Ana Gargaun
- University of Ottawa, Department of Chemistry, 10 Marie-Curie, D'Iorio Hall, Room 201 Ottawa, ON K1N 6N5, Canada
| | - Alexey E Sokolov
- Institute of Physics named after L.V. Kirenski Siberian Branch of Russian Academy of Science 50/38, Akademgorodok, Krasnoyarsk, 660036, Russia
| | - Andrey A Modestov
- Krasnoyarsk Regional Clinical Cancer Center named after A.I. Kryzhanovsky 1, Smolenskaya, Krasnoyarsk, 660022, Russia
| | - Ivan P Artyukhov
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Nikolay V Chesnokov
- Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, 50/24, Akademgorodok, Krasnoyarsk, 660036, Russia
| | - Marina M Petrova
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia
| | - Maxim V Berezovski
- University of Ottawa, Department of Chemistry, 10 Marie-Curie, D'Iorio Hall, Room 201 Ottawa, ON K1N 6N5, Canada
| | - Anna S Zamay
- Krasnoyarsk State Medical University named after prof. V.F. Voino-Yasenecki, Laboratory for Biomolecular and medical technologies, 1 P. Zheleznyaka, Krasnoyarsk 660022, Russia.,Institute of Chemistry and Chemical Technology of the Siberian Branch of the Russian Academy of Science, 50/24, Akademgorodok, Krasnoyarsk, 660036, Russia
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Khan N, Mironov G, Berezovski MV. Direct detection of endogenous MicroRNAs and their post-transcriptional modifications in cancer serum by capillary electrophoresis-mass spectrometry. Anal Bioanal Chem 2016; 408:2891-9. [DOI: 10.1007/s00216-015-9277-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/11/2015] [Accepted: 12/16/2015] [Indexed: 01/06/2023]
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Abstract
SELEXed to protect: aptamers to B-lymphocyte antigen CD20 decrease cell damage inducedviaantibody-dependent complement dependent cytotoxicity.
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Affiliation(s)
- Nadia L. Al-Youssef
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa
- Canada
| | | | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences
- University of Ottawa
- Ottawa
- Canada
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41
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Iqbal A, Labib M, Muharemagic D, Sattar S, Dixon BR, Berezovski MV. Detection of Cryptosporidium parvum Oocysts on Fresh Produce Using DNA Aptamers. PLoS One 2015; 10:e0137455. [PMID: 26334529 PMCID: PMC4559477 DOI: 10.1371/journal.pone.0137455] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 08/17/2015] [Indexed: 02/07/2023] Open
Abstract
There are currently no standard methods for the detection of Cryptosporidium spp., or other protozoan parasites, in foods, and existing methods are often inadequate, with low and variable recovery efficiencies. Food testing is difficult due to the low concentrations of parasites, the difficulty in eluting parasites from some foods, the lack of enrichment methods, and the presence of PCR inhibitors. The main objectives of the present study were to obtain DNA aptamers binding to the oocyst wall of C. parvum, and to use the aptamers to detect the presence of this parasite in foods. DNA aptamers were selected against C. parvum oocysts using SELEX (Systematic Evolution of Ligands by EXponential enrichment). Ten rounds of selection led to the discovery of 14 aptamer clones with high affinities for C. parvum oocysts. For detecting parasite-bound aptamers, a simple electrochemical sensor was employed, which used a gold nanoparticle-modified screen-printed carbon electrode. This aptasensor was fabricated by self-assembling a hybrid of a thiolated ssDNA primer and the anti- C. parvum aptamer. Square wave voltammetry was employed to quantitate C. parvum in the range of 150 to 800 oocysts, with a detection limit of approximately 100 oocysts. The high sensitivity and specificity of the developed aptasensor suggests that this novel method is very promising for the detection and identification of C. parvum oocysts on spiked fresh fruits, as compared to conventional methods such as microscopy and PCR.
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Affiliation(s)
- Asma Iqbal
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, Ontario, Canada
| | - Mahmoud Labib
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Darija Muharemagic
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Syed Sattar
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Brent R. Dixon
- Bureau of Microbial Hazards, Food Directorate, Health Canada, Ottawa, Ontario, Canada
- * E-mail: (BRD); Maxim. (MVB)
| | - Maxim V. Berezovski
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
- * E-mail: (BRD); Maxim. (MVB)
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Abstract
MicroRNAs (miRNAs) are potentially useful biomarkers for diagnosis, classification, and prognosis of many diseases, including cancer. Herein, we developed a protein-facilitated electrocatalytic quadroprobe sensor (Sens(PEQ)) for detection of miRNA signature of chronic lymphocytic leukemia (CLL) in human serum. The developed signal-ON sensor provides a compatible combination of two DNA adaptor strands modified with four methylene blue molecules and electrocatalysis using glucose oxidase in order to enhance the overall signal gain. This enhanced sensitivity provided the response necessary to detect the low-abundant serum miRNAs without preamplification. The developed Sens(PEQ) is exquisitely sensitive to subtle π-stack perturbations and capable of distinguishing single base mismatches in the target miRNA. Furthermore, the developed sensor was employed for profiling of three endogenous miRNAs characteristic to CLL, including hsa-miR-16-5p, hsa-miR-21-5p, and hsa-miR-150-5p in normal healthy serum, chronic lymphocytic leukemia Rai stage 1 (CLL-1), and stage 3 (CLL-3) sera, using a non-human cel-miR-39-3p as an internal standard. The sensor results were verified by conventional SYBR green-based quantitative reverse-transcription polymerase chain reaction (RT-qPCR) analysis.
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Affiliation(s)
- Mahmoud Labib
- Department of Chemistry, University of Ottawa , 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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Ghobadloo SM, Gargaun A, Casselman R, Muharemagic D, Berezovski MV. Aptamer-facilitated cryoprotection of viruses. ACS Med Chem Lett 2014; 5:1240-4. [PMID: 25408838 DOI: 10.1021/ml500322h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 08/01/2014] [Accepted: 09/23/2014] [Indexed: 11/29/2022] Open
Abstract
Global vaccination and gene therapy programs have an urgent demand for stabilization of viral vectors at low temperature. We used a quadramer, a bridge-connected DNA tetra-aptamer to antivesicular stomatitis virus (VSV), as a viral cryoprotectant. Results showed that the tetravalent antivirus DNA aptamers protect viral activity during multiple freeze-thaw cycles, shield from neutralizing antibodies, and decrease aggregation of viral particles.
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Affiliation(s)
- Shahrokh M. Ghobadloo
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Ana Gargaun
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Rebecca Casselman
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Darija Muharemagic
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Maxim V. Berezovski
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
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Wehbe M, Labib M, Muharemagic D, Zamay AS, Berezovski MV. Switchable aptamers for biosensing and bioseparation of viruses (SwAps-V). Biosens Bioelectron 2014; 67:280-6. [PMID: 25190090 DOI: 10.1016/j.bios.2014.08.033] [Citation(s) in RCA: 17] [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: 06/04/2014] [Revised: 08/08/2014] [Accepted: 08/18/2014] [Indexed: 11/29/2022]
Abstract
There is a widespread interest in the development of aptamer-based affinity chromatographic methods for purification of biomolecules. Regardless of the many advantages exhibited by aptamers when compared to other recognition elements, the lack of an efficient regeneration technique that can be generalized to all targets has encumbered further integration of aptamers into affinity-based purification methods. Here we offer switchable aptamers (SwAps) that have been developed to solve this problem and move aptamer-based chromatography forward. SwAps are controlled-affinity aptamers, which have been employed here to purify vesicular stomatitis virus (VSV) as a model case, however this technique can be extended to all biologically significant molecules. VSV is one oncolytic virus out of an arsenal of potential candidates shown to provide selective destruction of cancer cells both in vitro and in vivo. These SwAps were developed in the presence of Ca(2+) and Mg(2+) ions where they cannot bind to their target VSV in absence of these cations. Upon addition of EDTA and EGTA, the divalent cations were sequestered from the stabilized aptameric structure causing a conformational change and subsequently release of the virus. Both flow cytometry and electrochemical impedance spectroscopy were employed to estimate the binding affinities between the selected SwAps and VSV and to determine the coefficient of switching (CoS) upon elution. Among fifteen sequenced SwAps, four have exhibited high affinity to VSV and ability to switch upon elution and thus were further integrated into streptavidin-coated magnetic beads for purification of VSV.
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Affiliation(s)
- Mohamed Wehbe
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | - Mahmoud Labib
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Anna S Zamay
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada; Institute of Chemistry and Chemical Technology SB RAS, 50 Akademgorodok, Krasnoyarsk 660036, Russia
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Ghobadloo SM, Balcerzak AK, Gargaun A, Muharemagic D, Mironov GG, Capicciotti CJ, Briard JG, Ben RN, Berezovski MV. Carbohydrate-based ice recrystallization inhibitors increase infectivity and thermostability of viral vectors. Sci Rep 2014; 4:5903. [PMID: 25078058 PMCID: PMC4116624 DOI: 10.1038/srep05903] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [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: 03/21/2014] [Accepted: 07/16/2014] [Indexed: 12/28/2022] Open
Abstract
The inability of vaccines to retain sufficient thermostability has been an obstacle to global vaccination programs. To address this major limitation, we utilized carbohydrate-based ice recrystallization inhibitors (IRIs) to eliminate the cold chain and stabilize the potency of Vaccinia virus (VV), Vesicular Stomatitis virus (VSV) and Herpes virus-1 (HSV-1). The impact of these IRIs was tested on the potency of the viral vectors using a plaque forming unit assay following room temperature storage, cryopreservation with successive freeze-thaw cycles and lyophilization. Viral potency after storage with all three conditions demonstrated that N-octyl-gluconamide (NOGlc) recovered the infectivity of shelf stored VV, 5.6 Log10 PFU mL−1 during 40 days, and HSV-1, 2.7 Log10 PFU mL−1 during 9 days. Carbon-linked antifreeze glycoprotein analogue ornithine-glycine-glycine-galactose (OGG-Gal) increases the recovery of VV and VSV more than 1 Log10 PFU mL−1 after 10 freeze-thaw cycles. In VSV, cryostorage with OGG-Gal maintains high infectivity and reduces temperature-induced aggregation of viral particles by 2 times that of the control. In total, OGG-Gal and NOGlc preserve virus potency during cryostorage. Remarkably, NOGlc has potential to eliminate the cold chain and permit room temperature storage of viral vectors.
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Affiliation(s)
| | - Anna K Balcerzak
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Ana Gargaun
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Darija Muharemagic
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gleb G Mironov
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | | | - Jennie G Briard
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Robert N Ben
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Maxim V Berezovski
- Department of Chemistry, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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Mironov GG, Okhonin V, Khan N, Clouthier CM, Berezovski MV. Conformational Dynamics of DNA G-Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On-line with Mass Spectrometry. ChemistryOpen 2014; 3:58-64. [PMID: 24808992 PMCID: PMC4000168 DOI: 10.1002/open.201400002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Indexed: 12/03/2022] Open
Abstract
G-quadruplex-forming DNA/RNA sequences play an important role in the regulation of biological functions and development of new anticancer and anti-aging drugs. In this work, we couple on-line kinetic capillary electrophoresis with mass spectrometry (KCE-MS) to study conformational dynamics of DNA G-quadruplexes in solution. We show that peaks shift and its widening in KCE can be used for measuring rate and equilibrium constants for DNA–metal affinity interactions and G-quadruplex formation; and ion mobility mass spectrometry (IM-MS) provides information about relative sizes, absolute molecular masses and stoichiometry of DNA complexes. KCE-MS separates a thrombin-binding aptamer d[GGTTGGTGTGGTTGG] from mutated sequences based on affinity to potassium, and reveals the apparent equilibrium folding constant (KF≈150 μm), folding rate constant (kon≈1.70×103 s−1 m−1), unfolding rate constant (koff≈0.25 s−1), half-life time of the G-quadruplex (t1/2≈2.8 s), and relaxation time (τ≈3.9 ms at physiological 150 mm [K+]). In addition, KCE-MS screens for a GQ-stabilizing/-destabilizing effect of DNA binding dyes and an anticancer drug, cisplatin.
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Affiliation(s)
- Gleb G Mironov
- Department of Chemistry, University of Ottawa 10 Marie Curie, Ottawa K1N 6N5 (Canada)
| | - Victor Okhonin
- Department of Chemistry, University of Ottawa 10 Marie Curie, Ottawa K1N 6N5 (Canada)
| | - Nasrin Khan
- Department of Chemistry, University of Ottawa 10 Marie Curie, Ottawa K1N 6N5 (Canada)
| | | | - Maxim V Berezovski
- Department of Chemistry, University of Ottawa 10 Marie Curie, Ottawa K1N 6N5 (Canada)
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Mironov GG, Okhonin V, Khan N, Clouthier CM, Berezovski MV. Cover Picture: Conformational Dynamics of DNA G-Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On-line with Mass Spectrometry (ChemistryOpen 2/2014). ChemistryOpen 2014. [DOI: 10.1002/open.201480201] [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: 11/10/2022] Open
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48
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Berezovski MV. Conformational Dynamics of DNA G-Quadruplex in Solution Studied by Kinetic Capillary Electrophoresis Coupled On-line with Mass Spectrometry. ChemistryOpen 2014; 3:38. [PMID: 24808989 PMCID: PMC4000165 DOI: 10.1002/open.201400004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Maxim V Berezovski
- Department of Chemistry, University of Ottawa 10 Marie Curie, Ottawa K1N 6N5 (Canada)
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49
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Zamay TN, Kolovskaya OS, Glazyrin YE, Zamay GS, Kuznetsova SA, Spivak EA, Wehbe M, Savitskaya AG, Zubkova OA, Kadkina A, Wang X, Muharemagic D, Dubynina A, Sheina Y, Salmina AB, Berezovski MV, Zamay AS. DNA-aptamer targeting vimentin for tumor therapy in vivo. Nucleic Acid Ther 2014; 24:160-70. [PMID: 24410722 DOI: 10.1089/nat.2013.0471] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In recent years, new prospects for the use of nucleic acids as anticancer drugs have been discovered. Aptamers for intracellular targets can regulate cellular functions and cause cell death or proliferation. However, intracellular aptamers have limited use for therapeutic applications due to their low bioavailability. In this work, we selected DNA aptamers to cell organelles and nucleus of cancer cells, and showed that an aptamer NAS-24 binds to vimentin and causes apoptosis of mouse ascites adenocarcinoma cells in vitro and in vivo. To deliver the aptamer NAS-24 inside cells, natural polysaccharide arabinogalactan was used as a carrier reagent. The mixture of arabinogalactan and NAS-24 was injected intraperitonealy for 5 days into mice with adenocarcinoma and inhibited adenocarcinoma growth more effectively than free arabinogalactan or the aptamer alone. The use of aptamers to intracellular targets together with arabinogalactan becomes a promising approach for anticancer therapy.
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Affiliation(s)
- Tatyana N Zamay
- 1 Department of Biochemistry, Medical, Pharmaceutical, and Toxicological Chemistry, Krasnoyarsk State Medical University , Krasnoyarsk, Russia
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50
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Giamberardino A, Labib M, Hassan EM, Tetro JA, Springthorpe S, Sattar SA, Berezovski MV, DeRosa MC. Ultrasensitive norovirus detection using DNA aptasensor technology. PLoS One 2013; 8:e79087. [PMID: 24244426 PMCID: PMC3828344 DOI: 10.1371/journal.pone.0079087] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [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: 03/10/2013] [Accepted: 09/26/2013] [Indexed: 12/31/2022] Open
Abstract
DNA aptamers were developed against murine norovirus (MNV) using SELEX (Systematic Evolution of Ligands by EXponential enrichment). Nine rounds of SELEX led to the discovery of AG3, a promising aptamer with very high affinity for MNV as well as for lab-synthesized capsids of a common human norovirus (HuNoV) outbreak strain (GII.3). Using fluorescence anisotropy, AG3 was found to bind with MNV with affinity in the low picomolar range. The aptamer could cross-react with HuNoV though it was selected against MNV. As compared to a non-specific DNA control sequence, the norovirus-binding affinity of AG3 was about a million-fold higher. In further tests, the aptamer also showed nearly a million-fold higher affinity for the noroviruses than for the feline calicivirus (FCV), a virus similar in size and structure to noroviruses. AG3 was incorporated into a simple electrochemical sensor using a gold nanoparticle-modified screen-printed carbon electrode (GNPs-SPCE). The aptasensor could detect MNV with a limit of detection of approximately 180 virus particles, for possible on-site applications. The lead aptamer candidate and the aptasensor platform show promise for the rapid detection and identification of noroviruses in environmental and clinical samples.
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Affiliation(s)
- Amanda Giamberardino
- Department of Chemistry, Carleton University, Steacie Building, Ottawa, Ontario, Canada
| | - Mahmoud Labib
- Department of Chemistry, University of Ottawa, Ottawa, Ontario, Canada
| | - Eman M. Hassan
- Department of Chemistry, Carleton University, Steacie Building, Ottawa, Ontario, Canada
| | - Jason A. Tetro
- Centre for Research on Environmental Microbiology, University of Ottawa, Ottawa, Ontario, Canada
| | - Susan Springthorpe
- Centre for Research on Environmental Microbiology, University of Ottawa, Ottawa, Ontario, Canada
| | - Syed A. Sattar
- Centre for Research on Environmental Microbiology, University of Ottawa, Ottawa, Ontario, Canada
| | | | - Maria C. DeRosa
- Department of Chemistry, Carleton University, Steacie Building, Ottawa, Ontario, Canada
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