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Yoshida T, Kasuya Y, Yamamoto H, Kawai G, Hanaki KI, Matano T, Masuda T. HIV-1 RNAs whose transcription initiates from the third deoxyguanosine of GGG tract in the 5' long terminal repeat serve as a dominant genome for efficient provirus DNA formation. J Virol 2024; 98:e0182523. [PMID: 38289105 PMCID: PMC10878063 DOI: 10.1128/jvi.01825-23] [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: 11/21/2023] [Accepted: 12/20/2023] [Indexed: 02/21/2024] Open
Abstract
Unspliced HIV-1 RNAs function as messenger RNAs for Gag or Gag-Pol polyproteins and progeny genomes packaged into virus particles. Recently, it has been reported that fate of the RNAs might be primarily determined, depending on transcriptional initiation sites among three consecutive deoxyguanosine residues (GGG tract) downstream of TATA-box in the 5' long terminal repeat (LTR). Although HIV-1 RNA transcription starts mostly from the first deoxyguanosine of the GGG tract and often from the second or third deoxyguanosine, RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine, were predominant in HIV-1 particles. Despite selective packaging of G1-form RNAs into virus particles, its biological impact during viral replication remains to be determined. In this study, we revealed that G1-form RNAs are primarily selected as a template for provirus DNA rather than other RNAs. In competitions between HIV-1 and lentiviral vector transcripts in virus-producing cells, approximately 80% of infectious particles were found to generate provirus using HIV-1 transcripts, while lentiviral vector transcripts were conversely selected when we used HIV-1 mutants in which the third deoxyguanosine in the GGG tract was replaced with deoxythymidine or deoxycytidine (GGT or GGC mutants, respectively). In the other analyses of proviral sequences after infection with an HIV-1 mutant in which the GGG tract in 3' LTR was replaced with TTT, most proviral sequences of the GGG-tract region in 5' LTR were found to be TTG, which is reasonably generated using the G1-form transcripts. Our results indicate that the G1-form RNAs serve as a dominant genome to establish provirus DNA.IMPORTANCESince the promoter for transcribing HIV-1 RNA is unique, all viral elements including genomic RNA and viral proteins have to be generated by the unique transcripts through ingenious mechanisms including RNA splicing and frameshifting during protein translation. Previous studies suggested a new mechanism for diversification of HIV-1 RNA functions by heterogeneous transcriptional initiation site usage; HIV-1 RNAs whose transcription initiates from a certain nucleotide were predominant in virus particles. In this study, we established two methods to analyze heterogenous transcriptional initiation site usage by HIV-1 during viral infection and showed that RNAs beginning with one guanosine (G1-form RNAs), whose transcription initiates from the third deoxyguanosine of the GGG tract in 5' LTR, were primarily selected as viral genome in infectious particles and thus are used as a template to generate provirus for continuous replication. This study provides insights into the mechanism for diversification of unspliced RNA functions and requisites of lentivirus infectivity.
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Affiliation(s)
- Takeshi Yoshida
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuho Kasuya
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Hiroyuki Yamamoto
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Department of Biomedicine, University Hospital Basel, Basel, Switzerland
| | - Gota Kawai
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
| | - Ken-ichi Hanaki
- Management Department of Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tetsuro Matano
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto, Japan
| | - Takao Masuda
- Department of Life Science, Faculty of Advanced Engineering, Chiba Institute of Technology, Chiba, Japan
- Graduate school of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
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Yasuda H, Ito F, Hanaki KI, Suzuki K. Correction: COVID-19 pandemic vaccination strategies of early 2021 based on behavioral differences between residents of Tokyo and Osaka, Japan. Arch Public Health 2022; 80:205. [PMID: 36068620 PMCID: PMC9446555 DOI: 10.1186/s13690-022-00961-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Yasuda H, Ito F, Hanaki KI, Suzuki K. COVID-19 pandemic vaccination strategies of early 2021 based on behavioral differences between residents of Tokyo and Osaka, Japan. Arch Public Health 2022; 80:180. [PMID: 35927683 PMCID: PMC9351264 DOI: 10.1186/s13690-022-00933-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 07/17/2022] [Indexed: 12/11/2022] Open
Abstract
Background During the fourth COVID-19 wave in Japan, marked differences became apparent in the scale of the epidemic between metropolitan Tokyo in eastern Japan and Osaka prefecture in western Japan. Methods Public epidemic data were analyzed, with performance of mathematical simulations using simplified SEIR models. Results The increase in the number of infected persons per 100,000 population during the fourth wave of expansion was greater in Osaka than in Tokyo. The basic reproduction number in Osaka was greater than in Tokyo. Particularly, the number of infected people in their 20 s increased during the fourth wave: The generation-specific reproduction number for people in their 20 s was higher than for people of other generations. Both Tokyo and Osaka were found to have strong correlation between the increase in the number of infected people and the average number of people using the main downtown stations at night. Simulations showed vaccination of people in their 60 s and older reduced the number of infected people among the high-risk elderly population in the fourth wave. However, age-specific vaccination of people in their 20 s reduced the number of infected people more than vaccination of people in their 60 s and older. Conclusions Differences in the epidemic between Tokyo and Osaka are explainable by different behaviors of the most socially active generation. When vaccine supplies are adequate, priority should be assigned to high-risk older adults, but if vaccine supplies are scarce, simulation results suggest consideration of vaccinating specific groups among whom the epidemic is spreading rapidly.
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Watanabe S, Fujino M, Saito Y, Ahmed N, Sato H, Sugimoto C, Okamura T, Hanaki K, Nakayama EE, Shioda T, Matsushima K, Ansari AA, Villinger F, Mori K. Protective Immune Responses Elicited by Deglycosylated Live-Attenuated Simian Immunodeficiency Virus Vaccine Are Associated with IL-15 Effector Functions. J Immunol 2020; 205:1331-1344. [PMID: 32747501 PMCID: PMC7484436 DOI: 10.4049/jimmunol.1901431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/25/2020] [Indexed: 11/19/2022]
Abstract
Deglycosylated, live-attenuated SIV vaccines elicited protective immune responses against heterologous SIVsmE543-3, which differs from the vaccine strain SIVmac239 to levels similar to those across HIV-1 clades. Two thirds of the vaccinees contained the chronic SIVsmE543-3 infection (controllers), whereas one third did not (noncontrollers). In this study, we investigated immune correlates of heterologous challenge control in rhesus macaques of Burmese origin. Because depletion of CD8+ cells in the controllers by administration of anti-CD8α Ab abrogated the control of viral replication, CD8+ cells were required for the protective immune response. However, classical SIV-specific CD8+ T cells did not account for the protective immune response in all controllers. Instead, IL-15-responding CD8α+ cells, including CD8+ T and NK cells, were significantly higher in the controllers than those in the noncontrollers, before and after vaccination with deglycosylated SIV. It is well established that IL-15 signal transduction occurs through "trans-presentation" in which IL-15 complexed with IL-15Rα on monocytes, macrophages, and dendritic cells binds to IL-15 Rβ/γ expressed on CD8+ T and NK cells. Accordingly, levels of IL-15 stimulation were strongly affected by the depletion of monocytes from PBMCs, implying key roles of innate immune cells. These results suggest that intrinsic IL-15 responsiveness may dictate the outcome of protective responses and may lead to optimized formulations of future broadly protective HIV vaccines.
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Affiliation(s)
- Satoru Watanabe
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Masayuki Fujino
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Yohei Saito
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba 305-0843, Japan
| | - Nursarat Ahmed
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Hirotaka Sato
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | | | - Tomotaka Okamura
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba 305-0843, Japan
| | - Kenichi Hanaki
- Division of Experimental Animal Research, National Institute of Infectious Diseases, Tokyo 162-8640, Japan
| | - Emi E Nakayama
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Tatsuo Shioda
- Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda 278-0022, Japan
| | - Aftab A Ansari
- Emory University School of Medicine, Atlanta, GA 30322; and
| | - Francois Villinger
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA 70562
| | - Kazuyasu Mori
- AIDS Research Center, National Institute of Infectious Diseases, Tokyo 162-8640, Japan;
- Tsukuba Primate Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Tsukuba 305-0843, Japan
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, Noda 278-0022, Japan
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Hanaki KI, Ohka S, Yamamoto K, Nomoto A, Yoshikura H. Oligo(dA-dT)-dependent signal amplification for the detection of proteins in cells. Biotechniques 2004; 36:856-60, 862-3. [PMID: 15152606 DOI: 10.2144/04365pt01] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 11/23/2022] Open
Abstract
An ultrasensitive protein detection system in situ named the ImmunoAT-tailing method was developed. It consists of three elementary processes: (i) detection of a protein by a primary antibody and a biotinylated secondary antibody; (ii) linking of biotinylated 15-base oligo(dA-dT) to the biotinylated immunocomplex via streptavidin; and (iii) self-priming elongation of oligo(dA-dT) by the Klenow fragment, 3' to 5' exo-. After the elongation reaction in the presence of dATP, dTTP, and dye-labeled dUTP, the protein was labeled with a large number of the dye molecules. The poly(dA-dT) elongated without the labeled nucleotides was detected by 4',6-diamidino-2-phenylindole (DAPI) staining. By combining the different labelings, double staining was possible. This ImmunoAT-tailing method has a specificity and sensitivity higher than that of tyramide signal amplification.
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Affiliation(s)
- Ken-ichi Hanaki
- Japan Society for the Promotion of Science, University of Tokyo, Tokyo, Japan.
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Hoshino A, Hanaki KI, Suzuki K, Yamamoto K. Applications of T-lymphoma labeled with fluorescent quantum dots to cell tracing markers in mouse body. Biochem Biophys Res Commun 2004; 314:46-53. [PMID: 14715244 DOI: 10.1016/j.bbrc.2003.11.185] [Citation(s) in RCA: 219] [Impact Index Per Article: 11.0] [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
Photoluminescent semiconductor quantum dots (QDs) are novel nanometer-size probes that have found bioimaging. Here we imaged a cell line of mouse lymphocytes. QDs were actively taken into the target cells by endocytotic pathways. The fluorescence of QDs held in the endosomes could be studied for more than a week and remained stable luminescence against cell activation induced by concanavalin A, phytohemagglutinin, phorbol myristate acetate, and calcium ionophore A23187. These results suggested that QD-labeling was stable and did not affect either cell activation or cell function. When QD-labeled cells were intravenously injected into mouse, they remained in the peripheral blood in a concentration of approximately 10% up to 5 days after injection using both fluorescence microscopy and flow cytometry. In addition, approximately 20% of QDs were detected in the kidneys, liver, lung, and spleen and could still be observed 7 days after injection. These results suggested that fluorescent probes of QDs might be useful as bioimaging tools for tracing target cells over the period of a week in vivo.
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Affiliation(s)
- Akiyoshi Hoshino
- Department of Medical Ecology and Informatics, Research Institute, International Medical Center of Japan, Shinjuku, Tokyo, Japan
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Abstract
We have investigated the growth dynamics of Bacillus circulans colony exhibiting the knotted-branching pattern by swarming on a hard agar medium. The knotted-branching pattern consists of many circular clusters, so-called subcolonies, and their trajectories. We analysed the processes of a subcolony because they are presumably the key elements for the formation of knotted-branching pattern. It was found that a subcolony has three processes, i.e. "generation", "growth", and "migration" by microscopic and time-resolved observations. An embryonic small subcolony (child subcolony) formed around an existing subcolony (parent subcolony) grows larger and migrates away from the parent subcolony. We proposed a simple model to explain the migration and the growth processes. It is assumed that the internal part of the subcolony is unfavorable for the bacteria and that the motion of the child subcolony on the agar medium can be modeled using a frictional force. The experimental data were quantitatively analysed in order to compare with models. Our models are consistent with the experimental results on following three points: (1) the radius of a subcolony increases linearly with the incubation time, (2) a subcolony stops just after formation and then starts to migrate suddenly, and (3) the trajectory of a subcolony predicted by the model agrees with the experimental one.
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Affiliation(s)
- Atsushi Komoto
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Hanaki KI, Momo A, Oku T, Komoto A, Maenosono S, Yamaguchi Y, Yamamoto K. Semiconductor quantum dot/albumin complex is a long-life and highly photostable endosome marker. Biochem Biophys Res Commun 2003; 302:496-501. [PMID: 12615061 DOI: 10.1016/s0006-291x(03)00211-0] [Citation(s) in RCA: 262] [Impact Index Per Article: 12.5] [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: 11/16/2022]
Abstract
For the purpose of selecting the efficient dispersion condition of hydrophilic semiconductor quantum dots (QDs) in biological buffers, the dispersion of the QDs mixed with a serum albumin from 9 different species or an ovalbumin was compared by a fluorescence intensity analysis. The QDs mixed with sheep serum albumin (SSA) showed the highest fluorescence of all when the mixtures were dissolved in Dulbecco's MEM. QD/SSA complexes were accumulated in the endosome/lysosome of Vero cells and the fluorescence could be detected over a 5-day post-incubation period. The photostability of QD/SSA complexes associated with the endosomes was detectable, at least, 30 times as long as that of fluorescein-labeled dextran involved in endosomes. QD/SSA complex, therefore, can be used as a long-life and highly photostable endosome marker.
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Affiliation(s)
- Ken-ichi Hanaki
- Domestic Research Fellow, Japan Science and Technology Corporation, 4-1-8 Honmachi, Kawaguchi, Saitama 332-0012, Japan.
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Yanaka Y, Hanaki KI, Yoshikura H, Yamamoto K. Further simulation on survival of mutants under non-selective condition. Jpn J Infect Dis 2001; 54:84-5. [PMID: 11427752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Affiliation(s)
- Y Yanaka
- Department of Medical Ecology and Informatics, International Medical Center of Japan, Tokyo 162-8655, Japan
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