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Shmakova A, Hugot C, Kozhevnikova Y, Schwager Karpukhina A, Tsimailo I, Gérard L, Boutboul D, Oksenhendler E, Szewczyk-Roszczenko O, Roszczenko P, Buzun K, Sheval EV, Germini D, Vassetzky Y. Chronic HIV-1 Tat action induces HLA-DR downregulation in B cells: A mechanism for lymphoma immune escape in people living with HIV. J Med Virol 2024; 96:e29423. [PMID: 38285479 DOI: 10.1002/jmv.29423] [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: 09/25/2023] [Revised: 01/03/2024] [Accepted: 01/11/2024] [Indexed: 01/30/2024]
Abstract
Despite the success of combination antiretroviral therapy, people living with human immunodeficiency virus (HIV) still have an increased risk of Epstein-Barr virus (EBV)-associated B cell malignancies. In the HIV setting, B cell physiology is altered by coexistence with HIV-infected cells and the chronic action of secreted viral proteins, for example, HIV-1 Tat that, once released, efficiently penetrates noninfected cells. We modeled the chronic action of HIV-1 Tat on B cells by ectopically expressing Tat or TatC22G mutant in two lymphoblastoid B cell lines. The RNA-sequencing analysis revealed that Tat deregulated the expression of hundreds of genes in B cells, including the downregulation of a subset of major histocompatibility complex (MHC) class II-related genes. Tat-induced downregulation of HLA-DRB1 and HLA-DRB5 genes led to a decrease in HLA-DR surface expression; this effect was reproduced by coculturing B cells with Tat-expressing T cells. Chronic Tat presence decreased the NF-ᴋB pathway activity in B cells; this downregulated NF-ᴋB-dependent transcriptional targets, including MHC class II genes. Notably, HLA-DRB1 and surface HLA-DR expression was also decreased in B cells from people with HIV. Tat-induced HLA-DR downregulation in B cells impaired EBV-specific CD4+ T cell response, which contributed to the escape from immune surveillance and could eventually promote B cell lymphomagenesis in people with HIV.
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Affiliation(s)
- Anna Shmakova
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
- Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Coline Hugot
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
| | - Yana Kozhevnikova
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
| | - Anna Schwager Karpukhina
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
- Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Ivan Tsimailo
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
| | - Laurence Gérard
- Service d'Immunopathologie Clinique, Hôpital St Louis, APHP, Paris, France
| | - David Boutboul
- Service d'Immunopathologie Clinique, Hôpital St Louis, APHP, Paris, France
| | - Eric Oksenhendler
- Service d'Immunopathologie Clinique, Hôpital St Louis, APHP, Paris, France
| | - Olga Szewczyk-Roszczenko
- Department of Synthesis and Technology of Drugs, Medical University of Bialystok, Bialystok, Poland
| | - Piotr Roszczenko
- Department of Biotechnology, Medical University of Bialystok, Bialystok, Poland
| | - Kamila Buzun
- Department of Pharmaceutical Sciences, Poznan University of Medical Sciences, Poznan, Poland
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Department of Cell Biology and Histology, Lomonosov Moscow State University, Moscow, Russia
| | - Diego Germini
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
| | - Yegor Vassetzky
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France
- Koltzov Institute of Developmental Biology, Moscow, Russia
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2
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Potashnikova DM, Tvorogova AV, Saidova AA, Sotnikova TN, Arifulin EA, Lipina TV, Shirokova OM, Melnikov ES, Rodina TA, Valyaeva AA, Zharikova AA, Zayratyants GO, Zayratyants OV, Sheval EV, Vasilieva EJ. Lung inflammation is associated with lipid deposition. bioRxiv 2023:2022.12.30.522299. [PMID: 36789445 PMCID: PMC9928036 DOI: 10.1101/2022.12.30.522299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Lung inflammation, pneumonia, is an acute respiratory disease of varying etiology that has recently drawn much attention during the COVID-19 pandemic as lungs are among the main targets for SARS-CoV-2. Multiple other etiological agents are associated with pneumonias. Here, we describe a newly-recognized pathology, namely abnormal lipid depositions in the lungs of patients who died from COVID-19 as well as from non-COVID-19 pneumonias. Our analysis of both semi-thin and Sudan III-stained lung specimens revealed extracellular and intracellular lipid depositions irrespective of the pneumonia etiology. Most notably, lipid depositions were located within vessels adjacent to inflamed regions, where they apparently interfere with the blood flow. Structurally, the lipid droplets in the inflamed lung tissue were homogeneous and lacked outer membranes as assessed by electron microscopy. Morphometric analysis of lipid droplet deposition area allowed us to distinguish the non-pneumonia control lung specimens from the macroscopically intact area of the pneumonia lung and from the inflamed area of the pneumonia lung. Our measurements revealed a gradient of lipid deposition towards the inflamed region. The pattern of lipid distribution proved universal for all pneumonias. Finally, lipid metabolism in the lung tissue was assessed by the fatty acid analysis and by expression of genes involved in lipid turnover. Chromato-mass spectrometry revealed that unsaturated fatty acid content was elevated at inflammation sites compared to that in control non-inflamed lung tissue from the same individual. The expression of genes involved in lipid metabolism was altered in pneumonia, as shown by qPCR and in silico RNA-seq analysis. Thus, pneumonias of various etiologies are associated with specific lipid abnormalities; therefore, lipid metabolism can be considered to be a target for new therapeutic strategies.
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3
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Potashnikova DM, Sotnikova TN, Shirokova OM, Zayratyants OV, Vasilieva EY, Sheval EV. Cilia impairment in bronchial epithelial cells detected in autopsy material of SARS-CoV-2-infected patient. Ultrastruct Pathol 2023; 47:382-387. [PMID: 37306223 DOI: 10.1080/01913123.2023.2222167] [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: 04/18/2023] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 06/13/2023]
Abstract
Recent studies indicate that cilia impairment, accompanied by the axonema loss and the basal body misorientation, is a common pathological feature of SARS-CoV-2-infected bronchial epithelial cells. However, these data were obtained using either cultured cells, or animal models, while in human postmortem material, cilia impairment has not been described yet. Here, we present direct observation of cilia impairment in SARS-CoV-2-infected bronchial epithelial cells using transmission electron microscopy of the autopsy material. We were able to observe only single infected cells with cilia impairment in one of twelve examined specimens, while the large number of desquamated bronchial epithelial cells with undisturbed ciliary layer was visible in the bronchial lumens. Thus, it seems that in the lungs of infected patients, the majority of bronchial cells do not die as a direct result of infection, which may explain the rarity of this finding in the autopsy material.
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Affiliation(s)
- Daria M Potashnikova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
- Moscow Department of Healthcare, City Clinical Hospital Named After I.V. Davydovsky, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Tatiana N Sotnikova
- Moscow Department of Healthcare, City Clinical Hospital Named After I.V. Davydovsky, Moscow, Russia
| | - Olesya M Shirokova
- Central Scientific Research Laboratory, Institute of Fundamental Medicine, Privolzhsky Research Medical University, Nizhny Novgorod, Russia
| | - Oleg V Zayratyants
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Elena Yu Vasilieva
- Moscow Department of Healthcare, City Clinical Hospital Named After I.V. Davydovsky, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Eugene V Sheval
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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4
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Valyaeva AA, Zharikova AA, Sheval EV. SARS-CoV-2 cellular tropism and direct multiorgan failure in COVID-19 patients: Bioinformatic predictions, experimental observations, and open questions. Cell Biol Int 2023; 47:308-326. [PMID: 36229927 PMCID: PMC9874490 DOI: 10.1002/cbin.11928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/24/2022] [Accepted: 09/25/2022] [Indexed: 02/06/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), has led to an unprecedented public health emergency worldwide. While common cold symptoms are observed in mild cases, COVID-19 is accompanied by multiorgan failure in severe patients. Organ damage in COVID-19 patients is partially associated with the indirect effects of SARS-CoV-2 infection (e.g., systemic inflammation, hypoxic-ischemic damage, coagulopathy), but early processes in COVID-19 patients that trigger a chain of indirect effects are connected with the direct infection of cells by the virus. To understand the virus transmission routes and the reasons for the wide-spectrum of complications and severe outcomes of COVID-19, it is important to identify the cells targeted by SARS-CoV-2. This review summarizes the major steps of investigation and the most recent findings regarding SARS-CoV-2 cellular tropism and the possible connection between the early stages of infection and multiorgan failure in COVID-19. The SARS-CoV-2 pandemic is the first epidemic in which data extracted from single-cell RNA-seq (scRNA-seq) gene expression data sets have been widely used to predict cellular tropism. The analysis presented here indicates that the SARS-CoV-2 cellular tropism predictions are accurate enough for estimating the potential susceptibility of different cells to SARS-CoV-2 infection; however, it appears that not all susceptible cells may be infected in patients with COVID-19.
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Affiliation(s)
- Anna A. Valyaeva
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia,Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Anastasia A. Zharikova
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia,Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | - Eugene V. Sheval
- School of Bioengineering and BioinformaticsLomonosov Moscow State UniversityMoscowRussia,Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia,Department of Cell Biology and Histology, School of BiologyLomonosov Moscow State UniversityMoscowRussia
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5
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Valyaeva AA, Tikhomirova MA, Potashnikova DM, Bogomazova AN, Snigiryova GP, Penin AA, Logacheva MD, Arifulin EA, Shmakova AA, Germini D, Kachalova AI, Saidova AA, Zharikova AA, Musinova YR, Mironov AA, Vassetzky YS, Sheval EV. Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients. PeerJ 2022; 10:e13986. [PMID: 36275462 PMCID: PMC9586123 DOI: 10.7717/peerj.13986] [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: 05/12/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time.
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Affiliation(s)
- Anna A. Valyaeva
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria A. Tikhomirova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Daria M. Potashnikova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexandra N. Bogomazova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Eugene A. Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna A. Shmakova
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Diego Germini
- UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Anastasia I. Kachalova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleena A. Saidova
- Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - Anastasia A. Zharikova
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana R. Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Koltzov Institute of Developmental Biology, Moscow, Russia
| | - Andrey A. Mironov
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Institute for Information Transmission Problems, Moscow, Russia
| | - Yegor S. Vassetzky
- Koltzov Institute of Developmental Biology, Moscow, Russia,UMR9018 (CNRS – Institut Gustave Roussy – Université Paris Saclay), Centre National de Recherche Scientifique, Villejuif, France, France
| | - Eugene V. Sheval
- School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia,Department of Cell Biology and Histology, School of Biology, Lomonosov Moscow State University, Moscow, Russia
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6
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Valyaeva AA, Zharikova AA, Kasianov AS, Vassetzky YS, Sheval EV. Expression of SARS-CoV-2 entry factors in lung epithelial stem cells and its potential implications for COVID-19. Sci Rep 2020; 10:17772. [PMID: 33082395 PMCID: PMC7576138 DOI: 10.1038/s41598-020-74598-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 07/15/2020] [Accepted: 10/01/2020] [Indexed: 01/19/2023] Open
Abstract
SARS-CoV-2 can infiltrate the lower respiratory tract, resulting in severe respiratory failure and a high death rate. Normally, the airway and alveolar epithelium can be rapidly reconstituted by multipotent stem cells after episodes of infection. Here, we analyzed published RNA-seq datasets and demonstrated that cells of four different lung epithelial stem cell types express SARS-CoV-2 entry factors, including Ace2. Thus, stem cells can be potentially infected by SARS-CoV-2, which may lead to defects in regeneration capacity partially accounting for the severity of SARS-CoV-2 infection and its consequences.
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Affiliation(s)
- Anna A Valyaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Anastasia A Zharikova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119991
- The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia, 127051
| | - Artem S Kasianov
- The Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia, 127051
| | - Yegor S Vassetzky
- CNRS, UMR 9018, Université Paris-Saclay, Institut Gustave Roussy, Villejuif, France.
- Koltzov Institute of Developmental Biology, Moscow, Russia, 117334.
| | - Eugene V Sheval
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia, 119991.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia, 119991.
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia, 119991.
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7
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Shubina MY, Arifulin EA, Sorokin DV, Sosina MA, Tikhomirova MA, Serebryakova MV, Smirnova T, Sokolov SS, Musinova YR, Sheval EV. The GAR domain integrates functions that are necessary for the proper localization of fibrillarin (FBL) inside eukaryotic cells. PeerJ 2020; 8:e9029. [PMID: 32377452 PMCID: PMC7194090 DOI: 10.7717/peerj.9029] [Citation(s) in RCA: 4] [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: 10/17/2019] [Accepted: 03/31/2020] [Indexed: 01/25/2023] Open
Abstract
Fibrillarin (FBL) is an essential nucleolar protein that participates in pre-rRNA methylation and processing. The methyltransferase domain of FBL is an example of an extremely well-conserved protein domain in which the amino acid sequence was not substantially modified during the evolution from Archaea to Eukaryota. An additional N-terminal glycine–arginine-rich (GAR) domain is present in the FBL of eukaryotes. Here, we demonstrate that the GAR domain is involved in FBL functioning and integrates the functions of the nuclear localization signal and the nucleolar localization signal (NoLS). The methylation of the arginine residues in the GAR domain is necessary for nuclear import but decreases the efficiency of nucleolar retention via the NoLS. The presented data indicate that the GAR domain can be considered an evolutionary innovation that integrates several functional activities and thereby adapts FBL to the highly compartmentalized content of the eukaryotic cell.
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Affiliation(s)
- Maria Y Shubina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Eugene A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitry V Sorokin
- Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, Moscow, Russia
| | - Mariya A Sosina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria A Tikhomirova
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Smirnova
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Svyatoslav S Sokolov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Skobelkin State Scientific Center of Laser Medicine FMBA, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, France
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8
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Lisitsyna OM, Kurnaeva MA, Arifulin EA, Shubina MY, Musinova YR, Mironov AA, Sheval EV. Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins. Biol Direct 2020; 15:9. [PMID: 32345340 PMCID: PMC7189692 DOI: 10.1186/s13062-020-00263-6] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Background The origin of the selective nuclear protein import machinery, which consists of nuclear pore complexes and adaptor molecules interacting with the nuclear localization signals (NLSs) of cargo molecules, is one of the most important events in the evolution of eukaryotic cells. How proteins were selected for import into the forming nucleus remains an open question. Results Here, we demonstrate that functional NLSs may be integrated in the nucleotide-binding domains of both eukaryotic and prokaryotic proteins and may coevolve with these domains. Conclusion The presence of sequences similar to NLSs in the DNA-binding domains of prokaryotic proteins might have created an advantage for nuclear accumulation of these proteins during evolution of the nuclear-cytoplasmic barrier, influencing which proteins accumulated and became compartmentalized inside the forming nucleus (i.e., the content of the nuclear proteome). Reviewers This article was reviewed by Sergey Melnikov and Igor Rogozin. Open peer review Reviewed by Sergey Melnikov and Igor Rogozin. For the full reviews, please go to the Reviewers’ comments section.
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Affiliation(s)
- Olga M Lisitsyna
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Margarita A Kurnaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Eugene A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Maria Y Shubina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334, Moscow, Russia.,Skobelkin State Scientific Center of Laser Medicine FMBA, 121099, Moscow, Russia
| | - Andrey A Mironov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia.,Skolkovo Institute of Science and Technology, 121205, Moscow, Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, 127051, Moscow, Russia.,Faculty of Computer Science, National Research University Higher School of Economics, 101000, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. .,Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia. .,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
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9
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Eldarov CM, Vangely IM, Vays VB, Sheval EV, Holtze S, Hildebrandt TB, Kolosova NG, Popkov VA, Plotnikov EY, Zorov DB, Bakeeva LE, Skulachev VP. Mitochondria in the Nuclei of Rat Myocardial Cells. Cells 2020; 9:E712. [PMID: 32183238 PMCID: PMC7140638 DOI: 10.3390/cells9030712] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 12/12/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 01/01/2023] Open
Abstract
Electron microscopic study of cardiomyocytes taken from healthy Wistar and OXYS rats and naked mole rats (Heterocephalus glaber) revealed mitochondria in nuclei that lacked part of the nuclear envelope. The direct interaction of mitochondria with nucleoplasm is shown. The statistical analysis of the occurrence of mitochondria in cardiomyocyte nuclei showed that the percentage of nuclei with mitochondria was roughly around 1%, and did not show age and species dependency. Confocal microscopy of normal rat cardiac myocytes revealed a branched mitochondrial network in the vicinity of nuclei with an organization different than that of interfibrillar mitochondria. This mitochondrial network was energetically functional because it carried the membrane potential that responded by oscillatory mode after photodynamic challenge. We suggest that the presence of functional mitochondria in the nucleus is not only a consequence of certain pathologies but rather represents a normal biological phenomenon involved in mitochondrial/nuclear interactions.
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Affiliation(s)
- Chupalav M Eldarov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Irina M Vangely
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Valeriya B Vays
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Susanne Holtze
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Thomas B Hildebrandt
- Department of Reproduction Management, Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Natalia G Kolosova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Vasily A Popkov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Egor Y Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Dmitry B Zorov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Lora E Bakeeva
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir P Skulachev
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119992 Moscow, Russia
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10
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Abstract
Epoxy-embedded semithin sections are useful for the analysis of cell and tissue organization, as well as for the processing of samples for transmission electron microscopy. Because only a very limited number of staining protocols have been developed for epoxy-embedded sections; semithin sections are used infrequently compared to conventional paraffin sections. Here, we describe a simple and reproducible polychromatic protocol for the routine staining of epoxy-embedded semithin sections by adapting Twort's staining method (mixture of neutral red and fast green FCF). The method can be used for the visualization of cellular organization as well as for the detection of elastic and collagen fibers. The proposed protocol demonstrated the best results for samples fixed for transmission electron microscopy, which suggests, as we demonstrated here, that this staining protocol can also be used for correlative light and electron microscopy.
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Affiliation(s)
- Vasiliy N Manskikh
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, France.
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11
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Kharitonov AV, Shubina MY, Nosov GA, Mamontova AV, Arifulin EA, Lisitsyna OM, Nalobin DS, Musinova YR, Sheval EV. Switching of cardiac troponin I between nuclear and cytoplasmic localization during muscle differentiation. Biochim Biophys Acta Mol Cell Res 2019; 1867:118601. [PMID: 31733262 DOI: 10.1016/j.bbamcr.2019.118601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 11/02/2019] [Accepted: 11/11/2019] [Indexed: 11/18/2022]
Abstract
The nuclear accumulation of proteins may depend on the presence of short targeting sequences, which are known as nuclear localization signals (NLSs). Here, we found that NLSs are predicted in some cytosolic proteins and examined the hypothesis that these NLSs may be functional under certain conditions. As a model, human cardiac troponin I (hcTnI) was used. After expression in cultured non-muscle or undifferentiated muscle cells, hcTnI accumulated inside nuclei. Several NLSs were predicted and confirmed by site-directed mutagenesis in hcTnI. Nuclear import occurred via the classical karyopherin-α/β nuclear import pathway. However, hcTnI expressed in cultured myoblasts redistributed from the nucleus to the cytoplasm, where it was integrated into forming myofibrils after the induction of muscle differentiation. It appears that the dynamic retention of proteins inside cytoplasmic structures can lead to switching between nuclear and cytoplasmic localization.
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Affiliation(s)
- Alexey V Kharitonov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Maria Y Shubina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Georgii A Nosov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Institute of Medical Physics and Biophysics, 48149 Muenster, Germany
| | - Anastasia V Mamontova
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
| | - Eugene A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Olga M Lisitsyna
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Denis S Nalobin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Skobelkin State Scientific Center of Laser Medicine FMBA, 121165 Moscow, Russia
| | - Eugene V Sheval
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France.
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12
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Maximchik PV, Tamarov K, Sheval EV, Tolstik E, Kirchberger-Tolstik T, Yang Z, Sivakov V, Zhivotovsky B, Osminkina LA. Biodegradable Porous Silicon Nanocontainers as an Effective Drug Carrier for Regulation of the Tumor Cell Death Pathways. ACS Biomater Sci Eng 2019; 5:6063-6071. [DOI: 10.1021/acsbiomaterials.9b01292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Polina V. Maximchik
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russian Federation
| | - Konstantin Tamarov
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russian Federation
| | - Eugene V. Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russian Federation
| | - Elen Tolstik
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany
- Leibniz Institut für Analytische Wissenschaften - ISAS - e.V., Bunsen-Kirchhoff-Str. 11, 44139 Dortmund, Germany
| | - Tatiana Kirchberger-Tolstik
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany
- Jena University Hospital, Department of Internal Medicine IV, Gastroenterology, Hepatology, Infectious Disease, Am Klinikum, 1, 07747 Jena, Germany
| | - Zhang Yang
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russian Federation
- College of Science, Sichuan Agriculture University, Yaan, Sichuan 625014, People’s Republic of China
| | - Vladimir Sivakov
- Leibniz Institute of Photonic Technology, Albert Einstein Str. 9, 07745 Jena, Germany
| | - Boris Zhivotovsky
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russian Federation
- Institute of Environmental Medicine, Division of Toxicology, Karolinska Institutet, Box 210, Stockholm SE-171 77, Sweden
| | - Liubov A. Osminkina
- Faculty of Physics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russian Federation
- Institute for Biological Instrumentation of Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russian Federation
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13
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Iarovaia OV, Minina EP, Sheval EV, Onichtchouk D, Dokudovskaya S, Razin SV, Vassetzky YS. Nucleolus: A Central Hub for Nuclear Functions. Trends Cell Biol 2019; 29:647-659. [PMID: 31176528 DOI: 10.1016/j.tcb.2019.04.003] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [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: 12/17/2018] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/19/2022]
Abstract
The nucleolus is the largest and most studied nuclear body, but its role in nuclear function is far from being comprehensively understood. Much work on the nucleolus has focused on its role in regulating RNA polymerase I (RNA Pol I) transcription and ribosome biogenesis; however, emerging evidence points to the nucleolus as an organizing hub for many nuclear functions, accomplished via the shuttling of proteins and nucleic acids between the nucleolus and nucleoplasm. Here, we discuss the cellular mechanisms affected by shuttling of nucleolar components, including the 3D organization of the genome, stress response, DNA repair and recombination, transcription regulation, telomere maintenance, and other essential cellular functions.
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Affiliation(s)
- Olga V Iarovaia
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France
| | - Elizaveta P Minina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene V Sheval
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Daria Onichtchouk
- Developmental Biology Unit, Department of Biology I, University of Freiburg, Hauptstrasse 1, D-79104 Freiburg, Germany
| | - Svetlana Dokudovskaya
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; UMR8126, Université Paris-Sud, CNRS, Institut Gustave Roussy, 94805 Villejuif, France
| | - Sergey V Razin
- Institute of Gene Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Yegor S Vassetzky
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France; Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; UMR8126, Université Paris-Sud, CNRS, Institut Gustave Roussy, 94805 Villejuif, France.
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14
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Potashnikova DM, Saidova AA, Tvorogova AV, Sheval EV, Vorobjev IA. Non-linear Dose Response of Lymphocyte Cell Lines to Microtubule Inhibitors. Front Pharmacol 2019; 10:436. [PMID: 31068822 PMCID: PMC6491834 DOI: 10.3389/fphar.2019.00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 02/08/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022] Open
Abstract
Microtubule (MT) inhibitors show anti-cancer activity in a wide range of tumors in vitro and demonstrate high clinical efficacy. To date they are routinely included into many chemotherapeutic regimens. While the mechanisms of MT inhibitors’ interactions with tubulin have been well-established, the relationship between their concentration and effect on neoplastic cells is not completely understood. The common notion is that tumor cells are most vulnerable during division and all MT inhibitors block them in mitosis and induce mitotic checkpoint-associated cell death. At the same time multiple evidence of more subtle effects of lower doses of MT inhibitors on cell physiology exist. The extent of efficacy of the low-dose MT inhibitor treatment and the mechanisms of resulting cell death currently present a critical issue in oncology. The prospect of MT inhibitor dose reduction is promising as protocols at higher concentration have multiple side effects. We assessed cell cycle changes and cell death induced by MT inhibitors (paclitaxel, nocodazole, and vinorelbine) on human lymphoid B-cell lines in a broad concentration range. All inhibitors had similar accumulation effects and demonstrated “trigger” concentrations that induce cell accumulation in G2/M phase. Concentrations slightly below the “trigger” promoted cell accumulation in sub-G1 phase. Multi-label analysis of live cells showed that the sub-G1 population is heterogeneous and may include cells that are still viable after 24 h of treatment. Effects observed were similar for cells expressing Tat-protein. Thus cell cycle progression and cell death are differentially affected by high and low MT inhibitor concentrations.
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Affiliation(s)
- Daria M Potashnikova
- Department of Cell Biology and Histology, School of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Laboratory of Atherothrombosis, Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - Aleena A Saidova
- Department of Cell Biology and Histology, School of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Department of Cell Biotechnology, Center of Experimental Embryology and Reproductive Biotechnology, Moscow, Russia
| | - Anna V Tvorogova
- Department of Cell Biotechnology, Center of Experimental Embryology and Reproductive Biotechnology, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Ivan A Vorobjev
- Department of Cell Biology and Histology, School of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia.,Department of Biology, School of Science and Technology, Nazarbayev University, Astana, Kazakhstan
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15
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Kurnaeva MA, Sheval EV, Musinova YR, Vassetzky YS. Tat basic domain: A "Swiss army knife" of HIV-1 Tat? Rev Med Virol 2019; 29:e2031. [PMID: 30609200 DOI: 10.1002/rmv.2031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/19/2018] [Revised: 12/05/2018] [Accepted: 12/06/2018] [Indexed: 01/16/2023]
Abstract
Tat (transactivator of transcription) regulates transcription from the HIV provirus. It plays a crucial role in disease progression, supporting efficient replication of the viral genome. Tat also modulates many functions in the host genome via its interaction with chromatin and proteins. Many of the functions of Tat are associated with its basic domain rich in arginine and lysine residues. It is still unknown why the basic domain exhibits so many diverse functions. However, the highly charged basic domain, coupled with the overall structural flexibility of Tat protein itself, makes the basic domain a key player in binding to or associating with cellular and viral components. In addition, the basic domain undergoes diverse posttranslational modifications, which further expand and modulate its functions. Here, we review the current knowledge of Tat basic domain and its versatile role in the interaction between the virus and the host cell.
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Affiliation(s)
- Margarita A Kurnaeva
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, CNRS, Villejuif, France
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, CNRS, Villejuif, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yegor S Vassetzky
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, CNRS, Villejuif, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia.,Nuclear Organization and Pathologies, CNRS, UMR8126, Université Paris-Sud, Institut Gustave Roussy, Villejuif, France
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16
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Arifulin EA, Sorokin DV, Tvorogova AV, Kurnaeva MA, Musinova YR, Zhironkina OA, Golyshev SA, Abramchuk SS, Vassetzky YS, Sheval EV. Heterochromatin restricts the mobility of nuclear bodies. Chromosoma 2018; 127:529-537. [PMID: 30291421 DOI: 10.1007/s00412-018-0683-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 07/16/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/24/2022]
Abstract
Nuclear bodies are relatively immobile organelles. Here, we investigated the mechanisms underlying their movement using experimentally induced interphase prenucleolar bodies (iPNBs). Most iPNBs demonstrated constrained diffusion, exhibiting infrequent fusions with other iPNBs and nucleoli. Fusion events were actin-independent and appeared to be the consequence of stochastic collisions between iPNBs. Most iPNBs were surrounded by condensed chromatin, while fusing iPNBs were usually found in a single heterochromatin-delimited compartment ("cage"). The experimentally induced over-condensation of chromatin significantly decreased the frequency of iPNB fusion. Thus, the data obtained indicate that the mobility of nuclear bodies is restricted by heterochromatin.
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Affiliation(s)
- Eugene A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Dmitry V Sorokin
- Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Anna V Tvorogova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Margarita A Kurnaeva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilov str. 26, 119334, Moscow, Russia
| | - Oxana A Zhironkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Sergey A Golyshev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Sergey S Abramchuk
- Faculty of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yegor S Vassetzky
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Vavilov str. 26, 119334, Moscow, Russia.
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
- UMR8126, CNRS, Institut de Cancérologie Gustave Roussy, Université Paris-Sud, 94805, Villejuif, France.
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
- Department of Cell Biology and Histology, Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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17
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Abstract
Cell nucleus is characterized by strong compartmentalization of structural components in its three-dimensional space. Certain genomic functions are accompanied by changes in the localization of chromatin loci and nuclear bodies. Here we review recent data on the mobility of nuclear components and the role of this mobility in genome functioning.
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Affiliation(s)
- E A Arifulin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Y R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Y S Vassetzky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,UMR8126, CNRS, Université Paris-Sud, Institut de Cancérologie Gustave Roussy, Villejuif, 94805, France
| | - E V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, 94805, France
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18
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Shubina MY, Musinova YR, Sheval EV. Proliferation, cancer, and aging-novel functions of the nucleolar methyltransferase fibrillarin? Cell Biol Int 2018; 42:1463-1466. [PMID: 30080298 DOI: 10.1002/cbin.11044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 06/22/2018] [Accepted: 07/29/2018] [Indexed: 01/28/2023]
Abstract
Fibrillarin is an essential nucleolar protein that catalyzes the 2'-O-methylation of ribosomal RNAs. Recently, experimental data have begun to accumulate that suggest that fibrillarin can influence various cellular processes, development of pathological processes, and even aging. The exact mechanism by which fibrillarin can influence these processes has not been found, but some experimental data indicate that up- or downregulation of fibrillarin can modify the ribosome structure and, thus, causе an alteration in relative efficiency with which various mRNAs are translated. Here, we discuss recent studies on the potential roles of fibrillarin in the regulation of cell proliferation, cancer progression, and aging.
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Affiliation(s)
- Maria Y Shubina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Yana R Musinova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.,LIA 1066 French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France
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19
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Sheval EV. Analysis of Chromosome Condensation/Decondensation During Mitosis by EdU Incorporation in Nigella damascena L. Seedling Roots. Bio Protoc 2018; 8:e2726. [PMID: 34179260 DOI: 10.21769/bioprotoc.2726] [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: 01/12/2017] [Revised: 01/23/2018] [Accepted: 01/30/2018] [Indexed: 11/02/2022] Open
Abstract
To investigate the chromosome dynamics during mitosis, it is convenient to mark the discrete chromosome foci and then analyze their spatial rearrangements during prophase condensation and telophase decondensation. To label the chromosome regions in plant chromosomes, we incorporated the synthetic nucleotide, 5-ethynyl-2'-deoxyuridine (EdU), which can be detected by click-chemistry, into chromatin during replication. Here, we described a protocol of a method based on the application of semi-thin sections of Nigella damascena L. roots embedded in LR White acrylic resin. The thickness of semi-thin (100-250 nm) sections is significantly lower than that of optical sections even if a confocal microscope was used. This approach may also be suitable for work with any tissue fragments or large cells (oocytes, cells with polytene chromosomes, etc.).
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Affiliation(s)
- Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, Villejuif, France
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20
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El-Amine R, Germini D, Zakharova VV, Tsfasman T, Sheval EV, Louzada RAN, Dupuy C, Bilhou-Nabera C, Hamade A, Najjar F, Oksenhendler E, Lipinski M, Chernyak BV, Vassetzky YS. HIV-1 Tat protein induces DNA damage in human peripheral blood B-lymphocytes via mitochondrial ROS production. Redox Biol 2017; 15:97-108. [PMID: 29220699 PMCID: PMC5725280 DOI: 10.1016/j.redox.2017.11.024] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [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: 08/11/2017] [Revised: 10/25/2017] [Accepted: 11/27/2017] [Indexed: 12/12/2022] Open
Abstract
Human immunodeficiency virus (HIV) infection is associated with B-cell malignancies in patients though HIV-1 is not able to infect B-cells. The rate of B-cell lymphomas in HIV-infected individuals remains high even under the combined antiretroviral therapy (cART) that reconstitutes the immune function. Thus, the contribution of HIV-1 to B-cell oncogenesis remains enigmatic. HIV-1 induces oxidative stress and DNA damage in infected cells via multiple mechanisms, including viral Tat protein. We have detected elevated levels of reactive oxygen species (ROS) and DNA damage in B-cells of HIV-infected individuals. As Tat is present in blood of infected individuals and is able to transduce cells, we hypothesized that it could induce oxidative DNA damage in B-cells promoting genetic instability and malignant transformation. Indeed, incubation of B-cells isolated from healthy donors with purified Tat protein led to oxidative stress, a decrease in the glutathione (GSH) levels, DNA damage and appearance of chromosomal aberrations. The effects of Tat relied on its transcriptional activity and were mediated by NF-κB activation. Tat stimulated oxidative stress in B-cells mostly via mitochondrial ROS production which depended on the reverse electron flow in Complex I of respiratory chain. We propose that Tat-induced oxidative stress, DNA damage and chromosomal aberrations are novel oncogenic factors favoring B-cell lymphomas in HIV-1 infected individuals. B-cells of HIV-infected individuals exhibit elevated levels of oxidative stress, DNA damage and chromosomal aberrations. Purified HIV-1 Tat protein reproduces this effect and induces oxidative stress and DNA damage in B-cells. HIV-1 Tat induces mitochondrial oxidative stress and activates NF-kB in B-cells. This condition increases the risk of developing chromosomal abnormalities and translocations.
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Affiliation(s)
- Rawan El-Amine
- UMR 8126, Paris Saclay University, Paris-Sud University, Institut Gustave Roussy, CNRS, Villejuif 94805, France; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia; Doctoral school of Sciences and Technology (EDST), Lebanese University, Hadath, Lebanon; Department of Life and Earth Sciences, Faculty of Sciences II/Doctoral School of Sciences and Technology (EDST), Lebanese University, Jdeidet El Metn-Fanar, Lebanon; Department of Chemistry and Biochemistry, Faculty of Sciences II/EDST, Lebanese University, Jdeidet El Metn-Fanar, Lebanon
| | - Diego Germini
- UMR 8126, Paris Saclay University, Paris-Sud University, Institut Gustave Roussy, CNRS, Villejuif 94805, France; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia
| | - Vlada V Zakharova
- UMR 8126, Paris Saclay University, Paris-Sud University, Institut Gustave Roussy, CNRS, Villejuif 94805, France; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Tatyana Tsfasman
- UMR 8126, Paris Saclay University, Paris-Sud University, Institut Gustave Roussy, CNRS, Villejuif 94805, France; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia
| | - Eugene V Sheval
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Ruy A N Louzada
- UMR 8200, Institut Gustave Roussy, CNRS, Villejuif 94805, France
| | - Corinne Dupuy
- UMR 8200, Institut Gustave Roussy, CNRS, Villejuif 94805, France
| | - Chrystèle Bilhou-Nabera
- Biological Hematology Service-U.F. of Onco-Hematology Cytogenetics-Hôpital Saint-Antoine, 75012 Paris, France
| | - Aline Hamade
- Department of Life and Earth Sciences, Faculty of Sciences II/Doctoral School of Sciences and Technology (EDST), Lebanese University, Jdeidet El Metn-Fanar, Lebanon
| | - Fadia Najjar
- Department of Chemistry and Biochemistry, Faculty of Sciences II/EDST, Lebanese University, Jdeidet El Metn-Fanar, Lebanon
| | - Eric Oksenhendler
- Department of Clinical Immunology, Hôpital Saint-Louis, 75010 Paris, France
| | - Marс Lipinski
- UMR 8126, Paris Saclay University, Paris-Sud University, Institut Gustave Roussy, CNRS, Villejuif 94805, France; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia
| | - Boris V Chernyak
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Yegor S Vassetzky
- UMR 8126, Paris Saclay University, Paris-Sud University, Institut Gustave Roussy, CNRS, Villejuif 94805, France; LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif, France, 119334 Moscow, Russia; A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992 Moscow, Russia.
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Kuznetsova MA, Chaban IA, Sheval EV. Visualization of chromosome condensation in plants with large chromosomes. BMC Plant Biol 2017; 17:153. [PMID: 28899358 PMCID: PMC5596468 DOI: 10.1186/s12870-017-1102-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/07/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Most data concerning chromosome organization have been acquired from studies of a small number of model organisms, the majority of which are mammals. In plants with large genomes, the chromosomes are significantly larger than the animal chromosomes that have been studied to date, and it is possible that chromosome condensation in such plants was modified during evolution. Here, we analyzed chromosome condensation and decondensation processes in order to find structural mechanisms that allowed for an increase in chromosome size. RESULTS We found that anaphase and telophase chromosomes of plants with large chromosomes (average 2C DNA content exceeded 0.8 pg per chromosome) contained chromatin-free cavities in their axial regions in contrast to well-characterized animal chromosomes, which have high chromatin density in the axial regions. Similar to animal chromosomes, two intermediates of chromatin folding were visible inside condensing (during prophase) and decondensing (during telophase) chromosomes of Nigella damascena: approximately 150 nm chromonemata and approximately 300 nm fibers. The spatial folding of the latter fibers occurs in a fundamentally different way than in animal chromosomes, which leads to the formation of chromosomes with axial chromatin-free cavities. CONCLUSION Different compaction topology, but not the number of compaction levels, allowed for the evolution of increased chromosome size in plants.
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Affiliation(s)
- Maria A Kuznetsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Inna A Chaban
- All-Russian Research Institute of Agricultural Biotechnology, Timiryazevskaja 42, 127550, Moscow, Russia
| | - Eugene V Sheval
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992, Moscow, Russia.
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
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22
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Shevchenko SN, Burkhardt M, Sheval EV, Natashina UA, Grosse C, Nikolaev AL, Gopin AV, Neugebauer U, Kudryavtsev AA, Sivakov V, Osminkina LA. Antimicrobial Effect of Biocompatible Silicon Nanoparticles Activated Using Therapeutic Ultrasound. Langmuir 2017; 33:2603-2609. [PMID: 28211702 DOI: 10.1021/acs.langmuir.6b04303] [Citation(s) in RCA: 9] [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: 05/19/2023]
Abstract
In this study, we report a method for the suppression of Escherichia coli (E. coli) vitality by means of therapeutic ultrasound irradiation (USI) using biocompatible silicon nanoparticles as cavitation sensitizers. Silicon nanoparticles without (SiNPs) and with polysaccharide (dextran) coating (DSiNPs) were used. Both types of nanoparticles were nontoxic to Hep 2 cells up to a concentration of 2 mg/mL. The treatment of bacteria with nanoparticles and application of 1 W/cm2 USI resulted in the reduction of their viabilities up to 35 and 72% for SiNPs and DSiNPs, respectively. The higher bacterial viability reduction for DSiNPs as compared with SiNPs can be explained by the fact that the biopolymer shell of the polysaccharide provides a stronger adhesion of nanoparticles to the bacterial surface. Transmission electron microscopy (TEM) studies showed that the bacterial lipid shell was partially perforated after the combined treatment of DSiNPs and USI, which can be explained by the lysis of bacterial membrane due to the cavitation sensitized by the SiNPs. Furthermore, we have shown that 100% inhibition of E. coli bacterial colony growth is possible by coupling the treatments of DSiNPs and USI with an increased intensity of up to 3 W/cm2. The observed results reveal the application of SiNPs as promising antimicrobial agents.
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Affiliation(s)
| | - Markus Burkhardt
- Leibniz Institute of Photonic Technology , Albert Einstein Street 9, D-07745 Jena, Germany
| | | | | | - Christina Grosse
- Leibniz Institute of Photonic Technology , Albert Einstein Street 9, D-07745 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital , Erlanger Allee 101, 07747 Jena, Germany
| | | | | | - Ute Neugebauer
- Leibniz Institute of Photonic Technology , Albert Einstein Street 9, D-07745 Jena, Germany
- Center for Sepsis Control and Care, Jena University Hospital , Erlanger Allee 101, 07747 Jena, Germany
| | - Andrew A Kudryavtsev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science , Pushino 142290, Russian Federation
| | - Vladimir Sivakov
- Leibniz Institute of Photonic Technology , Albert Einstein Street 9, D-07745 Jena, Germany
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23
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Erokhina TN, Lazareva EA, Richert-Pöggeler KR, Sheval EV, Solovyev AG, Morozov SY. Subcellular Localization and Detection of Tobacco mosaic virus ORF6 Protein by Immunoelectron Microscopy. Biochemistry (Mosc) 2017; 82:60-66. [PMID: 28320287 DOI: 10.1134/s0006297917010060] [Citation(s) in RCA: 9] [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: 12/16/2023]
Abstract
Members of the genus Tobamovirus represent one of the best-characterized groups of plant positive, single stranded RNA viruses. Previous studies have shown that genomes of some tobamoviruses contain not only genes coding for coat protein, movement protein, and the cistron coding for different domains of RNA-polymerase, but also a gene, named ORF6, coding for a poorly conserved small protein. The amino acid sequences of ORF6 proteins encoded by different tobamoviruses are highly divergent. The potential role of ORF6 proteins in replication of tobamoviruses still needs to be elucidated. In this study, using biochemical and immunological methods, we have shown that ORF6 peptide is accumulated after infection in case of two isolates of Tobacco mosaic virus strain U1 (TMV-U1 common and TMV-U1 isolate A15). Unlike virus particles accumulating in the cytoplasm, the product of the ORF6 gene is found mainly in nuclei, which correlates with previously published data about transient expression of ORF6 isolated from TMV-U1. Moreover, we present new data showing the presence of ORF6 genes in genomes of several tobamoviruses. For example, in the genomes of other members of the tobamovirus subgroup 1, including Rehmannia mosaic virus, Paprika mild mottle virus, Tobacco mild green mosaic virus, Tomato mosaic virus, Tomato mottle mosaic virus, and Nigerian tobacco latent virus, sequence comparisons revealed the existence of a similar open reading frame like ORF6 of TMV.
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Affiliation(s)
- T N Erokhina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
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24
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Sheshukova EV, Komarova TV, Pozdyshev DV, Ershova NM, Shindyapina AV, Tashlitsky VN, Sheval EV, Dorokhov YL. The Intergenic Interplay between Aldose 1-Epimerase-Like Protein and Pectin Methylesterase in Abiotic and Biotic Stress Control. Front Plant Sci 2017; 8:1646. [PMID: 28993784 PMCID: PMC5622589 DOI: 10.3389/fpls.2017.01646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/07/2017] [Indexed: 05/22/2023]
Abstract
The mechanical damage that often precedes the penetration of a leaf by a pathogen promotes the activation of pectin methylesterase (PME); the activation of PME leads to the emission of methanol, resulting in a "priming" effect on intact leaves, which is accompanied by an increased sensitivity to Tobacco mosaic virus (TMV) and resistance to bacteria. In this study, we revealed that mRNA levels of the methanol-inducible gene encoding Nicotiana benthamiana aldose 1-epimerase-like protein (NbAELP) in the leaves of intact plants are very low compared with roots. However, stress and pathogen attack increased the accumulation of the NbAELP mRNA in the leaves. Using transiently transformed plants, we obtained data to support the mechanism underlying AELP/PME-related negative feedback The insertion of the NbAELP promoter sequence (proNbAELP) into the N. benthamiana genome resulted in the co-suppression of the natural NbAELP gene expression, accompanied by a reduction in the NbAELP mRNA content and increased PME synthesis. Knockdown of NbAELP resulted in high activity of PME in the cell wall and a decrease in the leaf glucose level, creating unfavorable conditions for Agrobacterium tumefaciens reproduction in injected leaves. Our results showed that NbAELP is capable of binding the TMV movement protein (MPTMV) in vitro and is likely to affect the cellular nucleocytoplasmic transport, which may explain the sensitivity of NbAELP knockdown plants to TMV. Although NbAELP was primarily detected in the cell wall, the influence of this protein on cellular PME mRNA levels might be associated with reduced transcriptional activity of the PME gene in the nucleus. To confirm this hypothesis, we isolated the N. tabacum PME gene promoter (proNtPME) and showed the inhibition of proNtPME-directed GFP and GUS expression in leaves when co-agroinjected with the NbAELP-encoding plasmid. We hypothesized that plant wounding and/or pathogen attack lead to PME activation and increased methanol emission, followed by increased NbAELP expression, which results in reversion of PME mRNA level and methanol emission to levels found in the intact plant.
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Affiliation(s)
| | - Tatiana V. Komarova
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | | | - Natalia M. Ershova
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Anastasia V. Shindyapina
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | | | - Eugene V. Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Yuri L. Dorokhov
- Vavilov Institute of General Genetics (RAS)Moscow, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
- *Correspondence: Yuri L. Dorokhov
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25
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Musinova YR, Lisitsyna OM, Sorokin DV, Arifulin EA, Smirnova TA, Zinovkin RA, Potashnikova DM, Vassetzky YS, Sheval EV. RNA-dependent disassembly of nuclear bodies. J Cell Sci 2016; 129:4509-4520. [PMID: 27875271 DOI: 10.1242/jcs.189142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 11/02/2016] [Indexed: 12/17/2022] Open
Abstract
Nuclear bodies are membraneless organelles that play important roles in genome functioning. A specific type of nuclear bodies known as interphase prenucleolar bodies (iPNBs) are formed in the nucleoplasm after hypotonic stress from partially disassembled nucleoli. iPNBs are then disassembled, and the nucleoli are reformed simultaneously. Here, we show that diffusion of B23 molecules (also known as nucleophosmin, NPM1) from iPNBs, but not fusion of iPNBs with the nucleoli, contributes to the transfer of B23 from iPNBs to the nucleoli. Maturation of pre-ribosomal RNAs (rRNAs) and the subsequent outflow of mature rRNAs from iPNBs led to the disassembly of iPNBs. We found that B23 transfer was dependent on the synthesis of pre-rRNA molecules in nucleoli; these pre-rRNA molecules interacted with B23 and led to its accumulation within nucleoli. The transfer of B23 between iPNBs and nucleoli was accomplished through a nucleoplasmic pool of B23, and increased nucleoplasmic B23 content retarded disassembly, whereas B23 depletion accelerated disassembly. Our results suggest that iPNB disassembly and nucleolus assembly might be coupled through RNA-dependent exchange of nucleolar proteins, creating a highly dynamic system with long-distance correlations between spatially distinct processes.
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Affiliation(s)
- Yana R Musinova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia.,LIA1066 French-Russian Joint Cancer Research Laboratory, Villejuif 94805, France
| | - Olga M Lisitsyna
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Dmitry V Sorokin
- Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Botanická 68a, Brno 602 00, Czech Republic.,Laboratory of Mathematical Methods of Image Processing, Faculty of Computational Mathematics and Cybernetics, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Eugene A Arifulin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Tatiana A Smirnova
- Department of Cell Biology and Histology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Roman A Zinovkin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Daria M Potashnikova
- Department of Cell Biology and Histology, Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia
| | - Yegor S Vassetzky
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia.,LIA1066 French-Russian Joint Cancer Research Laboratory, Villejuif 94805, France.,UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, Villejuif 94805, France
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119992, Russia .,LIA1066 French-Russian Joint Cancer Research Laboratory, Villejuif 94805, France
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26
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Kuznetsova MA, Sheval EV. Chromatin fibers: from classical descriptions to modern interpretation. Cell Biol Int 2016; 40:1140-1151. [PMID: 27569720 DOI: 10.1002/cbin.10672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 04/30/2016] [Accepted: 08/20/2016] [Indexed: 12/14/2022]
Abstract
The first description of intrachromosomal fibers was made by Baranetzky in 1880. Since that time, a plethora of fibrillar substructures have been described inside the mitotic chromosomes, and published data indicate that chromosomes may be formed as a result of the hierarchical folding of chromatin fibers. In this review, we examine the evolution and the current state of research on the morphological organization of mitotic chromosomes.
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Affiliation(s)
- Maria A Kuznetsova
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119992, Moscow, Russia. .,LIA1066 French-Russian Joint Cancer Research Laboratory, 119334, Moscow, Russia.
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27
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Musinova YR, Sheval EV, Dib C, Germini D, Vassetzky YS. Functional roles of HIV-1 Tat protein in the nucleus. Cell Mol Life Sci 2015; 73:589-601. [PMID: 26507246 DOI: 10.1007/s00018-015-2077-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [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: 06/15/2015] [Revised: 09/01/2015] [Accepted: 10/16/2015] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus-1 (HIV-1) Tat protein is one of the most important regulatory proteins for viral gene expression in the host cell and can modulate different cellular processes. In addition, Tat is secreted by the infected cell and can be internalized by neighboring cells; therefore, it affects both infected and uninfected cells. Tat can modulate cellular processes by interacting with different cellular structures and signaling pathways. In the nucleus, Tat might be localized either in the nucleoplasm or the nucleolus depending on its concentration. Here we review the distinct functions of Tat in the nucleoplasm and the nucleolus in connection with viral infection and HIV-induced oncogenesis.
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Affiliation(s)
- Yana R Musinova
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- LIA 1066 French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France
| | - Eugene V Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- LIA 1066 French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France
| | - Carla Dib
- LIA 1066 French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, 94805, Villejuif, France
| | - Diego Germini
- LIA 1066 French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, 94805, Villejuif, France
| | - Yegor S Vassetzky
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.
- LIA 1066 French-Russian Joint Cancer Research Laboratory, 94805, Villejuif, France.
- UMR8126, Université Paris-Sud, CNRS, Institut de cancérologie Gustave Roussy, 94805, Villejuif, France.
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28
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Volkova EG, Abramchuk SS, Sheval EV. The overexpression of nuclear envelope protein Lap2β induces endoplasmic reticulum reorganisation via membrane stacking. Biol Open 2012; 1:802-5. [PMID: 23213473 PMCID: PMC3507222 DOI: 10.1242/bio.20121537] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [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: 04/19/2012] [Accepted: 05/29/2012] [Indexed: 01/16/2023] Open
Abstract
Some nuclear envelope proteins are localised to both the nuclear envelope and the endoplasmic reticulum; therefore, it seems plausible that even small amounts of these proteins can influence the organisation of the endoplasmic reticulum. A simple method to study the possible effects of nuclear envelope proteins on endoplasmic reticulum organisation is to analyze nuclear envelope protein overexpression. Here, we demonstrate that Lap2β overexpression can induce the formation of cytoplasmic vesicular structures derived from endoplasmic reticulum membranes. Correlative light and electron microscopy demonstrated that these vesicular structures were composed of a series of closely apposed membranes that were frequently arranged in a circular fashion. Although stacked endoplasmic reticulum cisternae were highly ordered, Lap2β could readily diffuse into and out of these structures into the surrounding reticulum. It appears that low-affinity interactions between cytoplasmic domains of Lap2β can reorganise reticular endoplasmic reticulum into stacked cisternae. Although the effect of one protein may be insignificant at low concentrations, the cumulative effect of many non-specialised proteins may be significant.
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29
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Komarova TV, Sheval EV, Pozdyshev DV, Kolesnikova VS, Dorokhov YL. Rapid and massive green fluorescent protein production leads to formation of protein Y-bodies in plant cells. Biochemistry (Mosc) 2012; 77:603-8. [PMID: 22817459 DOI: 10.1134/s0006297912060065] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
Although high level of recombinant protein production can be achieved via transient expression in plant cells, the mechanism by which tolerance to the presence of recombinant protein is acquired remains unclear. Here we show that green fluorescent protein (GFP) encoded by an intron-optimized tobacco mosaic viral vector formed large membraneless GFP bodies called Y-bodies that demonstrated mainly perinuclear localization. The Y-bodies were heterogeneous in size, approaching the size of the cell nucleus. Experiments with extracted GFP and live cell imaging showed that Y-bodies included actively fluorescent, non-aggregated, tightly packed GFP molecules. The plant cells probably formed Y-bodies to exclude the recombinant protein from normal physiological turnover.
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Affiliation(s)
- T V Komarova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
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30
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Sheval EV, Prusov AN, Kireev II, Fais D, Polyakov VY. Organization of higher-level chromatin structures (chromomere, chromonema and chromatin block) examined using visible light-induced chromatin photo-stabilization. Cell Biol Int 2012; 26:579-91. [PMID: 12127937 DOI: 10.1006/cbir.2002.0879] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The method of chromatin photo-stabilization by the action of visible light in the presence of ethidium bromide was used for investigation of higher-level chromatin structures in isolated nuclei. As a model we used rat hepatocyte nuclei isolated in buffers which stabilized or destabilized nuclear matrix. Several higher-level chromatin structures were visualized: 100nm globules-chromomeres, chains of chromomeres-chromonemata, aggregates of chromomeres-blocks of condensed chromatin. All these structures were completely destroyed by 2M NaCl extraction independent of the matrix state, and DNA was extruded from the residual nuclei (nuclear matrices) into a halo. These results show that nuclear matrix proteins do not play the main role in the maintenance of higher-level chromatin structures. Preliminary irradiation led to the reduction of the halo width in the dose-dependent manner. In regions of condensed chromatin of irradiated nucleoids there were discrete complexes consisting of DNA fibers radiating from an electron-dense core and resembling the decondensed chromomeres or the rosette-like structures. As shown by the analysis of proteins bound to irradiated nuclei upon high-salt extraction, irradiation presumably stabilized the non-histone proteins. These results suggest that in interphase nuclei loop domains are folded into discrete higher-level chromatin complexes (chromomeres). These complexes are possibly maintained by putative non-histone proteins, which are extracted with high-salt buffers from non-irradiated nuclei.
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Affiliation(s)
- E V Sheval
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, 119899, Russia
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31
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Svistunova DM, Musinova YR, Polyakov VY, Sheval EV. A simple method for the immunocytochemical detection of proteins inside nuclear structures that are inaccessible to specific antibodies. J Histochem Cytochem 2011; 60:152-8. [PMID: 22114257 DOI: 10.1369/0022155411429704] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
It has been demonstrated elsewhere that a high concentration of an antigen within the nucleolus may prevent its proper recognition by specific antibodies. In this study, the authors found that a short proteinase treatment allowed for the detection of antigens in the nucleoli. The described approach is compatible with the simultaneous observation of proteins fused to fluorescent tags and with preembedding electron microscopy. It appears that the described method can be useful in situations when the proper recognition of antigens by specific antibodies is disturbed by a high density of cellular structures or a high concentration of antigens inside these structures.
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Affiliation(s)
- Darya M Svistunova
- AN Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia
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32
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Volkova EG, Kurchashova SY, Polyakov VY, Sheval EV. Self-organization of cellular structures induced by the overexpression of nuclear envelope proteins: a correlative light and electron microscopy study. J Electron Microsc (Tokyo) 2010; 60:57-71. [PMID: 20926432 DOI: 10.1093/jmicro/dfq067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The mechanisms by which the supramolecular order is formed inside the cell nucleus remain poorly understood. So far, two major hypotheses - ordered assembly and stochastic self-organization - have been discussed. To determine which mechanism is responsible for the formation of nuclear envelope, cells overexpressing one of the nuclear envelope proteins (lamin A, lamin B1, pom121 or ndc1) were investigated. According to the ordered assembly model, the presence of an excessive amount of a component has no effect in the formation of the normal structure of a nuclear envelope because it is programmed and cannot be distorted. In contrast, according to the self-organization concept, there is no such strictly determined cellular structures, and an excessive amount of even one component will affect the cellular organization. In the present study, formation of a redundant nuclear envelope was observed in the case of lamin B1 and lamin A overexpression. In the case of the nucleoporins pom121 and ndc1, no incorporation of the overexpressed proteins into the nuclear envelope was observed on the first day after transfection; however, the remodeling of endoplasmic reticulum elements and the formation of membrane aggregates in the cytoplasm were observed. After mitosis, pom121 from the cytoplasmic aggregates was translocated into the redundant nuclear envelope in which it induced inner nuclear membrane protrusions. Therefore, our results indicate that the formation of the nuclear envelope is not predetermined and that an excessive amount of even one protein component can affect cellular structure formation. This study concluded that nuclear envelope formation is achieved by the self-organization mechanism.
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Affiliation(s)
- Ekaterina G Volkova
- Department of Electron Microscopy, Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119991 Moscow, Russia
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Abstract
Both entero- and cardioviruses have been shown to suppress host mRNA synthesis. Enteroviruses are also known to inhibit the activity of rRNA genes, whereas this ability of cardioviruses is under debate. This study reported that mengovirus (a cardiovirus) suppressed rRNA synthesis but less efficiently than poliovirus (an enterovirus). In contrast to poliovirus infection, the incorporation of BrUTP, fluorouridine and [14C]uridine in rRNA precursors was observed even during the late stages of mengovirus infection, although at a significantly reduced level. The cleavage of TATA-binding protein, considered to be one of the central events in poliovirus-induced transcription shutoff, was not detected in mengovirus-infected cells, indicating a difference in the mechanisms of host RNA synthesis inhibition caused by these viruses. The results also showed that functional leader protein is redundant for the suppression of host RNA synthesis by cardiovirus.
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Affiliation(s)
- Ksenia A Krupina
- M. P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow Region 142782, Russia
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Sheval EV, Kazhura YI, Poleshuk NA, Lazareva EM, Smirnova EA, Maximova NP, Polyakov VY. Trifluralin-induced disorganization of microtubular cytoskeleton alters the development of roots in Hordeum vulgare L. Acta Biol Hung 2008; 59:465-78. [PMID: 19133502 DOI: 10.1556/abiol.59.2008.4.7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 11/19/2022]
Abstract
The extensive use of herbicides in agriculture becomes an important factor in environmental pollution, especially in case of slowly degradable compounds. Some agents act on plants during a long period of time, even if a very low concentration of the herbicide remains in the soil. Here, we investigated the toxicological effect of a low concentration of dinitroaniline herbicide, trifluralin, on growing seedlings of Hordeum vulgare L. Trifluralin in concentration of 1 microg/ml inhibited root growth. The mitotic activity of meristematic cells was suppressed due to the retardation of metaphase progression--alteration that can be caused by cytoskeleton disorder. Using antibodies to alpha-tubulin, we investigated the distribution of microtubules in root meristem cells. During all stages of mitosis, the highly regular system of microtubular cytoskeleton observed in control cells was slightly disorganized. An examination of root structure using light and electron microscopy demonstrated that the cell walls did not form normally during cell division that led to the appearance of large multinucleated cells. Also, the premature (pathological) cell differentiation was induced by trifluralin. A part of differentiating cells showed intracellular structural changes that are consistent with programmed cell death. It seems that the development of alterations in trifluralin-treated roots was due to the microtubular cytoskeleton disorganization.
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Affiliation(s)
- E V Sheval
- Department of Electron Microscopy, A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, GSP-1, Moscow 119991, Russia.
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Sheval EV, Polyakov VY. The peripheral chromosome scaffold, a novel structural component of mitotic chromosomes. Cell Biol Int 2008; 32:708-12. [PMID: 18337132 DOI: 10.1016/j.cellbi.2008.01.290] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 10/22/2007] [Accepted: 01/26/2008] [Indexed: 11/26/2022]
Abstract
Using an original high-salt extraction protocol, we observed a novel chromosome substructure, referred to as the peripheral chromosome scaffold. This chromosome domain contained the perichromosomal layer proteins pKi-67, B23/nucleophosmin and fibrillarin, but no DNA fragments (i.e., the loop domain bases were not associated with the peripheral scaffold). Modern models of chromosome organization do not predict the existence of a peripheral chromosome scaffold domain, and thus our observations have conceptual implications for understanding chromosome architecture.
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Affiliation(s)
- Eugene V Sheval
- Department of Electron Microscopy, AN Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119992, Russia.
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Plotnikov EY, Khryapenkova TG, Vasileva AK, Marey MV, Galkina SI, Isaev NK, Sheval EV, Polyakov VY, Sukhikh GT, Zorov DB. Cell-to-cell cross-talk between mesenchymal stem cells and cardiomyocytes in co-culture. J Cell Mol Med 2007; 12:1622-31. [PMID: 18088382 PMCID: PMC3918078 DOI: 10.1111/j.1582-4934.2007.00205.x] [Citation(s) in RCA: 161] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The goals of the study were: (1) to explore the communication between human mesenchymal stem cells (MSC) and rat cardiac myocytes resulting in differentiation of the stem cells and, (2) to evaluate the role of mitochondria in it. Light and fluorescence microscopy as well as scanning electron microscopy revealed that after co-cultivation, cells formed intercellular contacts and transient exchange with cytosolic elements could be observed. The transport of cytosolic entity had no specific direction. Noticeably, mitochondria also could be transferred to the recipient cells in a unidirectional fashion (towards cardiomyocytes only). Transmission electron microscopy revealed significant variability in both the diameter of intercellular contacting tubes and their shape. Inside of these nanotubes mitochondria-resembling structures were identified. Moreover, after co-cultivation with cardiomyocytes, expression of human-specific myosin was revealed in MSC. Thus, we speculate that: (1) transport of intracellular elements to MSC possibly can determine the direction of their differentiation and, (2) mitochondria may be involved in the mechanism of the stem cell differentiation. It looks plausible that mitochondrial transfer to recipient cardiomyocytes may be involved in the mechanism of failed myocardium repair after stem cells transplantation.
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Affiliation(s)
- E Y Plotnikov
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russian Federation
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37
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Caramyshev AV, Lobachov VM, Selivanov DV, Sheval EV, Vorobiev AK, Katasova ON, Polyakov VY, Makarov AA, Sakharov IY. Micellar Peroxidase-Catalyzed Synthesis of Chiral Polyaniline. Biomacromolecules 2007; 8:2549-55. [PMID: 17630690 DOI: 10.1021/bm070212p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Micellar peroxidase-catalyzed synthesis of chiral polyaniline (PANI) in the presence of dodecylbenzenesulfonic acid (DBSA) was developed. The effect of DBSA concentration on the catalytic efficiency of horseradish and palm tree peroxidases was examined. Favorable conditions for the enzymatic synthesis of chiral PANI, determined by a multiple factors design, demonstrated that the PANIs with the highest chirality were produced in the presence of low concentrations of optically active camphorsulphonic acid (CSA). Unexpectedly, the chiral PANI was also synthesized in the absence of CSA in feed. The favorable conditions for the enzymatic production of chiral and conducting PANIs were shown to be different. The morphology of the chiral PANI particles was examined by transmission and scanning electron microscopies.
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Affiliation(s)
- Alexei V Caramyshev
- Faculty of Chemistry and A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russia
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Karpova OV, Zayakina OV, Arkhipenko MV, Sheval EV, Kiselyova OI, Poljakov VY, Yaminsky IV, Rodionova NP, Atabekov JG. Potato virus X RNA-mediated assembly of single-tailed ternary ‘coat protein–RNA–movement protein’ complexes. J Gen Virol 2006; 87:2731-2740. [PMID: 16894214 DOI: 10.1099/vir.0.81993-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Different models have been proposed for the nature of the potexvirus transport form that moves from cell to cell over the infected plant: (i) genomic RNA moves as native virions; or (ii) in vitro-assembled non-virion ribonucleoprotein (RNP) complexes consisting of viral RNA, coat protein (CP) and movement protein (MP), termed TGBp1, serve as the transport form in vivo. As the structure of these RNPs has not been elucidated, the products assembled in vitro from potato virus X (PVX) RNA, CP and TGBp1 were characterized. The complexes appeared as single-tailed particles (STPs) with a helical, head-like structure composed of CP subunits located at the 5′-proximal region of PVX RNA; the TGBp1 was bound to the terminal CP molecules of the head. Remarkably, no particular non-virion RNP complexes were observed. These data suggest that the CP–RNA interactions resulting in head formation prevailed over TGBp1–RNA binding upon STP assembly from RNA, CP and TGBp1. STPs could be assembled from the 5′ end of PVX RNA and CP in the absence of TGBp1. The translational ability of STPs was characterized in a cell-free translation system. STPs lacking TGBp1 were entirely non-translatable; however, they were rendered translatable by binding of TGBp1 to the end of the head. It is suggested that the RNA-mediated assembly of STPs proceeds via two steps. Firstly, non-translatable CP–RNA STPs are produced, due to encapsidation of the 5′-terminal region. Secondly, the TGBp1 molecules bind to the end of a polar head, resulting in conversion of the STPs into a translatable form.
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Affiliation(s)
- O V Karpova
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - O V Zayakina
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - M V Arkhipenko
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - E V Sheval
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - O I Kiselyova
- Faculty of Physics, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - V Yu Poljakov
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - I V Yaminsky
- Faculty of Physics, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - N P Rodionova
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
| | - J G Atabekov
- Department of Virology and A. N. Belozersky Institute of Physico-Chemical Biology, Faculty of Chemistry of Moscow State University, Moscow 119992, Russia
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Sheval EV, Polyakov VY. Visualization of the chromosome scaffold and intermediates of loop domain compaction in extracted mitotic cells. Cell Biol Int 2006; 30:1028-40. [PMID: 17029868 DOI: 10.1016/j.cellbi.2006.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [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: 04/10/2006] [Revised: 07/13/2006] [Accepted: 07/28/2006] [Indexed: 11/28/2022]
Abstract
A novel extraction protocol for cells cultured on coverslips is described. Observations of the extraction process in a perfusion chamber reveal that cells of all mitotic stages are not detached from coverslips during extraction, and all stages can be recognized using phase contrast images. We studied the extracted cell morphology and distribution of a major scaffold component - topoisomerase IIalpha, in extracted metaphase and anaphase cells. An extraction using 2M NaCl leads to destruction of chromosomes at the light microscope level. Immunogold studies demonstrate that the only residual structure observed is an axial chromosome scaffold that contains topoisomerase IIalpha. In contrast, mitotic chromosomes are swelled only partially after an extraction using dextran sulphate and heparin, and it appears that this treatment does not lead to total destruction of loop domains. In this case, the chromosome scaffold and numerous structures resembling small rosettes are revealed inside extracted cells. The rosettes observed condense after addition of Mg2+-ions and do not contain topoisomerase IIalpha suggesting that these structures correspond to intermediates of loop domain compaction. We propose a model of chromosome structure in which the loop domains are condensed into highly regular structures with rosette organization.
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Affiliation(s)
- Eugene V Sheval
- Department of Electron Microscopy, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, GSP-2, Moscow 119992, Russia.
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Lidsky PV, Hato S, Bardina MV, Aminev AG, Palmenberg AC, Sheval EV, Polyakov VY, van Kuppeveld FJM, Agol VI. Nucleocytoplasmic traffic disorder induced by cardioviruses. J Virol 2006; 80:2705-17. [PMID: 16501080 PMCID: PMC1395435 DOI: 10.1128/jvi.80.6.2705-2717.2006] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Some picornaviruses, for example, poliovirus, increase bidirectional permeability of the nuclear envelope and suppress active nucleocytoplasmic transport. These activities require the viral protease 2A(pro). Here, we studied nucleocytoplasmic traffic in cells infected with encephalomyocarditis virus (EMCV; a cardiovirus), which lacks the poliovirus 2A(pro)-related protein. EMCV similarly enhanced bidirectional nucleocytoplasmic traffic. By using the fluorescent "Timer" protein, which contains a nuclear localization signal, we showed that the cytoplasmic accumulation of nuclear proteins in infected cells was largely due to the nuclear efflux of "old" proteins rather than impaired active nuclear import of newly synthesized molecules. The nuclear envelope of digitonin-treated EMCV-infected cells permitted rapid efflux of a nuclear marker protein. Inhibitors of poliovirus 2A(pro) did not prevent the EMCV-induced efflux. Extracts from EMCV-infected cells and products of in vitro translation of viral RNAs contained an activity increasing permeability of the nuclear envelope of uninfected cells. This activity depended on the expression of the viral leader protein. Mutations disrupting the zinc finger motif of this protein abolished its efflux-inducing ability. Inactivation of the L protein phosphorylation site (Thr47-->Ala) resulted in a delayed efflux, while a phosphorylation-mimicking (Thr47-->Asp) replacement did not significantly impair the efflux-inducing ability. Such activity of extracts from EMCV-infected cells was suppressed by the protein kinase inhibitor staurosporine. As evidenced by electron microscopy, cardiovirus infection resulted in alteration of the nuclear pores, but it did not trigger degradation of the nucleoporins known to be degraded in the poliovirus-infected cells. Thus, two groups of picornaviruses, enteroviruses and cardioviruses, similarly alter the nucleocytoplasmic traffic but achieve this by strikingly different mechanisms.
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Affiliation(s)
- Peter V Lidsky
- M. P. Chumakov Institute of Poliomyelitis and Viral Encephalitides, Russian Academy of Medical Sciences, Moscow Region, Russia
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Polyakov VY, Zatsepina OV, Kireev II, Prusov AN, Fais DI, Sheval EV, Koblyakova YV, Golyshev SA, Chentsov YS. Structural-functional model of the mitotic chromosome. Biochemistry (Moscow) 2006; 71:1-9. [PMID: 16457612 DOI: 10.1134/s0006297906010019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In the present review the structural role of noncoding DNA, mechanisms of differential staining of mitotic chromosomes, and structural organization of different levels of DNA compactization are discussed. A structural-functional model of the mitotic chromosome is proposed based on the principle of discreteness of structural levels of DNA compactization.
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Affiliation(s)
- V Yu Polyakov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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Sheval EV, Polzikov MA, Olson MOJ, Zatsepina OV. A higher concentration of an antigen within the nucleolus may prevent its proper recognition by specific antibodies. Eur J Histochem 2005; 49:117-23. [PMID: 15967739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
Transient transfection of HeLa cells with a plasmid encoding the full-length human fibrillarin fused to a green fluorescent protein (GFP) resulted in two major patterns of intensity of the nucleolar labeling for the chimeric protein: weak and strong. Both patterns were maintained in fibrillarin-GFP expressing cells after fixation with formaldehyde. When the fixed fibrillarin-GFP expressing cells were used for immunolabeling with antibodies to fibrillarin, only the nucleoli with a weak GFP-signal became strongly labeled, whereas those with the heavy signals were only lightly stained, if at all. A similar pattern was observed if the cells were immunolabeled with antibodies to GFP. These observations suggest that an increase in antigen accumulation within the nucleolus, which could take place under various physiological or experimental conditions, could prevent the antigen from being recognized by specific antibodies. These results have implications regarding contradictory data on localization of various nucleolar antigens obtained by conventional immunocytochemistry.
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Affiliation(s)
- E V Sheval
- A.N. Belozersky Institute of Physical and Chemical Biology, Moscow State University, Moscow, Russia
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Sheval EV, Kireev II, Polyakov VY. Stabilization of macromolecular chromatin complexes in mitotic chromosomes by light irradiation in the presence of ethidium bromide. Cell Biol Int 2004; 28:835-43. [PMID: 15566953 DOI: 10.1016/j.cellbi.2004.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Accepted: 07/30/2004] [Indexed: 10/26/2022]
Abstract
A method was developed for stabilizing mitotic chromosomes. Light irradiation of permeabilized cells in a low concentration of ethidium bromide made chromatin resistant to high salt concentrations and decondensing buffer. This resistance was abolished by proteinase treatment, but not by DNase or RNase treatment. In photostabilized and extracted chromosomes, chromatin appeared as thick fibers with discrete high electron density regions. These stabilized structures might correspond to the higher-level structures (chromonemata) observed in native chromatin. Moreover, the electron density was higher in the centromeric regions than the chromosome arm material. Thus, the method allows chromatin substructures (chromonemata and centromeric heterochromatin) to be stabilized inside mitotic chromosomes.
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Affiliation(s)
- Eugene V Sheval
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, GSP-2, Moscow 119992, Russia.
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Sheval EV, Churakova JV, Dudnik OA, Vorobjev IA. Examination of the proliferative activity of tumor cells in human lymphoid neoplasms using a morphometric approach. Cancer 2004; 102:174-85. [PMID: 15211477 DOI: 10.1002/cncr.20341] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [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: 11/07/2022]
Abstract
BACKGROUND The genesis of lymphoid neoplasia is accompanied by alterations in cell proliferation control mechanisms. Thus, proliferative indices (PIs) provide valuable prognostic information in this setting. Nonetheless, one shortcoming of PI measurements is that they depend not only on the proliferative activity of the neoplastic cells in a given lesion, but also on the activity of any admixed reactive cells. The current report describes an approach to identifying neoplastic and reactive subpopulations in cytologic preparations and to comparatively characterizing the morphologic features of neoplastic cells and assessing their proliferative activity. METHODS Reactive and malignant lymph node samples were obtained from 37 patients during surgical biopsy. Giemsa stained touch imprints were used for morphometric and high-resolution videomicroscopic analyses. Immunofluorescence-based detection of pKi-67-positive cells was used in conjunction with morphometric analysis to assess the proliferative activity of tumor cells. RESULTS Morphometric analysis allowed the selective identification of neoplastic cells in large cell lymphomas (LCLs). The morphologic characteristics of neoplastic cells in primary and secondary LCLs were found to be similar. The PI was highly dependent on the proportion of tumor cells present in the tissue sample analyzed, and in some samples with large proportions of reactive cells, the overall percentage of pKi-67-positive cells was low, but the majority of neoplastic cells nonetheless were positive for pKi-67. Most primary LCLs had very high tumor cell PIs (80-100%), whereas all secondary LCLs had moderate tumor cell PIs. CONCLUSIONS Neoplastic cell subpopulations in LCLs can be identified on morphometric analysis, which can be performed using touch imprints; this technique allows evaluation of the proliferative activity of tumor cells. The authors propose that the use of tumor cell PIs rather than PIs for overall cell populations will result in more accurate assessment of disease prognosis.
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Affiliation(s)
- Eugene V Sheval
- Hematology Research Center, Russian Academy of Medical Sciences, Moscow, Russia.
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