1
|
Biryukov M, Semenov D, Kryachkova N, Polyakova A, Patrakova E, Troitskaya O, Milakhina E, Poletaeva J, Gugin P, Ryabchikova E, Zakrevsky D, Schweigert I, Koval O. The Molecular Basis for Selectivity of the Cytotoxic Response of Lung Adenocarcinoma Cells to Cold Atmospheric Plasma. Biomolecules 2023; 13:1672. [PMID: 38002354 PMCID: PMC10669024 DOI: 10.3390/biom13111672] [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: 10/31/2023] [Revised: 11/15/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The interaction of cold atmospheric plasma (CAP) with biotargets is accompanied by chemical reactions on their surfaces and insides, and it has great potential as an anticancer approach. This study discovers the molecular mechanisms that may explain the selective death of tumor cells under CAP exposure. To reach this goal, the transcriptional response to CAP treatment was analyzed in A549 lung adenocarcinoma cells and in lung-fibroblast Wi-38 cells. We found that the CAP treatment induced the common trend of response from A549 and Wi-38 cells-the p53 pathway, KRAS signaling, UV response, TNF-alpha signaling, and apoptosis-related processes were up-regulated in both cell lines. However, the amplitude of the response to CAP was more variable in the A549 cells. The CAP-dependent death of A549 cells was accompanied by DNA damage, cell-cycle arrest in G2/M, and the dysfunctional response of glutathione peroxidase 4 (GPx4). The activation of the genes of endoplasmic reticulum stress and ER lumens was detected only in the A549 cells. Transmission-electron microscopy confirmed the alteration of the morphology of the ER lumens in the A549 cells after the CAP exposure. It can be concluded that the responses to nuclear stress and ER stress constitute the main differences in the sensitivity of tumor and healthy cells to CAP exposure.
Collapse
Affiliation(s)
- Mikhail Biryukov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| | - Dmitriy Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
| | - Nadezhda Kryachkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| | - Alina Polyakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| | - Ekaterina Patrakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
| | - Olga Troitskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| | - Elena Milakhina
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
- Department of Radio Engineering and Electronics, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Julia Poletaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
| | - Pavel Gugin
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Dmitriy Zakrevsky
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
- Department of Radio Engineering and Electronics, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Irina Schweigert
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| | - Olga Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (M.B.); (D.S.); (N.K.); (A.P.); (E.P.); (O.T.); (J.P.); (E.R.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.M.); (P.G.); (D.Z.); (I.S.)
| |
Collapse
|
2
|
Fokina A, Poletaeva Y, Dukova S, Klabenkova K, Rad’kova Z, Bakulina A, Zatsepin T, Ryabchikova E, Stetsenko D. Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides. Int J Mol Sci 2023; 24:15978. [PMID: 37958961 PMCID: PMC10650595 DOI: 10.3390/ijms242115978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.
Collapse
Affiliation(s)
- Alesya Fokina
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Yulia Poletaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (Y.P.); (E.R.)
| | | | - Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Zinaida Rad’kova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; (Z.R.); (A.B.)
| | - Anastasia Bakulina
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia; (Z.R.); (A.B.)
| | - Timofei Zatsepin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia;
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; (Y.P.); (E.R.)
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, Novosibirsk 630090, Russia; (A.F.); (K.K.)
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| |
Collapse
|
3
|
Patrakova E, Biryukov M, Troitskaya O, Gugin P, Milakhina E, Semenov D, Poletaeva J, Ryabchikova E, Novak D, Kryachkova N, Polyakova A, Zhilnikova M, Zakrevsky D, Schweigert I, Koval O. Chloroquine Enhances Death in Lung Adenocarcinoma A549 Cells Exposed to Cold Atmospheric Plasma Jet. Cells 2023; 12:cells12020290. [PMID: 36672225 PMCID: PMC9857254 DOI: 10.3390/cells12020290] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Cold atmospheric plasma (CAP) is an intensively-studied approach for the treatment of malignant neoplasms. Various active oxygen and nitrogen compounds are believed to be the main cytotoxic effectors on biotargets; however, the comprehensive mechanism of CAP interaction with living cells and tissues remains elusive. In this study, we experimentally determined the optimal discharge regime (or semi-selective regime) for the direct CAP jet treatment of cancer cells, under which lung adenocarcinoma A549, A427 and NCI-H23 cells demonstrated substantial suppression of viability, coupled with a weak viability decrease of healthy lung fibroblasts Wi-38 and MRC-5. The death of CAP-exposed cancer and healthy cells under semi-selective conditions was caspase-dependent. We showed that there was an accumulation of lysosomes in the treated cells. The increased activity of lysosomal protease Cathepsin D, the transcriptional upregulation of autophagy-related MAPLC3B gene in cancer cells and the changes in autophagy-related proteins may have indicated the activation of autophagy. The addition of the autophagy inhibitor chloroquine (CQ) after the CAP jet treatment increased the death of A549 cancer cells in a synergistic manner and showed a low effect on the viability of CAP-treated Wi-38 cells. Downregulation of Drp1 mitochondrial protein and upregulation of PINK1 protein in CAP + CQ treated cells indicated that CQ increased the CAP-dependent destabilization of mitochondria. We concluded that CAP weakly activated pro-survival autophagy in irradiated cells, and CQ promoted CAP-dependent cell death due to the destabilization of autophagosomes formation and mitochondria homeostasis. To summarize, the combination of CAP treatment with CQ could be useful for the development of cold plasma-based antitumor approaches for clinical application.
Collapse
Affiliation(s)
- Ekaterina Patrakova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Mikhail Biryukov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Troitskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Gugin
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Rzhanov Institute of Semiconductor Physic, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena Milakhina
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Rzhanov Institute of Semiconductor Physic, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Radio Engineering and Electronics, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Dmitriy Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Julia Poletaeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Diana Novak
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Nadezhda Kryachkova
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Alina Polyakova
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Maria Zhilnikova
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Dmitriy Zakrevsky
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Rzhanov Institute of Semiconductor Physic, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Radio Engineering and Electronics, Novosibirsk State Technical University, 630073 Novosibirsk, Russia
| | - Irina Schweigert
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Koval
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
- Khristianovich Institute of Theoretical and Applied Mechanics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Correspondence:
| |
Collapse
|
4
|
Ryabchikova E. Advances in Nanomaterials in Biomedicine. Nanomaterials (Basel) 2021; 11:nano11010118. [PMID: 33430171 PMCID: PMC7825609 DOI: 10.3390/nano11010118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 12/12/2022]
Affiliation(s)
- Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, 8 Lavrentiev Ave., 630090 Novosibirsk, Russia
| |
Collapse
|
5
|
Tamkovich S, Tutanov O, Efimenko A, Grigor'eva A, Ryabchikova E, Kirushina N, Vlassov V, Tkachuk V, Laktionov P. Blood Circulating Exosomes Contain Distinguishable Fractions of Free and Cell-Surface-Associated Vesicles. Curr Mol Med 2020; 19:273-285. [PMID: 30868953 DOI: 10.2174/1566524019666190314120532] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Considering exosomes as intercellular transporters, inevitably interacting with the plasma membrane and the large available surface of blood cells, we wonder if a fraction of circulating exosomes is associated with the surface of blood cells. OBJECTIVE The aim of this study was to develop an efficient protocol for isolating exosomes associated with the surface of blood cells and to further investigate the characteristics of this fraction in a healthy state and during the development of breast cancer, as well as its possible implication for use in diagnostic applications. METHODS Blood samples were collected from Healthy Females (HFs) and breast cancer patients (BCPs). Exosomes extracted from blood plasma and eluted from the surface of blood cells were isolated by ultrafiltration with subsequent ultracentrifugation. RESULTS Transmission Electron Microscopy (TEM), along with immunogold labeling, demonstrated the presence of exosomes among membrane-wrapped extracellular vesicles (EVs) isolated from both plasma and blood cell eluates. TEM, nanoparticle tracking analysis, and NanoOrange protein quantitation data showed that cell-associated exosomes constituted no less than 2/3 of total blood exosome number. Exosomes, ranging from 50-70 nm in size, prevailed in the blood of breast cancer patients, whereas smaller exosomes (30-50 nm) were mostly observed in the blood of healthy women. Analysis of specific proteins and RNAs in exosomes circulating in blood demonstrated the significant differences in the packing density of the polymers in exosomes of HFs and BCPs. Preliminary data indicated that detection of cancer-specific miRNA (miR-103, miR-191, miR-195) in exosomes associated with the fraction of red blood cells allowed to discriminate HFs and BCPs more precisely compared to cell-free exosomes circulating in plasma. CONCLUSION Our data provide the basis for using blood cell-associated exosomes for diagnostic applications.
Collapse
Affiliation(s)
- Svetlana Tamkovich
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation.,Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Oleg Tutanov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation
| | - Anastasia Efimenko
- Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alina Grigor'eva
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation
| | - Elena Ryabchikova
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Natalia Kirushina
- Department of Mammology, National Novosibirsk Regional Oncologic Dispensary, Novosibirsk, Russian Federation
| | - Valentin Vlassov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Faculty of Natural Science, Novosibirsk State University, Novosibirsk, Russian Federation
| | - Vsevolod Tkachuk
- Institute for Regenerative Medicine, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Pavel Laktionov
- Laboratory of Molecular Medicine, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russian Federation.,Novosibirsk Research Institute of Circulation Pathology of Academician E.N. Meshalkin, Novosibirsk, Russian Federation
| |
Collapse
|
6
|
Morozova V, Babkin I, Kozlova Y, Baykov I, Bokovaya O, Tikunov A, Ushakova T, Bardasheva A, Ryabchikova E, Zelentsova E, Tikunova N. Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8. Viruses 2019; 11:E1115. [PMID: 31810319 PMCID: PMC6950046 DOI: 10.3390/v11121115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 11/01/2019] [Revised: 11/29/2019] [Accepted: 11/29/2019] [Indexed: 12/31/2022] Open
Abstract
Klebsiella pneumoniae is a common pathogen, associated with a wide spectrum of infections, and clinical isolates of K. pneumoniae often possess multiple antibiotic resistances. Here, we describe a novel lytic N4-like bacteriophage KP8, specific to K. pneumoniae, including its genome, partial structural proteome, biological properties, and proposed taxonomy. Electron microscopy revealed that KP8 belongs to the Podoviridae family. The size of the KP8 genome was 73,679 bp, and it comprised 97 putative open reading frames. Comparative genome analysis revealed that the KP8 genome possessed the highest similarity to the genomes of Enquatrovirus and Gamaleyavirus phages, which are N4-like podoviruses. In addition, the KP8 genome showed gene synteny typical of the N4-like podoviruses and contained the gene encoding a large virion-encapsulated RNA polymerase. Phylogenetic analysis of the KP8 genome revealed that the KP8 genome formed a distinct branch within the clade, which included the members of Enquatrovirus and Gamaleyavirus genera besides KP8. The average evolutionary divergences KP8/Enquatrovirus and KP8/Gamaleyavirus were 0.466 and 0.447 substitutions per site (substitutes/site), respectively, similar to that between Enquatrovirus and Gamaleyavirus genera (0.468 substitutes/site). The obtained data suggested that Klebsiella phage KP8 differs from other similar phages and may represent a new genus within the N4-like phages.
Collapse
Affiliation(s)
- Vera Morozova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Igor Babkin
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Yuliya Kozlova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Ivan Baykov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Olga Bokovaya
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Artem Tikunov
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Tatyana Ushakova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Alevtina Bardasheva
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Elena Ryabchikova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| | - Ekaterina Zelentsova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
- International Tomography Center Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nina Tikunova
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia; (I.B.); (Y.K.); (I.B.); (O.B.); (A.T.); (T.U.); (A.B.); (E.R.); (E.Z.); (N.T.)
| |
Collapse
|
7
|
Tamkovich S, Grigor'eva A, Eremina A, Tupikin A, Kabilov M, Chernykh V, Vlassov V, Ryabchikova E. What information can be obtained from the tears of a patient with primary open angle glaucoma? Clin Chim Acta 2019; 495:529-537. [PMID: 31153869 DOI: 10.1016/j.cca.2019.05.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/29/2019] [Accepted: 05/29/2019] [Indexed: 12/22/2022]
Abstract
Since tears are a biological fluid, they have a potential diagnostic value for ophthalmic diseases. The aim of this study was to compare tear supernatants and pellets obtained from patients suffering from primary open angle glaucoma (POAG) and healthy persons (HPs) using transmission electron microscopy (TEM) and molecular biological methods. Tear supernatants and pellets were prepared using ultrafiltration and ultracentrifugation and were examined by negative staining and immunogold labelling TEM. DNA of the pellets was isolated, quantified and sequenced using a MiSeq (Illumina, USA) genomic sequencer with the Reagent Kit v3 (600 cycles, Illumina, USA). MicroRNA was isolated and quantified from the pellets; miR-146b, miR-16 and miR-126 were detected using TaqMan MicroRNA Assays (Applied Biosystems, USA). TEM of tear supernatants from both POAG patients and HPs revealed identical constituents: spherical or cup-shaped vesicles, "non-vesicles", cell debris and macromolecular aggregates. Pellets of POAG patients and HPs contained small extracellular vesicles (sEVs) non-labelled vesicles and "non-vesicles"; pellets of sick persons also contained sEVs with "a capsule". POAG-patient tear pellets showed elevated concentrations of genomic ds-DNA and SINE-repeats, and different expressions of miR-146b, miR-16 and miR-126 and a different set of bacterial DNA in comparison with pellets obtained from the tears of HPs. The data obtained indicate that the tears of HPs and POAG patients could serve as an object for TEM studies and as a source of sEV-containing preparations (pellets), which, in turn, could be used for the isolation and study of genomic ds-DNA and RNA. Our data provide the basis for using tears for diagnostic applications.
Collapse
Affiliation(s)
- Svetlana Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk National Research State University, Novosibirsk, Russia.
| | - Alina Grigor'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Alena Eremina
- Fyodorov Eye Microsurgery Complex, Novosibirsk Branch, Novosibirsk, Russia
| | - Alexey Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Marcel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Valerii Chernykh
- Fyodorov Eye Microsurgery Complex, Novosibirsk Branch, Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia; Novosibirsk National Research State University, Novosibirsk, Russia
| |
Collapse
|
8
|
Epanchintseva A, Dolodoev A, Grigor'eva A, Chelobanov B, Pyshnyi D, Ryabchikova E, Pyshnaya I. Non-covalent binding of nucleic acids with gold nanoparticles provides their stability and effective desorption in environment mimicking biological media. Nanotechnology 2018; 29:355601. [PMID: 29851383 DOI: 10.1088/1361-6528/aac933] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The ability of gold nanoparticles to bind different substances has resulted in the high interest of researchers determining their usage as a promising carrier of various biological substances including nucleic acids (NAs) for therapeutic applications. Most publications report covalent binding (conjugation) of an NA to spherical AuNPs via the Au-S bond. In this work, we obtained non-covalent associates of different ssDNA, ssRNA and siRNAs with spherical gold nanoparticles (AuNPs) and examined their physico-chemical properties and stability in media mimicking intracellular space (bacterial 'cytosol') and cell culture media (10% FBS in DMEM). The 'cytosol' was obtained from E. coli and possessed nuclease activity. For the first time, we used the phosphoryl guanidine (dimethylimidazolidin-2-imine, Dmi) group for modification of 3'-ends to enhance the stability of ssRNAs and siRNAs against nuclease destruction. Trying to evaluate the material balance, we analyzed the whole nucleotide species obtained after incubation of NA-AuNPs associates in 'cytosol' and FBS and evaluated the degree of NAs destruction, a share of full-size NAs remained on the surface of the AuNPs and in the solution. Native ss- and siRNAs, both free and in composition of non-covalent associates with AuNPs, were less resistant to degrading factors than ssDNA. The introduction of two Dmi-groups into the ssDNA increased its stability in 'cytosol' three times within 2.5 h. Dmi-modified siRNAs in non-covalent associates with AuNPs were two times more stable than unmodified siRNA within 4 h. We showed that non-covalent siRNA-AuNPs associates serve as a kind of storage for full-size NAs and thereby prolong their presence in nuclease-active media. Our study showed that non-covalent binding of siRNAs with a surface of AuNPs provides desorption of both strands, which is necessary for siRNA functioning in living cells, and could be considered as an important way to construct siRNA and ssDNA delivery systems based on AuNPs.
Collapse
Affiliation(s)
- Anna Epanchintseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia
| | | | | | | | | | | | | |
Collapse
|
9
|
Tutanov O, Tamkovich S, Grigoryeva A, Ryabchikova E, Duzhak T, Tsentalovich Y, Laktionov P, Vlassov V. 1PD Breast cancer blood-derived exosomes: Characterisation of protein composition in search for new biomarkers. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
10
|
Morozova V, Kozlova Y, Shedko E, Kurilshikov A, Babkin I, Tupikin A, Yunusova A, Chernonosov A, Baykov I, Кondratov I, Kabilov M, Ryabchikova E, Vlassov V, Tikunova N. Lytic bacteriophage PM16 specific for Proteus mirabilis: a novel member of the genus Phikmvvirus. Arch Virol 2016; 161:2457-72. [PMID: 27350061 DOI: 10.1007/s00705-016-2944-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 06/18/2016] [Indexed: 12/19/2022]
Abstract
Lytic Proteus phage PM16, isolated from human faeces, is a novel virus that is specific for Proteus mirabilis cells. Bacteriophage PM16 is characterized by high stability, a short latency period, large burst size and the occurrence of low phage resistance. Phage PM16 was classified as a member of the genus Phikmvvirus on the basis of genome organization, gene synteny, and protein sequences similarities. Within the genus Phikmvvirus, phage PM16 is grouped with Vibrio phage VP93, Pantoea phage LIMElight, Acinetobacter phage Petty, Enterobacter phage phiKDA1, and KP34-like bacteriophages. An investigation of the phage-cell interaction demonstrated that phage PM16 attached to the cell surface, not to the bacterial flagella. The study of P. mirabilis mutant cells obtained during the phage-resistant bacterial cell assay that were resistant to phage PM16 re-infection revealed a non-swarming phenotype, changes in membrane characteristics, and the absence of flagella. Presumably, the resistance of non-swarming P. mirabilis cells to phage PM16 re-infection is determined by changes in membrane macromolecular composition and is associated with the absence of flagella and a non-swarming phenotype.
Collapse
Affiliation(s)
- V Morozova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia.
| | - Yu Kozlova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - E Shedko
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Kurilshikov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - I Babkin
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Yunusova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - A Chernonosov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - I Baykov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - I Кondratov
- Limnological Institute of SB RAS, Ulan-Batorskaya Str., 3, Irkutsk, Russia
| | - M Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - E Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - V Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| | - N Tikunova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentieva Ave., 8, Novosibirsk, Russia
| |
Collapse
|
11
|
Zonov E, Kochneva G, Yunusova A, Grazhdantseva A, Richter V, Ryabchikova E. Features of the Antitumor Effect of Vaccinia Virus Lister Strain. Viruses 2016; 8:E20. [PMID: 26771631 PMCID: PMC4728580 DOI: 10.3390/v8010020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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: 07/28/2015] [Revised: 12/30/2015] [Accepted: 01/06/2016] [Indexed: 02/06/2023] Open
Abstract
Oncolytic abilities of vaccinia virus (VACV) served as a basis for the development of various recombinants for treating cancer; however, "natural" oncolytic properties of the virus are not examined in detail. Our study was conducted to know how the genetically unmodified L-IVP strain of VACV produces its antitumor effect. Human A431 carcinoma xenografts in nude mice and murine Ehrlich carcinoma in C57Bl mice were used as targets for VACV, which was injected intratumorally. A set of virological methods, immunohistochemistry, light and electron microscopy was used in the study. We found that in mice bearing A431 carcinoma, the L-IVP strain was observed in visceral organs within two weeks, but rapidly disappeared from the blood. The L-IVP strain caused decrease of sizes in both tumors, however, in different ways. Direct cell destruction by replicating virus plays a main role in regression of A431 carcinoma xenografts, while in Ehrlich carcinoma, which poorly supported VACV replication, the virus induced decrease of mitoses by pushing tumor cells into S-phase of cell cycle. Our study showed that genetically unmodified VACV possesses at least two mechanisms of antitumor effect: direct destruction of tumor cells and suppression of mitoses in tumor cells.
Collapse
Affiliation(s)
- Evgeniy Zonov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
| | - Galina Kochneva
- State Research Center of Virology and Biotechnology "Vector", Koltsovo 630559, Russia.
| | - Anastasiya Yunusova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
| | | | - Vladimir Richter
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.
| |
Collapse
|
12
|
Bryzgunova O, Lekhnov E, Skvortsova T, Morozkin E, Zaporozhchenko I, Grigorieva A, Zaripov M, Ryabchikova E, Vlassov V, Laktionov P. P67. European Journal of Cancer Supplements 2015. [DOI: 10.1016/j.ejcsup.2015.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
13
|
Kochneva G, Zonov E, Grazhdantseva A, Yunusova A, Sibolobova G, Popov E, Taranov O, Netesov S, Chumakov P, Ryabchikova E. Apoptin enhances the oncolytic properties of vaccinia virus and modifies mechanisms of tumor regression. Oncotarget 2014; 5:11269-82. [PMID: 25358248 PMCID: PMC4294355 DOI: 10.18632/oncotarget.2579] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 07/15/2014] [Accepted: 10/08/2014] [Indexed: 12/26/2022] Open
Abstract
A recombinant vaccinia virus VVdGF-ApoS24/2 expressing apoptin selectively kills human cancer cells in vitro [Kochneva et al., 2013]. We compared the oncolytic activity of this recombinant with that of the parental strain L-IVP using a model of human A431 carcinoma xenografts in nude mice. Single intratumoral injections (2×10^7 PFU/mouse) of the viruses produced a dramatic decrease in tumor volumes, which was higher after injection of apoptin-producing virus. The tumor dried out after the injection of recombinant while injection of L-IVP strain resulted in formation of cavities filled with cell debris and liquid. Both viruses rapidly spread in xenografts and replicate exclusively in tumor cells causing their destruction within 8 days. Both viruses induced insignificant level of apoptosis in tumors. Unlike the previously described nuclear localization of apoptin in cancer cells the apoptin produced by recombinant virus was localized to the cytoplasm. The apoptin did not induce a typical apoptosis, but it rather influenced pathway of cell death and thereby caused tumor shrinkage. The replacement of destroyed cells by filamentous material is the main feature of tumor regression caused by the VVdGF-ApoS24/2 virus. The study points the presence of complicated mechanisms of apoptin effects at the background of vaccinia virus replication.
Collapse
Affiliation(s)
- Galina Kochneva
- Novosibirsk State University, Novosibirsk, Russia
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Evgeniy Zonov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | | | - Anastasiya Yunusova
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Galina Sibolobova
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Evgeniy Popov
- Novosibirsk State University, Novosibirsk, Russia
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Oleg Taranov
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Sergei Netesov
- Novosibirsk State University, Novosibirsk, Russia
- State Research Center of Virology and Biotechnology “Vector”, Koltsovo, Russia
| | - Peter Chumakov
- Novosibirsk State University, Novosibirsk, Russia
- Engelhardt Institute of Molecular Biology, Moscow
| | - Elena Ryabchikova
- Novosibirsk State University, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| |
Collapse
|
14
|
Grigor'eva A, Saranina I, Tikunova N, Safonov A, Timoshenko N, Rebrov A, Ryabchikova E. Fine mechanisms of the interaction of silver nanoparticles with the cells of Salmonella typhimurium and Staphylococcus aureus. Biometals 2013; 26:479-88. [PMID: 23686387 DOI: 10.1007/s10534-013-9633-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2013] [Accepted: 05/11/2013] [Indexed: 10/26/2022]
Abstract
Silver nanoparticles possess antibacterial effect for various bacteria; however mechanisms of the interaction between Ag-NPs and bacterial cells remain unclear. The aim of our study was to obtain direct evidence of Ag-NPs penetration into cells of Gram-negative bacterium S. typhimurium and Gram-positive bacterium S. aureus, and to study cell responses to Ag-NPs. The Ag-NPs (most 8-10 nm) were obtained by gas-jet method. S. typhimurium (7.81 × 10⁷ CFU), or S. aureus (8.96 × 10⁷ CFU) were treated by Ag-NPs (0.05 mg/l of silver) in orbital shaker at 190 rpm, 37 °C. Bacteria were sampled at 0.5, 1, 1.5, 2, 5 and 23 h of the incubation for transmission electron microscopy of ultrathin sections. The Ag-NPs adsorbed on outer membrane of S. typhimurium and cell wall of S. auereus; penetrated and accumulated in cells without aggregation and damaging of neighboring cytoplasm. In cells of S. aureus Ag-NPs bound with DNA fibers. Cell responses to Ag-NPs differed morphologically in S. typhimurium and S. aureus, and mainly were presented by damage of cell structures. The cytoplasm of S. aureus became amorphous, while S. typhimurium showed lumping and lysis of cytoplasm which led to formation of "empty" cells. Other difference was fast change of cell shape in S. typhimurium, and late deformation of S. aureus cells. The obtained results showed how different could be responses induced by the same NPs in relatively simple prokaryotic cells. Evidently, Ag-NPs directly interact with macromolecular structures of living cells and are exert an active influence on their metabolism.
Collapse
Affiliation(s)
- Alina Grigor'eva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Lavrent'eva Av., 8, Novosibirsk 630090, Russia
| | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
Marburg and Ebola viruses cause a severe hemorrhagic disease in humans with high fatality rates. Early target cells of filoviruses are monocytes, macrophages, and dendritic cells. The infection spreads to the liver, spleen and later other organs by blood and lymph flow. A hallmark of filovirus infection is the depletion of non-infected lymphocytes; however, the molecular mechanisms leading to the observed bystander lymphocyte apoptosis are poorly understood. Also, there is limited knowledge about the fate of infected cells in filovirus disease. In this review we will explore what is known about the intracellular events leading to virus amplification and cell damage in filovirus infection. Furthermore, we will discuss how cellular dysfunction and cell death may correlate with disease pathogenesis.
Collapse
Affiliation(s)
- Judith Olejnik
- Department of Microbiology, School of Medicine, Boston University, 72 East Concord Street, Boston, MA 02118, USA; E-Mails: (J.O.); (R.B.C.)
- National Emerging Infectious Diseases Laboratories Institute, Boston University, 72 East Concord Street, Boston, MA 02118, USA
| | - Elena Ryabchikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, Pr. Lavrent’eva, 8, Novosibirsk 630090, Russian Federation; E-Mail:
| | - Ronald B. Corley
- Department of Microbiology, School of Medicine, Boston University, 72 East Concord Street, Boston, MA 02118, USA; E-Mails: (J.O.); (R.B.C.)
- National Emerging Infectious Diseases Laboratories Institute, Boston University, 72 East Concord Street, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Microbiology, School of Medicine, Boston University, 72 East Concord Street, Boston, MA 02118, USA; E-Mails: (J.O.); (R.B.C.)
- National Emerging Infectious Diseases Laboratories Institute, Boston University, 72 East Concord Street, Boston, MA 02118, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-617-638-0336; Fax: +1-617-638-4286
| |
Collapse
|
16
|
Patutina O, Mironova N, Ryabchikova E, Popova N, Nikolin V, Kaledin V, Vlassov V, Zenkova M. Inhibition of metastasis development by daily administration of ultralow doses of RNase A and DNase I. Biochimie 2010; 93:689-96. [PMID: 21194552 DOI: 10.1016/j.biochi.2010.12.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Accepted: 12/16/2010] [Indexed: 12/18/2022]
Abstract
Recent data on the involvement of miRNA and circulating tumor-derived DNA in regulation of tumorigenesis showed a great prospect for these molecules as a novel class of therapeutic targets and gave a new start for the study of enzymes cleaving nucleic acids as potential antitumor and antimetastatic agents. In the present paper using two murine tumor models with pulmonary or liver metastases we studied the antimetastatic potential of RNase A and DNase I and performed a search for possible molecular targets of the enzymes. Herein, we show for the first time that daily administration of ultralow doses of RNase A (0.5-50 μg/kg) and DNase I (0.02-2.3 mg/kg) inhibits the development of metastasis to 60-90% and RNase A exerts 30% retardation of tumor growth. Remarkably, the increase in RNase A dose from 50 μg/kg to 10mg/kg leads to a disappearance of antitumor and antimetastatic effects. Simultaneous treatment of tumor-bearing animals with RNase A and DNase I leads to an additive effect and results in almost total absence of metastases. The use of RNase A as an adjuvant in conjunction with conventional cytostatic cyclophosphamide results in a reliable enhancement of antitumor and antimetastatic effect of the therapy compared with the use of these agents individually. The search for possible molecular mechanism of antimetastatic effect of nucleases showed that daily administration of the enzymes reduced the pathologically increased level of extracellular nucleic acids and increased nuclease activity of the blood plasma of tumor-bearing mice back to the level of healthy animals. Thus, we unequivocally show that the proposed protocol of treatment of tumor-bearing animals with RNase A and DNase I has a general systemic and immunomodulatory effect, leads to a drastic suppression of metastasis development, and in perspective may become an effective component of intensive complex therapy of cancer.
Collapse
Affiliation(s)
- Olga Patutina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russian Federation
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Rak S, Goncharova E, Vinogradov I, Ryabchikova E, Chinarev A, Tuzikov A, Bovin N, Ryzhikov A. Comparative Study of the Efficacy of Low- and High-Molecular Inhibitors of Influenza Virus Hemagglutinin. Antiviral Res 2009. [DOI: 10.1016/j.antiviral.2009.02.068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
18
|
Kolesnikova L, Ryabchikova E, Shestopalov A, Becker S. Basolateral Budding of Marburg Virus: VP40 Retargets Viral Glycoprotein GP to the Basolateral Surface. J Infect Dis 2007; 196 Suppl 2:S232-6. [DOI: 10.1086/520584] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
|
19
|
Kochneva G, Kolosova I, Maksyutova T, Ryabchikova E, Shchelkunov S. Effects of deletions of kelch-like genes on cowpox virus biological properties. Arch Virol 2005; 150:1857-70. [PMID: 15824883 DOI: 10.1007/s00705-005-0530-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2004] [Accepted: 02/17/2005] [Indexed: 11/28/2022]
Abstract
Cowpox virus (CPXV) strain GRI-90 contains six genes encoding kelch-like proteins. All six proteins contain both, the N-terminal BTB domain and the C-terminal kelch domain. We constructed mutant variants of a CPXV strain with targeted deletions of one to four genes of the kelch family, namely D11L, C18L, G3L, and A57R. As kelch genes are located in terminal variable regions of the CPXV genome, we studied the relationship of these genes with integral biological characteristics such as virulence, host range, reproduction in vitro and in ovo (in chicken embryos). It was demonstrated that the following effects occurred in a gene dose dependent manner with an increase of the number of genes deleted: (1) range of sensitive cells altered--deletion mutants lacking three genes displayed a considerably decreased ability to reproduce in MDCK cells; mutants lacking four genes lost this ability completely; (2) analysis of pocks formed by mutants with deletion of three and four kelch-like genes on chorioallantoic membranes of chicken embryos demonstrated that pock size and virus yield were significantly decreased; (3) light microscopic analysis of the pocks revealed impaired proliferation and reduced vascularisation in the pock region. More alterations were detected by electron microscopic analysis: the reproduction of mutants results in a reduction of the number of mature virions formed, and in many cells this process was arrested at the stage of assembly of immature virions; and (4) the evaluation of LD(50) and body weight loss in BALB/c mice infected intranasally with CPXVs revealed a reduction of the virulence of the deletion mutants, which became statistically significant when four kelch-like genes were excised.
Collapse
Affiliation(s)
- G Kochneva
- State Research Center of Virology and Biotechnology Vector, Koltsovo, Novosibirsk, Russia
| | | | | | | | | |
Collapse
|
20
|
Sänger C, Mühlberger E, Ryabchikova E, Kolesnikova L, Klenk HD, Becker S. Sorting of Marburg virus surface protein and virus release take place at opposite surfaces of infected polarized epithelial cells. J Virol 2001; 75:1274-83. [PMID: 11152500 PMCID: PMC114033 DOI: 10.1128/jvi.75.3.1274-1283.2001] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marburg virus, a filovirus, causes severe hemorrhagic fever with hitherto poorly understood molecular pathogenesis. We have investigated here the vectorial transport of the surface protein GP of Marburg virus in polarized epithelial cells. To this end, we established an MDCKII cell line that was able to express GP permanently (MDCK-GP). The functional integrity of GP expressed in these cells was analyzed using vesicular stomatitis virus pseudotypes. Further experiments revealed that GP is transported in MDCK-GP cells mainly to the apical membrane and is released exclusively into the culture medium facing the apical membrane. When MDCKII cells were infected with Marburg virus, the majority of GP was also transported to the apical membrane, suggesting that the protein contains an autonomous apical transport signal. Release of infectious progeny virions, however, took place exclusively at the basolateral membrane of the cells. Thus, vectorial budding of Marburg virus is presumably determined by factors other than the surface protein.
Collapse
Affiliation(s)
- C Sänger
- Institut für Virologie, Philipps-Universität Marburg, D-35037 Marburg, Germany
| | | | | | | | | | | |
Collapse
|
21
|
Kolesnikova L, Mühlberger E, Ryabchikova E, Becker S. Ultrastructural organization of recombinant Marburg virus nucleoprotein: comparison with Marburg virus inclusions. J Virol 2000; 74:3899-904. [PMID: 10729166 PMCID: PMC111900 DOI: 10.1128/jvi.74.8.3899-3904.2000] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/1999] [Accepted: 01/20/2000] [Indexed: 11/20/2022] Open
Abstract
HeLa cells expressing the recombinant Marburg virus (MBGV) nucleoprotein (NP) have been studied by immunoelectron microscopy. It was found that MBGV NPs assembled into large aggregates which were in close association with membranes of the rough endoplasmic reticulum. Further analysis of these aggregates revealed that NPs formed tubule-like structures which were arranged in a hexagonal pattern. A similar pattern of preformed nucleocapsids was detected in intracellular inclusions induced by MBGV infection. Our data indicated that MBGV NP is able to form nucleocapsid-like structures in the absence of the authentic viral genome and other nucleocapsid-associated proteins.
Collapse
Affiliation(s)
- L Kolesnikova
- State Scientific Research Center of Virology, Vector Institute of Molecular Biology, Laboratory of Ultrastructure, 633159 Koltsovo, Novosibirsk Region, Russia
| | | | | | | |
Collapse
|
22
|
Abstract
Marburg virus (MV) reproduction in organs, hematological and pathological changes were studied by virological and clinical methods, light and electron microscopy in guinea pigs respiratory challenged by the virus. Liver and spleen were most affected by MV, as in parenteral infection. The sequential involvement of cells in virus replication was also the same as in parenteral infection, with monocytoid-macrophagal cells infected first, followed by hepatocytes, spongiocytes, endotheliocytes and fibroblasts. Hemopoietic cells showed evidence of severe damage in respiratory infected guinea pigs. A distinguishing feature of the respiratory infection was close contact of leucocytes with MV infected cells. It is suggested that the entrapment and accumulation of MV in the lungs of respiratory infected guinea pigs makes possible the enfoldment leucocyte attack which does not, however, result in destruction of the infected cells.
Collapse
Affiliation(s)
- E Ryabchikova
- State Research Center of Virology and Biotechnology Vector, Research Institute of Molecular Biology Koltsovo, Novosibirsk Region, Russia
| | | | | | | | | |
Collapse
|
23
|
Ryabchikova E, Kolesnikova L, Smolina M, Tkachev V, Pereboeva L, Baranova S, Grazhdantseva A, Rassadkin Y. Ebola virus infection in guinea pigs: presumable role of granulomatous inflammation in pathogenesis. Arch Virol 1996; 141:909-21. [PMID: 8678836 DOI: 10.1007/bf01718165] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
An approach combining virology with light and electron microscopy was used to study the organs of guinea pigs during nine serial passages of Ebola virus, strain Zaire. It was observed that the wild type of Ebola virus causes severe granulomatous inflammation in the liver and reproduces in the cells of the mononuclear phagocyte system (MPS). Based on morphological characterization, two types of virus-cell interactions were demonstrated. The obtained data evidenced for heterogeneity of the population of wild type of Ebola virus. The virus accumulated in the liver of the infected animals, and the lesions became more pronounced with passage. Degenerative changes appeared, and their severity was increased with passage in the other organs as well. The set of target cells diversified and, as a result, not only the MPS cells, but also hepatocytes, spongiocytes, endotheliocytes and fibroblasts became involved in the reproduction of Ebola virus. The possible role of granulomatous inflammation in the development of the adaptive mechanism of Ebola virus to guinea pigs is discussed.
Collapse
Affiliation(s)
- E Ryabchikova
- State Research Center of Virology and Biotechnology "Vector" Research Institute of Molecular Biology, Koltsovo, Novosibirsk Region, Russia
| | | | | | | | | | | | | | | |
Collapse
|