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Toh H, Sasaki H. Spatiotemporal DNA methylation dynamics shape megabase-scale methylome landscapes. Life Sci Alliance 2024; 7:e202302403. [PMID: 38233073 PMCID: PMC10794778 DOI: 10.26508/lsa.202302403] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 01/19/2024] Open
Abstract
DNA methylation is an essential epigenetic mechanism that regulates cellular reprogramming and development. Studies using whole-genome bisulfite sequencing have revealed distinct DNA methylome landscapes in human and mouse cells and tissues. However, the factors responsible for the differences in megabase-scale methylome patterns between cell types remain poorly understood. By analyzing publicly available 258 human and 301 mouse whole-genome bisulfite sequencing datasets, we reveal that genomic regions rich in guanine and cytosine, when located near the nuclear center, are highly susceptible to both global DNA demethylation and methylation events during embryonic and germline reprogramming. Furthermore, we found that regions that generate partially methylated domains during global DNA methylation are more likely to resist global DNA demethylation, contain high levels of adenine and thymine, and are adjacent to the nuclear lamina. The spatial properties of genomic regions, influenced by their guanine-cytosine content, are likely to affect the accessibility of molecules involved in DNA (de)methylation. These properties shape megabase-scale DNA methylation patterns and change as cells differentiate, leading to the emergence of different megabase-scale methylome patterns across cell types.
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Affiliation(s)
- Hidehiro Toh
- https://ror.org/02xg1m795 Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
- https://ror.org/00p4k0j84 Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- https://ror.org/00p4k0j84 Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Tamakoshi M, Hijikata A, Yura K, Oshima K, Toh H, Mitsuoka K, Oshima T, Bessho Y. Isolation and genomic analysis of a type IV pili-independent Thermus thermophilus phage, φMN1 from a Japanese hot spring. J GEN APPL MICROBIOL 2023; 69:117-124. [PMID: 37423744 DOI: 10.2323/jgam.2023.06.008] [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] [Indexed: 07/11/2023]
Abstract
A Thermus thermophilus lytic phage was isolated from a Japanese hot spring using a type IV pili-deficient strain as an indicator host, and designated as φMN1. Electron microscopic (EM) examination revealed that φMN1 had an icosahedral head and a contractile tail, suggesting that φMN1 belonged to Myoviridae. An EM analysis focused on φMN1 adsorption to the Thermus host cell showed that the receptor molecules for the phage were uniformly distributed on the outer surface of the cells. The circular double-stranded DNA of φMN1 was 76,659 base pairs in length, and the guanine and cytosine content was 61.8%. It was predicted to contain 99 open reading frames, and its putative distal tail fiber protein, which is essential for non-piliated host cell surface receptor recognition, was dissimilar in terms of sequence and length with its counterpart in the type IV pili-dependent φYS40. A phage proteomic tree revealed that φMN1 and φYS40 are in the same cluster, but many genes had low sequence similarities and some seemed to be derived from both mesophilic and thermophilic organisms. The gene organization suggested that φMN1 evolved from a non-Thermus phage through large-scale recombination events of the genes determining the host specificity, followed by gradual evolution by recombination of both the thermophilic and mesophilic DNAs assimilated by the host Thermus cells. This newly isolated phage will provide evolutionary insights into thermophilic phages.
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Affiliation(s)
- Masatada Tamakoshi
- Department of Applied Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Atsushi Hijikata
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- Graduate School of Advanced Science and Engineering, Waseda University
| | | | - Hidehiro Toh
- Advanced Genomics Center, National Institute of Genetics
| | - Kaoru Mitsuoka
- Research Center for Ultra-High Voltage Electron Microscopy, Osaka University
| | - Tairo Oshima
- Institute of Environmental Microbiology, Kyowa Kako Co., Ltd
| | - Yoshitaka Bessho
- Center for Interdisciplinary AI and Data Science, Ochanomizu University
- RIKEN SPring-8 Center, Harima Institute
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Uehara R, Au Yeung WK, Toriyama K, Ohishi H, Kubo N, Toh H, Suetake I, Shirane K, Sasaki H. The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes. PLoS Genet 2023; 19:e1010855. [PMID: 37527244 PMCID: PMC10393158 DOI: 10.1371/journal.pgen.1010855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-DNMT3-DNMT3L (ADD) domain that interacts with histone H3 tail unmethylated at lysine-4 (H3K4me0). The domain normally blocks the methyltransferase domain via intramolecular interaction and binding to histone H3K4me0 releases the autoinhibition. However, H3K4me0 is widespread in chromatin and the role of the ADD-histone interaction has not been studied in vivo. We herein show that amino-acid substitutions in the ADD domain of mouse DNMT3A cause dwarfism. Oocytes derived from homozygous females show mosaic loss of CG methylation and almost complete loss of non-CG methylation. Embryos derived from such oocytes die in mid-to-late gestation, with stochastic and often all-or-none-type CG-methylation loss at imprinting control regions and misexpression of the linked genes. The stochastic loss is a two-step process, with loss occurring in cleavage-stage embryos and regaining occurring after implantation. These results highlight an important role for the ADD domain in efficient, and likely processive, de novo CG methylation and pose a model for stochastic inheritance of epigenetic perturbations in germ cells to the next generation.
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Affiliation(s)
- Ryuji Uehara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Keisuke Toriyama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Division of Gene Expression Dynamics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Japan
| | - Isao Suetake
- Department of Nutrition Science, Nakamura Gakuen University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Maruyama O, Li Y, Narita H, Toh H, Au Yeung WK, Sasaki H. CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers. BMC Bioinformatics 2022; 23:371. [PMID: 36096737 PMCID: PMC9469632 DOI: 10.1186/s12859-022-04916-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine CpG island (CGI) sequences to predict whether a mouse blastocyst CGI inherits oocyte-derived DNA methylation from the maternal genome. Recurrent neural networks (RNNs), including that based on gated recurrent units (GRUs), have recently been employed for variable-length inputs in classification and regression analyses. One advantage of this strategy is the ability of RNNs to automatically learn latent features embedded in inputs by learning their model parameters. However, the available CGI dataset applied for the prediction of oocyte-derived DNA methylation inheritance are not large enough to train the neural networks. Results We propose a GRU-based model called CMIC (CGI Methylation Inheritance Classifier) to augment CGI sequence by converting it into variable-length k-mers, where the length k is randomly selected from the range \documentclass[12pt]{minimal}
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\begin{document}$$k_{\max }$$\end{document}kmax, N times, which were then used as neural network input. N was set to 1000 in the default setting. In addition, we proposed a new embedding vector generator for k-mers called splitDNA2vec. The randomness of this procedure was higher than the previous work, dna2vec. Conclusions We found that CMIC can predict the inheritance of oocyte-derived DNA methylation at CGIs in the maternal genome of blastocysts with a high F-measure (0.93). We also show that the F-measure can be improved by increasing the parameter N, that is, the number of sequences of variable-length k-mers derived from a single CGI sequence. This implies the effectiveness of augmenting input data by converting a DNA sequence to N sequences of variable-length k-mers. This approach can be applied to different DNA sequence classification and regression analyses, particularly those involving a small amount of data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04916-3.
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Affiliation(s)
| | - Yinuo Li
- Graduate School of Design, Kyushu University, Fukuoka, Japan
| | | | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Wan Kin Au Yeung
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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Kibe K, Shirane K, Ohishi H, Uemura S, Toh H, Sasaki H. The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes. PLoS Genet 2021; 17:e1009570. [PMID: 34048432 PMCID: PMC8162659 DOI: 10.1371/journal.pgen.1009570] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/30/2021] [Indexed: 12/28/2022] Open
Abstract
DNA methylation at CG sites is important for gene regulation and embryonic development. In mouse oocytes, de novo CG methylation requires preceding transcription-coupled histone mark H3K36me3 and is mediated by a DNA methyltransferase DNMT3A. DNMT3A has a PWWP domain, which recognizes H3K36me2/3, and heterozygous mutations in this domain, including D329A substitution, cause aberrant CG hypermethylation of regions marked by H3K27me3 in somatic cells, leading to a dwarfism phenotype. We herein demonstrate that D329A homozygous mice show greater CG hypermethylation and severer dwarfism. In oocytes, D329A substitution did not affect CG methylation of H3K36me2/3-marked regions, including maternally methylated imprinting control regions; rather, it caused aberrant hypermethylation in regions lacking H3K36me2/3, including H3K27me3-marked regions. Thus, the role of the PWWP domain in CG methylation seems similar in somatic cells and oocytes; however, there were cell-type-specific differences in affected regions. The major satellite repeat was also hypermethylated in mutant oocytes. Contrary to the CA hypomethylation in somatic cells, the mutation caused hypermethylation at CH sites, including CA sites. Surprisingly, oocytes expressing only the mutated protein could support embryonic and postnatal development. Our study reveals that the DNMT3A PWWP domain is important for suppressing aberrant CG hypermethylation in both somatic cells and oocytes but that D329A mutation has little impact on the developmental potential of oocytes.
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Affiliation(s)
- Kanako Kibe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - Shuhei Uemura
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- * E-mail:
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Hiramoto T, Tahara M, Liao J, Soda Y, Miura Y, Kurita R, Hamana H, Inoue K, Kohara H, Miyamoto S, Hijikata Y, Okano S, Yamaguchi Y, Oda Y, Ichiyanagi K, Toh H, Sasaki H, Kishi H, Ryo A, Muraguchi A, Takeda M, Tani K. Non-transmissible MV Vector with Segmented RNA Genome Establishes Different Types of iPSCs from Hematopoietic Cells. Mol Ther 2019; 28:129-141. [PMID: 31677955 DOI: 10.1016/j.ymthe.2019.09.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/30/2019] [Accepted: 09/06/2019] [Indexed: 01/11/2023] Open
Abstract
Recent advances in gene therapy technologies have enabled the treatment of congenital disorders and cancers and facilitated the development of innovative methods, including induced pluripotent stem cell (iPSC) production and genome editing. We recently developed a novel non-transmissible and non-integrating measles virus (MV) vector capable of transferring multiple genes simultaneously into a wide range of cells through the CD46 and CD150 receptors. The MV vector expresses four genes for iPSC generation and the GFP gene for a period of time sufficient to establish iPSCs from human fibroblasts as well as peripheral blood T cells. The transgenes were expressed differentially depending on their gene order in the vector. Human hematopoietic stem/progenitor cells were directly and efficiently reprogrammed to naive-like cells that could proliferate and differentiate into primed iPSCs by the same method used to establish primed iPSCs from other cell types. The novel MV vector has several advantages for establishing iPSCs and potential future applications in gene therapy.
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Affiliation(s)
- Takafumi Hiramoto
- Department of Biochemistry, Jichi Medical University, Tochigi 329-0498, Japan
| | - Maino Tahara
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo 208-0011, Japan
| | - Jiyuan Liao
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasushi Soda
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshie Miura
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Ryo Kurita
- Central Blood Institute (Blood Service Headquarters), Japanese Red Cross Society, Tokyo 135-8521, Japan
| | - Hiroshi Hamana
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Kota Inoue
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroshi Kohara
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Shohei Miyamoto
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yasuki Hijikata
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan
| | - Shinji Okano
- Section of Pathology, Department of Morphological Biology, Fukuoka Dental College, Fukuoka 814-0193, Japan
| | | | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hidehiro Toh
- Division of Epigenetics and Development, Medical Institute of Bioregulation, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Sasaki
- Division of Epigenetics and Development, Medical Institute of Bioregulation, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Kishi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Akihide Ryo
- Department of Microbiology, Yokohama City University, Kanagawa 236-0004, Japan
| | - Atsushi Muraguchi
- Department of Immunology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Makoto Takeda
- Department of Virology 3, National Institute of Infectious Diseases, Tokyo 208-0011, Japan.
| | - Kenzaburo Tani
- Project Division of ALA Advanced Medical Research, The Institute of Medical Science, The University of Tokyo, Tokyo 108-8639, Japan.
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Hagiwara D, Sato K, Miyazaki M, Kamada M, Moriwaki N, Nakano T, Shiotsuka S, Tokushige C, Toh H, Kamimura H, Togawa A, Takata T. The impact of earlier intervention by an antimicrobial stewardship team for specific antimicrobials in a single weekly intervention. Int J Infect Dis 2018; 77:34-39. [PMID: 30292892 DOI: 10.1016/j.ijid.2018.09.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVE The objective of this study was to evaluate the effects of earlier intervention by an antimicrobial stewardship team (AST) on antimicrobial use, antimicrobial resistance rates, and the clinical outcomes, without changing the weekly intervention schedule. METHODS A retrospective study was conducted at Fukuoka University Hospital between April 2013 and March 2016. The effects were compared among three study periods (SP): SP1 (patients receiving anti-methicillin-resistant Staphylococcus aureus agents and carbapenems for ≥14 days), SP2 (patients receiving specific antimicrobials for ≥14 days), and SP3 (patients receiving specific antimicrobials regardless of the duration of treatment). RESULTS The timing of AST intervention was shortened from an average of 15.5days after administration in SP1 to 4.2 days in SP3. The antimicrobial use density (AUD) of carbapenems and piperacillin-tazobactam decreased significantly (SP2 vs. SP3, p<0.05), and the costs of specific antimicrobials decreased (SP1, US$ 1080000; SP2, US$ 944000; SP3, US$ 763000). The rates of carbapenem resistance among Pseudomonas aeruginosa isolates showed a significant reduction from 16.2% in SP2 to 8.7% in SP3 (p<0.05). The mortality rate and length of stay did not change during the study period. CONCLUSIONS Earlier intervention by an AST could contribute to the proper use of antimicrobials without adversely affecting patient outcomes.
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Affiliation(s)
- D Hagiwara
- Department of Pharmacy, Fukuoka University Hospital, Fukuoka, Japan
| | - K Sato
- Department of Pharmacy, Fukuoka University Hospital, Fukuoka, Japan
| | - M Miyazaki
- Department of Pharmacy, Fukuoka University Chikushi Hospital, Fukuoka, Japan
| | - M Kamada
- Department of Pharmacy, Fukuoka University Hospital, Fukuoka, Japan
| | - N Moriwaki
- Department of Pharmacy, Fukuoka University Hospital, Fukuoka, Japan
| | - T Nakano
- Department of Pharmacology, Faculty of Pharmaceutical Sciences, Fukuoka University, Fukuoka, Japan
| | - S Shiotsuka
- Department of Pharmacy, Fukuoka University Hospital, Fukuoka, Japan
| | - C Tokushige
- Department of Clinical Laboratory, Fukuoka University Hospital, Fukuoka, Japan
| | - H Toh
- Department of Clinical Laboratory, Fukuoka University Hospital, Fukuoka, Japan
| | - H Kamimura
- Department of Pharmacy, Fukuoka University Hospital, Fukuoka, Japan
| | - A Togawa
- Department of Infection Control, Fukuoka University Hospital, Fukuoka, Japan; Department of Medical Oncology, Hematology, and Infectious Diseases, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - T Takata
- Department of Infection Control, Fukuoka University Hospital, Fukuoka, Japan; Department of Medical Oncology, Hematology, and Infectious Diseases, Faculty of Medicine, Fukuoka University, Fukuoka, Japan.
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Thakur U, Levy S, Sivaratnam D, Herath D, Nadesapillai S, Toh H, Westcott J, Lichtenstein M, Hepworth G, Better N. The Relationship Between Ischaemia on Myocardial Perfusion Imaging and Chest Pain or Electrocardiogram Changes During Exercise. Heart Lung Circ 2018. [DOI: 10.1016/j.hlc.2018.06.532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Okae H, Toh H, Sato T, Hiura H, Takahashi S, Shirane K, Kabayama Y, Suyama M, Sasaki H, Arima T. Derivation of Human Trophoblast Stem Cells. Cell Stem Cell 2017; 22:50-63.e6. [PMID: 29249463 DOI: 10.1016/j.stem.2017.11.004] [Citation(s) in RCA: 464] [Impact Index Per Article: 66.3] [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: 05/16/2017] [Revised: 09/20/2017] [Accepted: 11/02/2017] [Indexed: 11/25/2022]
Abstract
Trophoblast cells play an essential role in the interactions between the fetus and mother. Mouse trophoblast stem (TS) cells have been derived and used as the best in vitro model for molecular and functional analysis of mouse trophoblast lineages, but attempts to derive human TS cells have so far been unsuccessful. Here we show that activation of Wingless/Integrated (Wnt) and EGF and inhibition of TGF-β, histone deacetylase (HDAC), and Rho-associated protein kinase (ROCK) enable long-term culture of human villous cytotrophoblast (CT) cells. The resulting cell lines have the capacity to give rise to the three major trophoblast lineages, which show transcriptomes similar to those of the corresponding primary trophoblast cells. Importantly, equivalent cell lines can be derived from human blastocysts. Our data strongly suggest that the CT- and blastocyst-derived cell lines are human TS cells, which will provide a powerful tool to study human trophoblast development and function.
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Affiliation(s)
- Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hitoshi Hiura
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Sota Takahashi
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuka Kabayama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
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Maenohara S, Unoki M, Toh H, Ohishi H, Sharif J, Koseki H, Sasaki H. Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos. PLoS Genet 2017; 13:e1007042. [PMID: 28976982 PMCID: PMC5643148 DOI: 10.1371/journal.pgen.1007042] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/16/2017] [Accepted: 09/22/2017] [Indexed: 01/05/2023] Open
Abstract
The methylation of cytosine at CG sites in the mammalian genome is dynamically reprogrammed during gametogenesis and preimplantation development. It was previously shown that oocyte-derived DNMT1 (a maintenance methyltransferase) is essential for maintaining and propagating CG methylation at imprinting control regions in preimplantation embryos. In mammalian somatic cells, hemimethylated-CG-binding protein UHRF1 plays a critical role in maintaining CG methylation by recruiting DNMT1 to hemimethylated CG sites. However, the role of UHRF1 in oogenesis and preimplantation development is unknown. In the present study, we show that UHRF1 is mainly, but not exclusively, localized in the cytoplasm of oocytes and preimplantation embryos. However, smaller amounts of UHRF1 existed in the nucleus, consistent with the expected role in DNA methylation. We then generated oocyte-specific Uhrf1 knockout (KO) mice and found that, although oogenesis was itself unaffected, a large proportion of the embryos derived from the KO oocytes died before reaching the blastocyst stage (a maternal effect). Whole genome bisulfite sequencing revealed that blastocysts derived from KO oocytes have a greatly reduced level of CG methylation, suggesting that maternal UHRF1 is essential for maintaining CG methylation, particularly at the imprinting control regions, in preimplantation embryos. Surprisingly, UHRF1 was also found to contribute to de novo CG and non-CG methylation during oocyte growth: in Uhrf1 KO oocytes, transcriptionally-inactive regions gained less methylation, while actively transcribed regions, including the imprinting control regions, were unaffected or only slightly affected. We also found that de novo methylation was defective during the late stage of oocyte growth. To the best of our knowledge, this is the first study to demonstrate the role of UHRF1 in de novo DNA methylation in vivo. Our study reveals multiple functions of UHRF1 during the global epigenetic reprogramming of oocytes and early embryos. The methylation of cytosine at CG sites in the mammalian genome is an epigenetic modification that is important for cell differentiation and embryonic development. During oocyte growth, the actively transcribed regions gain both CG and non-CG methylation. However, after fertilization, such methylation is globally erased, except for certain gene control regions and a subset of retrotransposons that retain CG methylation. We examined the role of UHRF1, a protein essential for the maintenance of CG methylation in somatic cells, in oocytes and preimplantation embryos by generating oocyte-specific Uhrf1 gene knockout mice. We found that oocyte-derived maternal UHRF1 protein was important for nuclear localization of DNMT1 (a maintenance DNA methyltransferase) and for CG maintenance methylation, particularly at the imprinting control regions, in preimplantation embryos. Unexpectedly, we found that the gain in CG and non-CG methylation in oocytes was also affected by Uhrf1 knockout in certain genomic regions. To the best of our knowledge, this is the first study to demonstrate a role of UHRF1 in de novo DNA methylation in vivo. Our study reveals multiple functions of UHRF1 during the global epigenetic reprogramming of oocytes and preimplantation embryos.
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Affiliation(s)
- Shoji Maenohara
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- * E-mail: (HS); (MU)
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hiroaki Ohishi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Jafar Sharif
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan
- * E-mail: (HS); (MU)
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11
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Toh H, Ong S, Swe M, Chua M, Chen Q, Lam S, Zhang J. Objective vs subjective identification of the difficult airway: A retrospective audit of their incidences in A tertiary hospital in Singapore. Trends in Anaesthesia and Critical Care 2017. [DOI: 10.1016/j.tacc.2017.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Kabayama Y, Toh H, Katanaya A, Sakurai T, Chuma S, Kuramochi-Miyagawa S, Saga Y, Nakano T, Sasaki H. Roles of MIWI, MILI and PLD6 in small RNA regulation in mouse growing oocytes. Nucleic Acids Res 2017; 45:5387-5398. [PMID: 28115634 PMCID: PMC5435931 DOI: 10.1093/nar/gkx027] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/14/2017] [Indexed: 11/13/2022] Open
Abstract
The mouse PIWI-interacting RNA (piRNA) pathway produces a class of 26–30-nucleotide (nt) small RNAs and is essential for spermatogenesis and retrotransposon repression. In oocytes, however, its regulation and function are poorly understood. In the present study, we investigated the consequences of loss of piRNA-pathway components in growing oocytes. When MILI (or PIWIL2), a PIWI family member, was depleted by gene knockout, almost all piRNAs disappeared. This severe loss of piRNA was accompanied by an increase in transcripts derived from specific retrotransposons, especially IAPs. MIWI (or PIWIL1) depletion had a smaller effect. In oocytes lacking PLD6 (or ZUCCHINI or MITOPLD), a mitochondrial nuclease/phospholipase involved in piRNA biogenesis in male germ cells, the piRNA level was decreased to 50% compared to wild-type, a phenotype much milder than that in males. Since PLD6 is essential for the creation of the 5΄ ends of primary piRNAs in males, the presence of mature piRNA in PLD6-depleted oocytes suggests the presence of compensating enzymes. Furthermore, we identified novel 21–23-nt small RNAs, termed spiRNAs, possessing a 10-nt complementarity with piRNAs, which were produced dependent on MILI and independent of DICER. Our study revealed the differences in the biogenesis and function of the piRNA pathway between sexes.
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Affiliation(s)
- Yuka Kabayama
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.,Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Ami Katanaya
- Department of Development and Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Sakurai
- Division of Mammalian Development, Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Shinichiro Chuma
- Department of Development and Differentiation, Institute for Frontier Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Satomi Kuramochi-Miyagawa
- Department of Pathology, Medical school and Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Yumiko Saga
- Division of Mammalian Development, Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan
| | - Toru Nakano
- Department of Pathology, Medical school and Graduate School of Frontier Biosciences, Osaka University, Suita 565-0871, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
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13
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Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H. Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing. BMC Genomics 2017; 18:31. [PMID: 28056787 PMCID: PMC5217569 DOI: 10.1186/s12864-016-3392-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 12/07/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Methylation of cytosine in genomic DNA is a well-characterized epigenetic modification involved in many cellular processes and diseases. Whole-genome bisulfite sequencing (WGBS), such as MethylC-seq and post-bisulfite adaptor tagging sequencing (PBAT-seq), uses the power of high-throughput DNA sequencers and provides genome-wide DNA methylation profiles at single-base resolution. However, the accuracy and consistency of WGBS outputs in relation to the operating conditions of high-throughput sequencers have not been explored. RESULTS We have used the Illumina HiSeq platform for our PBAT-based WGBS, and found that different versions of HiSeq Control Software (HCS) and Real-Time Analysis (RTA) installed on the system provided different global CpG methylation levels (approximately 5% overall difference) for the same libraries. This problem was reproduced multiple times with different WGBS libraries and likely to be associated with the low sequence diversity of bisulfite-converted DNA. We found that HCS was the major determinant in the observed differences. To determine which version of HCS is most suitable for WGBS, we used substrates with predetermined CpG methylation levels, and found that HCS v2.0.5 is the best among the examined versions. HCS v2.0.12 showed the poorest performance and provided artificially lower CpG methylation levels when 5-methylcytosine is read as guanine (first read of PBAT-seq and second read of MethylC-seq). In addition, paired-end sequencing of low diversity libraries using HCS v2.2.38 or the latest HCS v2.2.58 was greatly affected by cluster densities. CONCLUSIONS Software updates in the Illumina HiSeq platform can affect the outputs from low-diversity sequencing libraries such as WGBS libraries. More recent versions are not necessarily the better, and HCS v2.0.5 is currently the best for WGBS among the examined HCS versions. Thus, together with other experimental conditions, special care has to be taken on this point when CpG methylation levels are to be compared between different samples by WGBS.
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Affiliation(s)
- Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Ichiyanagi
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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14
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Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T. Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. Am J Hum Genet 2016; 99:1045-1058. [PMID: 27843122 DOI: 10.1016/j.ajhg.2016.08.021] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 08/31/2016] [Indexed: 10/20/2022] Open
Abstract
DNA methylation is globally reprogrammed after fertilization, and as a result, the parental genomes have similar DNA-methylation profiles after implantation except at the germline differentially methylated regions (gDMRs). We and others have previously shown that human blastocysts might contain thousands of transient maternally methylated gDMRs (transient mDMRs), whose maternal methylation is lost in embryonic tissues after implantation. In this study, we performed genome-wide allelic DNA methylation analyses of purified trophoblast cells from human placentas and, surprisingly, found that more than one-quarter of the transient-in-embryo mDMRs maintained their maternally biased DNA methylation. RNA-sequencing-based allelic expression analyses revealed that some of the placenta-specific mDMRs were associated with expression of imprinted genes (e.g., TIGAR, SLC4A7, PROSER2-AS1, and KLHDC10), and three imprinted gene clusters were identified. This approach also identified some X-linked gDMRs. Comparisons of the data with those from other mammals revealed that genomic imprinting in the placenta is highly variable. These findings highlight the incomplete erasure of germline DNA methylation in the human placenta; understanding this erasure is important for understanding normal placental development and the pathogenesis of developmental disorders with imprinting effects.
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15
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Matsumoto S, Noda N, Hotta T, Uchiumi T, Kang D. [Neuraminidase Amino Acid Sequences of Influenza A/H3N2 and B Viruses Isolated from Influenza Patients in the 2014/15 Japanese Influenza Season]. Fukuoka Igaku Zasshi 2016; 107:98-104. [PMID: 29210538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Neuraminidase (NA) is a surface protein essential for influenza virus replication. NA inhibitors are commonly used for the treatment of influenza patients in Japan. Several mutations that reduce the effect of NA inhibitors have been reported. We sequenced the whole NA segment of isolated virus from influenza patients and investigated the relation between the NA amino acid sequence and the 50% inhibitory concentration (IC_50) of four NA inhibitors. MATERIALS AND METHODS Forty A/H3N2 and 19 B influenza virus isolated from patients in the 2014/15 influenza season were analyzed. The IC_50 was determined by a neuraminidase inhibition assay using a fluorescent substrate. Viral RNA was amplified by RT-PCR and the genome was sequenced using a next generation sequencer. The deduced amino acid sequences were analyzed. RESULTS There was no AA change in the NA catalytic site of the A/H3N2 and B viruses isolated in the 2014-15 influenza season. There was no significant relation between the NA amino acids and the IC_50 of the four NA inhibitors for A/H3N2 or B viruses. CONCLUSION The catalytic site of NA was highly conserved for these A/H3N2 and B viruses. No emergence of NA amino acid mutations related to the sensitivity of the four currently used NA inhibitors was observed.
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16
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Toh H, Morita H, Tsuji H, Iwashita K, Goto N, Nakayama J, Sekine M, Kato Y, Suzuki KI, Fujita N. Complete genome sequence of Lactobacillus acetotolerans RIB 9124 (NBRC 13120) isolated from putrefied (hiochi) Japanese sake. J Biotechnol 2015; 214:214-5. [PMID: 26376472 DOI: 10.1016/j.jbiotec.2015.09.006] [Citation(s) in RCA: 7] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/10/2015] [Indexed: 11/28/2022]
Abstract
Lactobacillus acetotolerans RIB 9124 (NBRC 13120) was isolated from putrefied (hiochi) Japanese sake. Here we report the complete genome sequence of this organism. This paper is the first report demonstrating the fully sequenced and completely annotated genome of a L. acetotolerans strain.
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Affiliation(s)
- Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Hiroyuki Tsuji
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima, Japan
| | - Kazuhiro Iwashita
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima, Japan
| | - Nami Goto
- National Research Institute of Brewing, Higashi-hiroshima, Hiroshima, Japan
| | - Jiro Nakayama
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Mitsuo Sekine
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan
| | - Yumiko Kato
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan
| | - Ken-ichiro Suzuki
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan
| | - Nobuyuki Fujita
- Biological Resource Center, National Institute of Technology and Evaluation, Tokyo, Japan.
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17
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Kubo N, Toh H, Shirane K, Shirakawa T, Kobayashi H, Sato T, Sone H, Sato Y, Tomizawa SI, Tsurusaki Y, Shibata H, Saitsu H, Suzuki Y, Matsumoto N, Suyama M, Kono T, Ohbo K, Sasaki H. DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis. BMC Genomics 2015; 16:624. [PMID: 26290333 PMCID: PMC4546090 DOI: 10.1186/s12864-015-1833-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
Background In the male germline, neonatal prospermatogonia give rise to spermatogonia, which include stem cell population (undifferentiated spermatogonia) that supports continuous spermatogenesis in adults. Although the levels of DNA methyltransferases change dynamically in the neonatal and early postnatal male germ cells, detailed genome-wide DNA methylation profiles of these cells during the stem cell formation and differentiation have not been reported. Results To understand the regulation of spermatogonial stem cell formation and differentiation, we examined the DNA methylation and gene expression dynamics of male mouse germ cells at the critical stages: neonatal prospermatogonia, and early postntal (day 7) undifferentiated and differentiating spermatogonia. We found large partially methylated domains similar to those found in cancer cells and placenta in all these germ cells, and high levels of non-CG methylation and 5-hydroxymethylcytosines in neonatal prospermatogonia. Although the global CG methylation levels were stable in early postnatal male germ cells, and despite the reported scarcity of differential methylation in the adult spermatogonial stem cells, we identified many regions showing stage-specific differential methylation in and around genes important for stem cell function and spermatogenesis. These regions contained binding sites for specific transcription factors including the SOX family members. Conclusions Our findings show a distinctive and dynamic regulation of DNA methylation during spermatogonial stem cell formation and differentiation in the neonatal and early postnatal testes. Furthermore, we revealed a unique accumulation and distribution of non-CG methylation and 5hmC marks in neonatal prospermatogonia. These findings contrast with the reported scarcity of differential methylation in adult spermatogonial stem cell differentiation and represent a unique phase of male germ cell development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1833-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Naoki Kubo
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.,Research Institute for Disease of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hidehiro Toh
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Kenjiro Shirane
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Takayuki Shirakawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hidetoshi Sone
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Yasuyuki Sato
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Shin-ichi Tomizawa
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Yoshinori Tsurusaki
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba, 277-8568, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Graduate School of Medicine, Yokohama City University, Yokohama, 236-0004, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tomohiro Kono
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, 156-8502, Japan.,Department of BioScience, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Kazuyuki Ohbo
- Department of Histology and Cell Biology, Yokohama City University School of Medicine, Yokohama, 236-0004, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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18
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Koga Y, Matsumoto S, Hotta T, Uchiumi T, Kang D. [Analysis of the Neuraminidase Amino Acid Sequences of Influenza A/H1N1pdm09, A/H3N2, and B Viruses Isolated from Influenza Patients in the 2013/14 Japanese Influenza Season]. Fukuoka Igaku Zasshi 2015; 106:231-239. [PMID: 26630841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Neuraminidase (NA) is an essential surface protein for influenza virus replication. NA inhibitors are commonly used for the treatment of influenza patients in Japan. Several mutations that reduce the effect of NA inhibitors have been reported. We sequenced the whole NA segment of isolated virus from influenza patients and investigated the relation between the NA amino acid sequence and the 50% inhibitory concentration (IC50) of four NA inhibitors. MATERIALS AND METHODS A total of 20 viruses that showed high or low IC50 of NA inhibitors were selected from A/H1N1pdm09, A/H3N2, and B isolates from the viruses isolated from patients in the 2013-14 influenza season. Viral RNA was extracted and RT-PCR was done. The amplified genome was sequenced using a next generation sequencer", and the deduced amino acid sequences were analyzed. RESULTS Two A/H1N1pdm09 viruses that showed very high IC50 for oseltamivir (150 nM and 130 nM) contained the H275Y mutation. Otherwise, no significant relation was found between the NA amino acids and the IC50 of the four NA inhibitors. There was no significant relation between the NA amino acids and the IC50 of the four NA inhibitors for A/H3N2 viruses. The B viruses that showed a high IC50 for oseltamivir and laninamivir shared some amino acids. The B viruses that showed a high IC50 of zanamivir and peramivir also shared some amino acids. They were different from the shared amino acids found for oseltamivir and laninamivir. CONCLUSION The previously reported H275Y mutation that causes oseltamivir resistance was found in the two A/H1N1pdm09 viruses that showed a very high IC50 for oseltamivir. No additional NA amino acid sequences related to the IC50 of the four NA inhibitors was found. The meaning of the shared amino acids among B viruses that showed a high IC50 would be an interesting target for further investigation.
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Morita H, Toh H, Oshima K, Nakano A, Kiuchi M, Kuroyanagi H, Arakawa K, Suda W, Honda K, Hattori M. Complete genome sequence of Bifidobacterium angulatum JCM 7096(T) isolated from human feces. J Biotechnol 2015; 211:10-1. [PMID: 26142062 DOI: 10.1016/j.jbiotec.2015.06.412] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 11/19/2022]
Abstract
Bifidobacterium angulatum JCM 7096(T) was isolated from human feces. Here we report the complete genome sequence of this organism. This paper is the first report demonstrating the fully sequenced and completely annotated genome of a B. angulatum strain.
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Affiliation(s)
- Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenshiro Oshima
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Misa Kiuchi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiromi Kuroyanagi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kensuke Arakawa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Wataru Suda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenya Honda
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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20
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Morita H, Toh H, Oshima K, Nakano A, Omori E, Hattori Y, Arakawa K, Suda W, Honda K, Hattori M. Complete genome sequence of Bifidobacterium breve JCM 1192(T) isolated from infant feces. J Biotechnol 2015; 210:81-2. [PMID: 26142063 DOI: 10.1016/j.jbiotec.2015.06.414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
Bifidobacterium breve JCM 1192(T) was isolated from infant feces. Here, we report the complete genome sequence of this organism.
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Affiliation(s)
- Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenshiro Oshima
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Emi Omori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yasue Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kensuke Arakawa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Wataru Suda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenya Honda
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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Morita H, Toh H, Oshima K, Nakano A, Yamashita N, Iioka E, Arakawa K, Suda W, Honda K, Hattori M. Complete genome sequence of Bifidobacterium catenulatum JCM 1194(T) isolated from human feces. J Biotechnol 2015; 210:25-6. [PMID: 26133930 DOI: 10.1016/j.jbiotec.2015.06.415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 11/29/2022]
Abstract
Bifidobacterium catenulatum JCM 1194(T) was isolated from human feces. This paper is the first report demonstrating the fully sequenced and completely annotated genome of a B. catenulatum strain.
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Affiliation(s)
- Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenshiro Oshima
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Naoko Yamashita
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Erica Iioka
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kensuke Arakawa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Wataru Suda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenya Honda
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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22
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Morita H, Toh H, Oshima K, Nakano A, Arakawa K, Takayama Y, Kurokawa R, Takanashi K, Honda K, Hattori M. Complete genome sequence of Bifidobacterium pseudocatenulatum JCM 1200(T) isolated from infant feces. J Biotechnol 2015; 210:68-9. [PMID: 26133926 DOI: 10.1016/j.jbiotec.2015.06.416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
Bifidobacterium pseudocatenulatum JCM 1200(T) was isolated from infant feces. This paper is the first report demonstrating the fully sequenced and completely annotated genome of a B. pseudocatenulatum strain.
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Affiliation(s)
- Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenshiro Oshima
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Kensuke Arakawa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yukiko Takayama
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Rina Kurokawa
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kageyasu Takanashi
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenya Honda
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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23
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Morita H, Toh H, Oshima K, Nakano A, Shindo C, Komiya K, Arakawa K, Suda W, Honda K, Hattori M. Complete genome sequence of Bifidobacterium bifidum JCM 1255(T) isolated from feces of a breast-fed infant. J Biotechnol 2015; 210:66-7. [PMID: 26133927 DOI: 10.1016/j.jbiotec.2015.06.413] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
Bifidobacterium bifidum JCM 1255(T) was isolated from feces of a breast-fed infant. Here we report the complete genome sequence of this organism.
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Affiliation(s)
- Hidetoshi Morita
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan; CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
| | - Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenshiro Oshima
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- Department of Microbiology and Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Chie Shindo
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Keiko Komiya
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kensuke Arakawa
- Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Wataru Suda
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Kenya Honda
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; Department of Microbiology and Immunology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
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Ikematsu H, Chong Y, Shirane K, Toh H, Sasaki H, Koga Y, Urata M, Hotta T, Uchiumi T, Kang D. [Analysis of influenza A/H3N2 neuraminidase genes obtained from influenza patients in the 2011/12 and 2012/13 seasons in Japan]. Fukuoka Igaku Zasshi 2015; 106:16-22. [PMID: 25942938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
BACKGROUND Influenza virus has neuraminidase (NA), a surface protein with enzymatic activity that is essential for virus replication. Mutation may affect the effectiveness of NA inhibitors that are used for the treatment of influenza patients. In this study, we determined the NA gene sequences from the clinical isolates of influenza patients to examine the chronological genetic changes and the relation to drug susceptibility. METHODS For 96 A/H3N2 virus isolates the 50% inhibitory concentration (IC50) (48 each from the 2011-12 and 12-13 influenza seasons) was measured. RT-PCR was done with extracted viral RNA, followed by nucleotide sequencing. RESULTS One putative amino acid mutation, D151N, was found in an NA activity-related cite in five of ninety-six tested isolate. The mutation did not affect the IC50 value. The mutations identified at amino acid positions 387 and 400 were statistically correlated with an increased IC50 value, although the change was less than ten times, suggesting no significant difference in the clinical effectiveness. A small number .of isolates showed mutation in the T and/or B cell epitope region of NA. CONCLUSION No mutation that affected the IC50 value or effectiveness of NAIs was detected. Antigenic mutations of NA, which influence the selection of epidemic strains, were not determined. Continuous observation will be necessary to further clarify the genetic features of NA.
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Kosaka T, Toh H, Fujiyama A, Sakaki Y, Watanabe K, Meng XY, Hanada S, Toyoda A. Physiological and genetic basis for self-aggregation of a thermophilic hydrogenotrophic methanogen, Methanothermobacter strain CaT2. Environ Microbiol Rep 2014; 6:268-277. [PMID: 24983531 DOI: 10.1111/1758-2229.12128] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/05/2013] [Indexed: 06/03/2023]
Abstract
Several thermophilic hydrogenotrophic methanogens naturally aggregate in their habitats in association with hydrogen-producing bacteria for efficient transfer of the methane fermentation intermediates to produce methane. However, physiology of aggregation and the identity of aggregation-specific genes remain to be elucidated. Here, we isolated and characterized a hydrogen and formate-utilizing Methanothermobacter sp. CaT2 that is capable of self-aggregation and utilizing formate. CaT2 produced methane from propionate oxidation in association with a syntrophic propionate-oxidizing bacterium faster than other methanogens, including Methanothermobacter thermautotrophicus ΔH and Methanothermobacter thermautotrophicus Z-245. CaT2 also aggregated throughout the culture period and was coated with polysaccharides, which was not found on the ΔH and Z-245 cells. Sugar content (particularly of rhamnose and mannose) was also higher in the CaT2 cells than the ΔH and Z-245 cells. Comparative genomic analysis of CaT2 indicated that four candidate genes, all of which encode glycosyltransferase, were involved in aggregation of CaT2. Transcriptional analysis showed that one glycosyltransferase gene was expressed at relatively high levels under normal growth conditions. The polysaccharide layer on the CaT2 cell surface, which is probably assembled by these glycosyltransferases, may be involved in cell aggregation.
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Affiliation(s)
- Tomoyuki Kosaka
- Department of Biological Chemistry, Faculty of Agriculture, Yamaguchi University, 1677-1 Yoshida, Yamaguchi, 753-8515, Japan; PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama, 332-0012, Japan; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8566, Japan
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26
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Toh H, Oshima K, Nakano A, Takahata M, Murakami M, Takaki T, Nishiyama H, Igimi S, Hattori M, Morita H. Genomic adaptation of the Lactobacillus casei group. PLoS One 2013; 8:e75073. [PMID: 24116025 PMCID: PMC3792948 DOI: 10.1371/journal.pone.0075073] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2013] [Accepted: 08/10/2013] [Indexed: 11/23/2022] Open
Abstract
Lactobacillus casei, L. paracasei, and L. rhamnosus form a closely related taxonomic group (Lactobacillus casei group) within the facultatively heterofermentative lactobacilli. Here, we report the complete genome sequences of L. paracasei JCM 8130 and L. casei ATCC 393, and the draft genome sequence of L. paracasei COM0101, all of which were isolated from daily products. Furthermore, we re-annotated the genome of L. rhamnosus ATCC 53103 (also known as L. rhamnosus GG), which we have previously reported. We confirmed that ATCC 393 is distinct from other strains previously described as L. paracasei. The core genome of 10 completely sequenced strains of the L. casei group comprised 1,682 protein-coding genes. Although extensive genome-wide synteny was found among the L. casei group, the genomes of ATCC 53103, JCM 8130, and ATCC 393 contained genomic islands compared with L. paracasei ATCC 334. Several genomic islands, including carbohydrate utilization gene clusters, were found at the same loci in the chromosomes of the L. casei group. The spaCBA pilus gene cluster, which was first identified in GG, was also found in other strains of the L. casei group, but several L. paracasei strains including COM0101 contained truncated spaC gene. ATCC 53103 encoded a higher number of proteins involved in carbohydrate utilization compared with intestinal lactobacilli, and extracellular adhesion proteins, several of which are absent in other strains of the L. casei group. In addition to previously fully sequenced L. rhamnosus and L. paracasei strains, the complete genome sequences of L. casei will provide valuable insights into the evolution of the L. casei group.
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Affiliation(s)
- Hidehiro Toh
- Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Akiyo Nakano
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Muneaki Takahata
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | - Masaru Murakami
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
| | | | | | - Shizunobu Igimi
- Division of Biomedical Food Research, National Institute of Health Sciences, Kamiyoga, Setagaya, Tokyo, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
- * E-mail:
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Takahata M, Toh H, Nakano A, Takagi M, Murakami M, Ishii Y, Takizawa T, Tanabe S, Morita H. Complete sequence analysis of two cryptic plasmids from Bifidobacterium kashiwanohense JCM 15439 (type strain) isolated from healthy infant feces. Anim Sci J 2013; 85:158-63. [PMID: 23865717 DOI: 10.1111/asj.12095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 04/18/2013] [Indexed: 11/26/2022]
Abstract
Bifidobacterial plasmids reported so far are derived from a limited number of strains and plasmids of bifidobacterial type strains isolated from humans are unknown. We found that Bifidobacterium kashiwanohense JCM 15439 (type strain) isolated from a healthy infant contained two cryptic plasmids, designated pBBKW-1 and pBBKW-2. We determined and analyzed the complete sequences of both plasmids. pBBKW-1 (7716 bp) was predicted to replicate by a rolling-circle mechanism and encode six protein-coding genes, two of which are putative replication proteins. pBBKW-1 seems to be a cointegrate plasmid containing two copies of the plasmid pMG1 from Bifidobacterium longum. pBBKW-2 (2920 bp) was predicted to encode six protein-coding genes and be a theta-type replicating plasmid, which has been reported to be more stable than a rolling circle-type replicating plasmid frequently found in bifidobacteria. Our finding will provide new insights into safe recombinant plasmid constructions for humans.
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Affiliation(s)
- Muneaki Takahata
- School of Veterinary Medicine, Azabu University, Sagamihara; BioBank Co., Ltd, Okayama
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Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H. Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases. PLoS Genet 2013; 9:e1003439. [PMID: 23637617 PMCID: PMC3630097 DOI: 10.1371/journal.pgen.1003439] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 02/23/2013] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian development, retrotransposon silencing, and cellular reprogramming. Although methylation mainly occurs on the cytosine in a CG site, non-CG methylation is prevalent in pluripotent stem cells, brain, and oocytes. We previously identified non-CG methylation in several CG-rich regions in mouse germinal vesicle oocytes (GVOs), but the overall distribution of non-CG methylation and the enzymes responsible for this modification are unknown. Using amplification-free whole-genome bisulfite sequencing, which can be used with minute amounts of DNA, we constructed the base-resolution methylome maps of GVOs, non-growing oocytes (NGOs), and mutant GVOs lacking the DNA methyltransferase Dnmt1, Dnmt3a, Dnmt3b, or Dnmt3L. We found that nearly two-thirds of all methylcytosines occur in a non-CG context in GVOs. The distribution of non-CG methylation closely resembled that of CG methylation throughout the genome and showed clear enrichment in gene bodies. Compared to NGOs, GVOs were over four times more methylated at non-CG sites, indicating that non-CG methylation accumulates during oocyte growth. Lack of Dnmt3a or Dnmt3L resulted in a global reduction in both CG and non-CG methylation, showing that non-CG methylation depends on the Dnmt3a-Dnmt3L complex. Dnmt3b was dispensable. Of note, lack of Dnmt1 resulted in a slight decrease in CG methylation, suggesting that this maintenance enzyme plays a role in non-dividing oocytes. Dnmt1 may act on CG sites that remain hemimethylated in the de novo methylation process. Our results provide a basis for understanding the mechanisms and significance of non-CG methylation in mammalian oocytes.
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Affiliation(s)
- Kenjiro Shirane
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hidehiro Toh
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
| | - Hisato Kobayashi
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Fumihito Miura
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hatsune Chiba
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ito
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomohiro Kono
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics, Medical Institute of Bioregulation, and Epigenome Network Research Center, Kyushu University, Fukuoka, Japan
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- * E-mail:
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Fukao M, Oshima K, Morita H, Toh H, Suda W, Kim SW, Suzuki S, Yakabe T, Hattori M, Yajima N. Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PLoS One 2013; 8:e60521. [PMID: 23544154 PMCID: PMC3609814 DOI: 10.1371/journal.pone.0060521] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 02/28/2013] [Indexed: 11/18/2022] Open
Abstract
We determined the complete genome sequence of Lactobacillus brevis KB290, a probiotic lactic acid bacterium isolated from a traditional Japanese fermented vegetable. The genome contained a 2,395,134-bp chromosome that housed 2,391 protein-coding genes and nine plasmids that together accounted for 191 protein-coding genes. KB290 contained no virulence factor genes, and several genes related to presumptive cell wall-associated polysaccharide biosynthesis and the stress response were present in L. brevis KB290 but not in the closely related L. brevis ATCC 367. Plasmid-curing experiments revealed that the presence of plasmid pKB290-1 was essential for the strain's gastrointestinal tract tolerance and tendency to aggregate. Using next-generation deep sequencing of current and 18-year-old stock strains to detect low frequency variants, we evaluated genome stability. Deep sequencing of four periodic KB290 culture stocks with more than 1,000-fold coverage revealed 3 mutation sites and 37 minority variation sites, indicating long-term stability and providing a useful method for assessing the stability of industrial bacteria at the nucleotide level.
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Affiliation(s)
- Masanori Fukao
- Research Institute, KAGOME Co., Ltd., Nasushiobara, Tochigi, Japan.
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Fukuda S, Toh H, Taylor TD, Ohno H, Hattori M. Acetate-producing bifidobacteria protect the host from enteropathogenic infection via carbohydrate transporters. Gut Microbes 2013; 3:449-54. [PMID: 22825494 DOI: 10.4161/gmic.21214] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The human gut harbors a large and diverse community of commensal bacteria. Among them, Bifidobacterium is known to exhibit various probiotic effects including protection of hosts from infectious diseases. We recently discovered that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting gnotobiotic mice from death induced by enterohemorrhagic Escherichia coli O157:H7. We elucidated the molecular mechanism on lethal infection in mice associated with several bifidobacterial strains by a multi-omics approach combining genomics, transcriptomics and metabolomics. The combined data clearly show that acetate produced by protective bifidobacteria acts in vivo to promote defense functions of the host epithelial cells and thereby protects the host from lethal infection. As demonstrated here, our multi-omics approach provides a powerful strategy for evaluation of host-microbial interactions in the complex gut ecosystem.
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Affiliation(s)
- Shinji Fukuda
- Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, Yokohama, Japan
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Abstract
Zinc finger transcription factor Zfp57 recognizes the methylated CpG within the TGCCGC element. We determined the structure of the DNA-binding domain of Zfp57, consisting of two adjacent zinc fingers, in complex with fully methylated DNA at 1.0 Å resolution. The first zinc finger contacts the 5' half (TGC), and the second recognizes the 3' half (CGC) of the recognition sequence. Zfp57 recognizes the two 5-methylcytosines (5mCs) asymmetrically: One involves hydrophobic interactions with Arg178, which also interacts with the neighboring 3' guanine and forms a 5mC-Arg-G interaction, while the other involves a layer of ordered water molecules. Two point mutations in patients with transient neonatal diabetes abolish DNA-binding activity. Zfp57 has reduced binding affinity for unmodified DNA and the oxidative products of 5mC.
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Affiliation(s)
- Yiwei Liu
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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Hira D, Toh H, Migita CT, Okubo H, Nishiyama T, Hattori M, Furukawa K, Fujii T. Anammox organism KSU-1 expresses a NirK-type copper-containing nitrite reductase instead of a NirS-type with cytochromecd1. FEBS Lett 2012; 586:1658-63. [DOI: 10.1016/j.febslet.2012.04.041] [Citation(s) in RCA: 100] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 04/19/2012] [Accepted: 04/20/2012] [Indexed: 10/28/2022]
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Morita H, Nakano A, Onoda H, Toh H, Oshima K, Takami H, Murakami M, Fukuda S, Takizawa T, Kuwahara T, Ohno H, Tanabe S, Hattori M. Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant faeces. Int J Syst Evol Microbiol 2011; 61:2610-2615. [DOI: 10.1099/ijs.0.024521-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Strains HM2-1 and HM2-2T were isolated from the faeces of a healthy infant and were characterized by determining their phenotypic and biochemical features and phylogenetic positions based on partial 16S rRNA gene sequence analysis. They were Gram-positive, obligately anaerobic, non-spore-forming, non-gas-producing, and catalase-negative non-motile rods. They did not grow at 15 or 45 °C in anaerobic bacterial culture medium, and their DNA G+C content was in the range 56–59 mol%. In enzyme activity tests, strains HM2-1 and HM2-2T were positive for α/β-galactosidases and α/β-glucosidases but negative for β-glucuronidase and cystine arylamidase. An analysis of the cell-wall composition of strains HM2-1 and HM2-2T revealed the presence of glutamic acid, alanine and lysine. The presence of fructose-6-phosphate phosphoketolase shows that isolates HM2-1 and HM2-2T are members of the genus Bifidobacterium. These two isolates belong to the same species of the genus Bifidobacterium. Strain HM2-2T was found to be related to Bifidobacterium catenulatum JCM 1194T (97.4 % 16S rRNA gene sequence identity: 1480/1520 bp), Bifidobacterium pseudocatenulatum JCM 1200T (97.2 %: 1472/1514 bp), Bifidobacterium dentium ATCC 27534T (96.7 %: 1459/1509 bp) and Bifidobacterium angulatum ATCC 27535T (96.5 %: 1462/1515 bp). The predominant cellular fatty acids of strains HM2-1 and HM2-2T were 16 : 0 and 18 : 1ω9c, with proportions greater than 18 % of the total. Phylogenetic analyses involving phenotypic characterization, DNA–DNA hybridization and partial 16S rRNA gene sequencing proves that the strains represent a novel species of the genus Bifidobacterium, for which the name Bifidobacterium kashiwanohense sp. nov. is proposed. The type strain is HM2-2T ( = JCM 15439T = DSM 21854T).
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Affiliation(s)
- Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Akiyo Nakano
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Hiromi Onoda
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Hidehiro Toh
- Advanced Science Institute, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Masaru Murakami
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Shinji Fukuda
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Tatsuya Takizawa
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Tomomi Kuwahara
- Department of Molecular Bacteriology, Institute of Health Biosciences, University of Tokushima, Graduate School, 3-18-15 Kuramoto-cho, Tokushima 770-8503, Japan
| | - Hiroshi Ohno
- Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Soichi Tanabe
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Morita H, Toh H, Oshima K, Yoshizaki M, Kawanishi M, Nakaya K, Suzuki T, Miyauchi E, Ishii Y, Tanabe S, Murakami M, Hattori M. Complete genome sequence and comparative analysis of the fish pathogen Lactococcus garvieae. PLoS One 2011; 6:e23184. [PMID: 21829716 PMCID: PMC3150408 DOI: 10.1371/journal.pone.0023184] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 07/11/2011] [Indexed: 11/21/2022] Open
Abstract
Lactococcus garvieae causes fatal haemorrhagic septicaemia in fish such as yellowtail. The comparative analysis of genomes of a virulent strain Lg2 and a non-virulent strain ATCC 49156 of L. garvieae revealed that the two strains shared a high degree of sequence identity, but Lg2 had a 16.5-kb capsule gene cluster that is absent in ATCC 49156. The capsule gene cluster was composed of 15 genes, of which eight genes are highly conserved with those in exopolysaccharide biosynthesis gene cluster often found in Lactococcus lactis strains. Sequence analysis of the capsule gene cluster in the less virulent strain L. garvieae Lg2-S, Lg2-derived strain, showed that two conserved genes were disrupted by a single base pair deletion, respectively. These results strongly suggest that the capsule is crucial for virulence of Lg2. The capsule gene cluster of Lg2 may be a genomic island from several features such as the presence of insertion sequences flanked on both ends, different GC content from the chromosomal average, integration into the locus syntenic to other lactococcal genome sequences, and distribution in human gut microbiomes. The analysis also predicted other potential virulence factors such as haemolysin. The present study provides new insights into understanding of the virulence mechanisms of L. garvieae in fish.
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Affiliation(s)
- Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa, Japan
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35
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Tamakoshi M, Murakami A, Sugisawa M, Tsuneizumi K, Takeda S, Saheki T, Izumi T, Akiba T, Mitsuoka K, Toh H, Yamashita A, Arisaka F, Hattori M, Oshima T, Yamagishi A. Genomic and proteomic characterization of the large Myoviridae bacteriophage ϕTMA of the extreme thermophile Thermus thermophilus. Bacteriophage 2011; 1:152-164. [PMID: 22164349 DOI: 10.4161/bact.1.3.16712] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 07/21/2011] [Accepted: 07/22/2011] [Indexed: 11/19/2022]
Abstract
A lytic phage, designated as ϕTMA, was isolated from a Japanese hot spring using Thermus thermophilus HB27 as an indicator strain. Electron microscopic examination showed that ϕTMA had an icosahedral head and a contractile tail. The circular double-stranded DNA sequence of ϕTMA was 151,483 bp in length, and its organization was essentially same as that of ϕYS40 except that the ϕTMA genome contained genes for a pair of transposase and resolvase, and a gene for a serine to asparagine substituted ortholog of the protein involved in the initiation of the ϕYS40 genomic DNA synthesis. The different host specificities of ϕTMA and ϕYS40 could be explained by the sequence differences in the C-terminal regions of their distal tail fiber proteins. The ΔpilA knockout strains of T. thermophilus showed simultaneous loss of sensitivity to their cognate phages, pilus structure, twitching motility and competence for natural transformation, thus suggesting that the phage infection required the intact host pili. Pulsed-field gel electrophoresis analysis of the ϕTMA and ϕYS40 genomes revealed that the length of their DNA exceeded 200 kb, indicating that the terminal redundancy is more than 30% of the closed circular form. Proteomic analysis of the ϕTMA virion using a combination of N-terminal sequencing and mass spectrometric analysis of peptide fragments suggested that the maturation of several proteins involved in the phage assembly process was mediated by a trypsin-like protease. The gene order of the phage structural proteins was also discussed.
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Affiliation(s)
- Masatada Tamakoshi
- Department of Molecular Biology; Tokyo University of Pharmacy and Life Sciences; Hachioji, Tokyo
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36
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Fukuda S, Toh H, Hase K, Oshima K, Nakanishi Y, Yoshimura K, Tobe T, Clarke JM, Topping DL, Suzuki T, Taylor TD, Itoh K, Kikuchi J, Morita H, Hattori M, Ohno H. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011. [PMID: 21270894 DOI: 10.1083/nature09646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The human gut is colonized with a wide variety of microorganisms, including species, such as those belonging to the bacterial genus Bifidobacterium, that have beneficial effects on human physiology and pathology. Among the most distinctive benefits of bifidobacteria are modulation of host defence responses and protection against infectious diseases. Nevertheless, the molecular mechanisms underlying these effects have barely been elucidated. To investigate these mechanisms, we used mice associated with certain bifidobacterial strains and a simplified model of lethal infection with enterohaemorrhagic Escherichia coli O157:H7, together with an integrated 'omics' approach. Here we show that genes encoding an ATP-binding-cassette-type carbohydrate transporter present in certain bifidobacteria contribute to protecting mice against death induced by E. coli O157:H7. We found that this effect can be attributed, at least in part, to increased production of acetate and that translocation of the E. coli O157:H7 Shiga toxin from the gut lumen to the blood was inhibited. We propose that acetate produced by protective bifidobacteria improves intestinal defence mediated by epithelial cells and thereby protects the host against lethal infection.
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Affiliation(s)
- Shinji Fukuda
- Laboratory for Epithelial Immunobiology, RIKEN Research Center for Allergy and Immunology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Ng E, Ang S, Li H, Lim K, Choo S, Ngeow JY, Toh H, Chow PK, Tan M. The Singapore liver cancer recurrence (SLICER) score for relapse prediction in patients with resected hepatocellular carcinoma. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.4_suppl.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
169 Background: Hepatocellular carcinoma (HCC) is a common worldwide cancer associated with extremely poor survival, with surgery the only option for cure in patients with localized disease. Current prognostic models for HCC are algorithms developed on datasets of mainly patients with metastatic or unresectable cancer, and may be less relevant to resectable HCC. Nomograms provide individualized outcome estimates. We constructed a postoperative nomogram, the Singapore liver cancer recurrence (SLICER) score, to predict outcomes of HCC patients who have undergone surgical resection. Methods: Records for Singaporean patients undergoing first-line curative surgery for localized HCC in one institution between 1992 and 2007 were retrospectively reviewed (n=405). Freedom from relapse (FFR) was the primary outcome measure. An outcome-blinded modeling strategy including clustering, data reduction and transformation, was used. Calibration was tested with bootstrapping (n=200). We compared the performance of this model with other alternative models including CLIP, CUPI, BCLC, and Okuda scores using c-indices and likelihood analysis. Results: A nomogram (SLICER score) predicting FFR was designed, incorporating vascular invasion, tumor size, multifocality, ECOG status, pre-operative AFP, Childs-Pugh score and cirrhosis. Bootstrap estimates show good calibration at 1, 2, 3, and 5 years postsurgery Comparison of the SLICER score with alternative prognostic models shows superior performance (Table). Conclusions: The SLICER score enables individualized relapse predictions for patients following curative resection of localized HCC. It permits optimal patient selection for adjuvant therapy trials, biomarker development, and individual counseling. [Table: see text] No significant financial relationships to disclose.
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Affiliation(s)
- E. Ng
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - S. Ang
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - H. Li
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - K. Lim
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - S. Choo
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - J. Y. Ngeow
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - H. Toh
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - P. K. Chow
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
| | - M. Tan
- Singapore General Hospital, Singapore, Singapore; Department of Pathology, Singapore General Hospital, Singapore, Singapore; National Cancer Centre Singapore, Singapore, Singapore
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Morita H, Nakano A, Shimazu M, Toh H, Nakajima F, Nagayama M, Hisamatsu S, Kato Y, Takagi M, Takami H, Akita H, Matsumoto M, Masaoka T, Murakami M. Lactobacillus hayakitensis, L. equigenerosi and L. equi, predominant lactobacilli in the intestinal flora of healthy thoroughbreds. Anim Sci J 2010; 80:339-46. [PMID: 20163646 DOI: 10.1111/j.1740-0929.2009.00633.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To detect the predominant lactobacilli in the intestinal flora of healthy thoroughbreds, we isolated lactobacilli from the feces of nine thoroughbreds (five males and four females; 0-15-year-old). The isolated lactobacilli comprise 17 species (37 strains), and they were classified into five groups: Lactobacillus salivarius (6 species), L. reuteri (6 species), Lactobacillus delbrueckii (3 species), L. buchneri (1 species) and L. vitulinus (1 species). On the basis of 16S rRNA gene sequences, we identified 3 other phylogenetic relatives belonging to the genus Lactobacillus. These results suggest that the intestinal flora of thoroughbreds may comprise many species of the genus Lactobacillus. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses of the 340-bp fragments of the 16S rRNA genes from the same nine fecal samples showed that L. hayakitensis, L. equigenerosi and L. equi are contained in all the samples, suggesting that these species are predominant lactobacilli in the intestinal flora of thoroughbreds.
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Affiliation(s)
- Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, Sagamihara, Japan.
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Choo S, Chowbay B, Ng Q, Thng C, Li H, Huynh H, Poon D, Ang M, Chang S, Toh H. A phase I dose-finding and pharmacodynamic study of rapamycin in combination with bevacizumab in patients with unresectable hepatocellular carcinoma. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.4097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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40
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Toh H, Chen P, Carr BI, Knox JJ, Gill S, Qian J, Qin Q, Ricker JL, Carlson DM, Yong W. Linifanib phase II trial in patients with advanced hepatocellular carcinoma (HCC). J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.4038] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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41
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Ang S, Wang W, Soe Y, Tan C, Chow W, Kwee AK, Toh H. Identification of three potential biomarkers in early resectable hepatocellular carcinoma. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.4131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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42
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Morita H, Shimazu M, Shiono H, Toh H, Nakajima F, Akita H, Takagi M, Takami H, Murakami M, Masaoka T, Tanabe S, Hattori M. Lactobacillus equicursoris sp. nov., isolated from the faeces of a thoroughbred racehorse. Int J Syst Evol Microbiol 2010; 60:109-112. [DOI: 10.1099/ijs.0.009290-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We previously isolated five strains of putative lactobacilli from the faeces of a thoroughbred horse (a 4-year-old male). Of the five strains, four were identified as members of existing Lactobacillus species; however, sequence analysis of the 16S rRNA gene revealed that the fifth isolate, DI70T, showed approximately 97 % identity (1325/1366 bp) with the type strain of Lactobacillus delbrueckii. Therefore, we considered the possibility that DI70T represents a novel species of the genus Lactobacillus. Cells of strain DI70T were Gram-stain-positive, catalase-negative, non-spore-forming, non-motile rods. In phylogenetic trees constructed on the basis of 16S rRNA gene sequences, strain DI70T formed a subcluster in the L. delbrueckii phylogenetic group and was closely related to L. delbrueckii, Lactobacillus crispatus and Lactobacillus jensenii. However, analysis of DNA–DNA relatedness showed that DI70T was genetically distinct from its phylogenetic relatives. The isolate also exhibited distinct biochemical and physiological characteristics when compared with its phylogenetic relatives. It required anaerobic conditions for growth on agar medium. The results indicate that isolate DI70T indeed represents a novel species of the genus Lactobacillus, for which we propose the name Lactobacillus equicursoris sp. nov. The type strain is DI70T (=JCM 14600T =DSM 19284T).
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Affiliation(s)
- Hidetoshi Morita
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Mitsuharu Shimazu
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Hiroshi Shiono
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Hidehiro Toh
- RIKEN Advanced Science Institute, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Fumihiko Nakajima
- Northern Farm, 275 Hayakita-genbu, Abira-cho, Yufutsu-gun, Hokkaido 059-1432, Japan
| | - Hiroaki Akita
- Northern Farm, 275 Hayakita-genbu, Abira-cho, Yufutsu-gun, Hokkaido 059-1432, Japan
| | - Misako Takagi
- Crossfield-Bio Inc., 1-1-20 Higashi-nihonbashi, Chuo, Tokyo 103-0004, Japan
| | - Hideto Takami
- Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Masaru Murakami
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Toshio Masaoka
- School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
| | - Soichi Tanabe
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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Toh H, Hamano Y, Goto T, Utada H. Long-Term Seafloor Electromagnetic Observation in the Northwest Pacific May Detect the Vector Geomagnetic Secular Variation. Data Sci J 2010. [DOI: 10.2481/dsj.ss_igy-004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Toh H, Chen P, Carr BI, Knox JJ, Gill S, Steinberg J, Carlson DM, Qian J, Qin Q, Yong W. A phase II study of ABT-869 in hepatocellular carcinoma (HCC): Interim analysis. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.4581] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
4581 Background: ABT-869 is a novel orally active, potent and selective inhibitor of the vascular endothelial growth factor and platelet derived growth factor families of receptor tyrosine kinases. Results of an interim analysis of a phase 2 trial of ABT-869 in HCC are presented. Methods: An open-label, multicenter phase II trial (M06–879) of oral ABT-869 at 0.25 mg/kg daily in Child-Pugh A (C-PA) or QOD in Child-Pugh B (C-PB) patients (pts) until progressive disease (PD) or intolerable toxicity, is ongoing. Key eligibility criteria included unresectable or metastatic HCC; up to one prior line of systemic treatment; and at least one measurable lesion by computed tomography (CT) scan. The primary endpoint was the progression free (PF) rate at 16 weeks. Secondary endpoints included objective response rate (ORR), time to progression (TTP), progression free survival (PFS) and overall survival (OS). CT scans were assessed centrally and by the investigators; presented results are from central assessment. Results: 44 pts were enrolled from 09/07 to 08/08 at 6 centers internationally, with interim data available for 34 pts. There were 28 C-PA pts (median age, 63.5 y [range, 20- 81]) and 6 C-PB pts (median age, 64.5 y [range, 36–69]) and 73.5% received no prior systemic therapy. For the 19 evaluable C-PA pts included in the per-protocol interim analysis, 8 (42.1%) were progression free at 16 weeks [95% CI 20.3, 66.5]. The estimated ORR was 8.7% [95% CI, 1.1, 28] for the 23 C-PA pts and 0% for the 2 C-PB pts who had at least one post-baseline CT scan reviewed by central imaging. For all 34 pts, median TTP was 112 d [95% CI, 110, -], median PFS was 112 d [95% CI, 61, 168] and median OS was 295 d [95% CI, 182, 333]. The most common adverse events (AEs) for all pts were hypertension (41%), fatigue (47%), diarrhea (38%), rash (35%), proteinuria (24%), vomiting (24%), cough (24%) and oedema peripheral (24%). The most common grade 3/4 AEs for all pts were hypertension (20.6%) and fatigue (11.8%). Most AEs were mild/moderate and reversible with interruption/dose reductions/or discontinuation of ABT-869. Conclusions: ABT-869 appears to benefit HCC patients, with an estimated TTP of 112 days and an acceptable safety profile. Updated results from this ongoing study will be presented. [Table: see text]
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Affiliation(s)
- H. Toh
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - P. Chen
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - B. I. Carr
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - J. J. Knox
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - S. Gill
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - J. Steinberg
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - D. M. Carlson
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - J. Qian
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - Q. Qin
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
| | - W. Yong
- National Cancer Centre, Singapore; National Taiwan University Hospital, Taipei, Taiwan; Thomas Jefferson University, Philadelphia, PA; University of Toronto, Toronto, ON, Canada; British Columbia Cancer Agency, Vancouver, BC, Canada; Abbott Laboratories, Abbott Park, IL; National University Hospital, Singapore
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Yong W, Goh B, Toh H, Soo R, Diermayr V, Goh A, Ethirajulu K, Lee S, Seah E, Zhu J. Phase I study of SB939 three times weekly for 3 weeks every 4 weeks in patients with advanced solid malignancies. J Clin Oncol 2009. [DOI: 10.1200/jco.2009.27.15_suppl.2560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
2560 Background: SB939 is a novel orally bioavailable inhibitor of class 1 and 2 histone deacetylases. We conducted a phase I study to assess the safety, maximum tolerated dose (MTD), pharmacokinetics, pharmacodynamics and preliminary efficacy of SB939 in patients with advanced solid malignancies. Methods: SB939 was administered orally every other day 3 times a week for 3 consecutive weeks, in a 4-week cycle. Cohorts of patient were treated with escalating doses of SB939 starting from 10 mg. PK and PD (Acetylated Histone 3 in PBMCs) samples were collected in the first cycle. Results: 31 patients were enrolled at 10 mg (n=3), 20 mg (4), 40 mg (8), 60 mg (10) and 80 mg (6). The median number of treatment cycles received was 3.6. Fatigue, elevation of troponin T and QTc prolongation were the observed dose-limiting toxicities (DLT). At 80mg, one patient each (3/6) experienced a DLT of grade 3 fatigue, grade 3 asymptomatic elevation of troponin T and grade 3 QTc prolongation respectively. All DLTs were reversible and no treatment mortality was observed. Grade 1–2 fatigue occurred in 56% of patients occurring mainly at the 4th week, and 37% of pts had G1–2 anorexia. Grade 3–4 thrombocytopenia was observed in 2 patients at 60 mg at cycles 1 and 6 of treatment. SB939 was rapidly absorbed reaching Tmax between 1–3 h after ingestion, and mean elimination half-life and oral clearance of SB939 were 7.2 + 0.6 hrs and 53 + 8.5 L/h respectively. Cmax and AUC (0-∞) were dose-proportionally increased at this dose range. There was no substantial accumulation of SB939 on day 15 following repeated dosing. Concentrations above IC50 of SB939 for HDAC I was reached at all doses. Acetylation of H3 was dose dependent and consistent at 60mg. Of the 13 patients evaluable for response, stable disease was seen in 1 patient with follicular thyroid carcinoma and 1 with hepatocellular carcinoma for 51 and 164 days respectively. Conclusions: SB939 has similar toxicity profiles as that of other HDAC inhibitors and a favorable PK/PD profile. The MTD of SB939 in this regimen was 80 mg and 60mg is the recommended dose, at which acetylation of H3 is consistently observed. Further phase 2 studies with SB939 in specific indications are being planned. No significant financial relationships to disclose.
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Affiliation(s)
- W. Yong
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - B. Goh
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - H. Toh
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - R. Soo
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - V. Diermayr
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - A. Goh
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - K. Ethirajulu
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - S. Lee
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - E. Seah
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
| | - J. Zhu
- National University Health System, Singapore; National Cancer Center, Singapore; S*BIO Pte Ltd, Singapore
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Hongoh Y, Sharma VK, Prakash T, Noda S, Toh H, Taylor TD, Kudo T, Sakaki Y, Toyoda A, Hattori M, Ohkuma M. Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut. Science 2008; 322:1108-9. [PMID: 19008447 DOI: 10.1126/science.1165578] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Termites harbor diverse symbiotic gut microorganisms, the majority of which are as yet uncultivable and their interrelationships unclear. Here, we present the complete genome sequence of the uncultured Bacteroidales endosymbiont of the cellulolytic protist Pseudotrichonympha grassii, which accounts for 70% of the bacterial cells in the gut of the termite Coptotermes formosanus. Functional annotation of the chromosome (1,114,206 base pairs) unveiled its ability to fix dinitrogen and recycle putative host nitrogen wastes for biosynthesis of diverse amino acids and cofactors, and import glucose and xylose as energy and carbon sources. Thus, nitrogen fixation and cellulolysis are coupled within the protist's cells. This highly evolved symbiotic system probably underlies the ability of the worldwide pest termites Coptotermes to use wood as their sole food.
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Affiliation(s)
- Yuichi Hongoh
- Ecomolecular Biorecycling Science Research Team, RIKEN Advanced Science Institute, Saitama 351-0198, Japan.
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Morita H, Shiratori C, Murakami M, Takami H, Toh H, Kato Y, Nakajima F, Takagi M, Akita H, Masaoka T, Hattori M. Sharpea azabuensis gen. nov., sp. nov., a Gram-positive, strictly anaerobic bacterium isolated from the faeces of thoroughbred horses. Int J Syst Evol Microbiol 2008; 58:2682-6. [DOI: 10.1099/ijs.0.65543-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Oshima K, Toh H, Ogura Y, Sasamoto H, Morita H, Park SH, Ooka T, Iyoda S, Taylor TD, Hayashi T, Itoh K, Hattori M. Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult. DNA Res 2008; 15:375-86. [PMID: 18931093 PMCID: PMC2608844 DOI: 10.1093/dnares/dsn026] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We sequenced and analyzed the genome of a commensal Escherichia coli (E. coli) strain SE11 (O152:H28) recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B1. SE11 harbored a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes. None of the SE11 genes had sequence similarity to known genes encoding phage- and plasmid-borne virulence factors found in pathogenic E. coli strains. The comparative genome analysis with the laboratory strain K-12 MG1655 identified 62 poorly conserved genes between these two non-pathogenic strains and 1186 genes absent in MG1655. These genes in SE11 were mostly encoded in large insertion regions on the chromosome or in the plasmids, and were notably abundant in genes of fimbriae and autotransporters, which are cell surface appendages that largely contribute to the adherence ability of bacteria to host cells and bacterial conjugation. These data suggest that SE11 may have evolved to acquire and accumulate the functions advantageous for stable colonization of intestinal cells, and that the adhesion-associated functions are important for the commensality of E. coli in human gut habitat.
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Affiliation(s)
- Kenshiro Oshima
- Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
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Naito M, Hirakawa H, Yamashita A, Ohara N, Shoji M, Yukitake H, Nakayama K, Toh H, Yoshimura F, Kuhara S, Hattori M, Hayashi T, Nakayama K. Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis. DNA Res 2008; 15:215-25. [PMID: 18524787 PMCID: PMC2575886 DOI: 10.1093/dnares/dsn013] [Citation(s) in RCA: 202] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The gram-negative anaerobic bacterium Porphyromonas gingivalis is a major causative agent of chronic periodontitis. Porphyromonas gingivalis strains have been classified into virulent and less-virulent strains by mouse subcutaneous soft tissue abscess model analysis. Here, we present the whole genome sequence of P. gingivalis ATCC 33277, which is classified as a less-virulent strain. We identified 2090 protein-coding sequences (CDSs), 4 RNA operons, and 53 tRNA genes in the ATCC 33277 genome. By genomic comparison with the virulent strain W83, we identified 461 ATCC 33277-specific and 415 W83-specific CDSs. Extensive genomic rearrangements were observed between the two strains: 175 regions in which genomic rearrangements have occurred were identified. Thirty-five of those genomic rearrangements were inversion or translocation and 140 were simple insertion, deletion, or replacement. Both strains contained large numbers of mobile elements, such as insertion sequences, miniature inverted-repeat transposable elements (MITEs), and conjugative transposons, which are frequently associated with genomic rearrangements. These findings indicate that the mobile genetic elements have been deeply involved in the extensive genome rearrangement of P. gingivalis and the occurrence of many of the strain-specific CDSs. We also describe here a very unique feature of MITE400, which we renamed MITEPgRS (MITE of P. gingivalis with Repeating Sequences).
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Affiliation(s)
- Mariko Naito
- Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, Sakamoto 1-7-1, Nagasaki, Japan
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Hsu C, Yang T, Hsu C, Toh H, Epstein R, Hsiao L, Lin Z, Cheng A. Phase II study of bevacizumab (A) plus capecitabine (X) in patients (pts) with advanced/metastatic hepatocellular carcinoma (HCC): Final report. J Clin Oncol 2008. [DOI: 10.1200/jco.2008.26.15_suppl.4603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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