Updated on 2024/05/01

写真a

 
Takashi Koda
 
Organization
Graduate Faculty of Interdisciplinary Research Faculty of Life and Environmental Sciences Bioagronomy (Biotechnology) Professor
Title
Professor
Contact information
メールアドレス

Education

  • The University of Tokyo   Graduate School of Agricultural and Life Sciences   Department of Agricultural Biochemistry

    1986.4 - 1989.3

      More details

    Country: Japan

    Course: Doctor course

  • The University of Tokyo   Graduate School of Agricultural and Life Sciences   Department of Agricultural Biochemistry

    1984.4 - 1986.3

      More details

    Country: Japan

    Course: Master course

  • The University of Tokyo   Faculty of Agriculture   Department of Agricultural Biochemistry

    1980.4 - 1984.3

      More details

    Country: Japan

Degree

  • Doctor of Agriculture ( 1989.3   The University of Tokyo )

Research Areas

  • Life Science / Genome biology

Research Projects

  • Development of analytical method for DNA hydroxymethylcytosine and biological significance of hemi-modification of cytosine.

    2021.4 - 2024.3

    Takashi Kohda

      More details

    Authorship:Principal investigator  Type of fund::Science research expense

  • A proposal for "anti-dementia dietary habits" based on healthy longevity epigenomics that links dietary habits and cognitive function.

    2021.4 - 2024.3

      More details

    Authorship:Coinvestigator(s)  Type of fund::Science research expense

  • Development of analytical method for DNA hydroxymethylcytosine and biological significance of hemi-modification of cytosine.

    Grant number:21H02154  2021.4 - 2024.3

    Japan Society for the Promotion of Science  University of Yamanashi  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

  • 胎児期化学物質曝露による真のエピゲノム影響の評価

    2020.4 - 2022.3

    挑戦的研究(萌芽)

    三宅邦夫

      More details

    Authorship:Coinvestigator(s)  Type of fund::Science research expense

  • 精子のエピゲノム修飾と経世代変化

    2017.4 - 2020.3

    日本学術振興会  科学研究費補助金  基盤研究(B) (一般)

    幸田 尚

      More details

    Authorship:Principal investigator  Type of fund::Science research expense

  • マイクロカプセルを用いた単一細胞解像度bisulfite法の確立

    2016.4 - 2019.3

    日本学術振興会  科学研究費補助金  挑戦的萌芽研究

    幸田 尚

      More details

    Authorship:Principal investigator  Type of fund::Science research expense

  • The improvement of oocyte and ovarian function in aged infertile women.

    2016.4 - 2019.3

    AMED 

    Toshiro Kubota

      More details

    Authorship:Coinvestigator(s) 

  • Establishment of bisulfite conversion method in microcapsules for single-cell analysis.

    Grant number:16K14667  2016.4 - 2019.3

    Japan Society for the Promotion of Science  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Exploratory Research

    KOHDA Takashi

      More details

    The bisulfite method, which is an analytical technique for methyl cytosine, is an essential experimental method in epigenetics. However, since this reaction requires a high temperature reaction under acidic conditions, DNA cleavage occurs simultaneously with the conversion reaction. Therefore, analysis from a small amount of material was difficult. In this study, an experimental system was established in which a small amount of DNA or cells were encapsulated in alginate microcapsules, bisulfite treatment and subsequent PCR amplification were performed. This method makes it possible to handle the bisulfite treatment of trace amounts of samples much more easily and reliably, that has been previously difficult.

  • The effects of the intracytoplasmic sperm injection on the gene expression regulation in the human preimplantation embryo.

    Grant number:24310141  2012.4 - 2015.3

    Japan Society for the Promotion of Science  Tokyo Medical and Dental University  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    KOHDA Takashi, KUBOTA Toshiro, TSUTSUMI Osamu

      More details

    The application of the in vitro fertilization (IVF) in assisted reproductive technology has been increased since its first introduction. Recently, the intracytoplasmic sperm injection (ICSI) technique is used in about half of the IVF cases in Japan.
    The aim of this study is to evaluate the effects of ICSI on the transcription regulation in human early development and to improve the ICSI method. First, we successfully established the RNA amplification protocol for single embryo RNA-seq analysis using T7 RNA polymerase. Then we analyzed the gene expression profile of the human blastocysts that were not transferred in assisted reproductive technologies. As the results, we identified the genes that affected their expression by ICSI procedure. These genes expected to be the useful markers to improve the ICSI technique.

  • Establishment of a novel method to identify the hydroxymethylcytosine in single base resolution.

    Grant number:24651210  2012.4 - 2014.3

    Japan Society for the Promotion of Science  Tokyo Medical and Dental University  Grants-in-Aid for Scientific Research  Grant-in-Aid for Challenging Exploratory Research

    KOHDA Takashi

      More details

    DNA methylation is one of the important modifications in epigenetic regulation of mammalian genome system. Recently, the oxidation reaction of methylcytosine to hydroxymethylcytosine is discovered. Thus, it is important to establish a method to identify the hydroxymethylcytosine of the genome in single base resolution. Here I provide a novel method to identify the methylcytosine and the hydroxymethylcytosine with high accuracy (more than 95%) using DNMT1 enzyme.

  • Role of mammalian-specific genes related to genomic imprinting in mammalian development and evolution

    Grant number:18GS0315  2006 - 2010

    Japan Society for the Promotion of Science  Tokyo Medical and Dental University  Grants-in-Aid for Scientific Research  Grant-in-Aid for Creative Scientific Research

    ISHINO Fumitoshi, KANEKO Tomoko, KOHDA Takashi, ONO Ryuichi

      More details

    Sushi-ichi retrotransposon-derived genes (Sirh family genes) are mammalian-specific genes. Among them, we have previously reported that Peg10 and Peg11/Rtl1 play essential roles in placenta formation and function. In this project, we have produced knockout mice of each gene and demonstrated that Sirh7 has mammalian-specific functions concerning implantation and pregnancy as well as placenta formation. Our systematic analysis suggests that other Sirh genes also have such functions.

  • Functional analysis of imprinted gene Peg3.

    Grant number:13680909  2001 - 2002

    Japan Society for the Promotion of Science  Tokyo Institute of Technology  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (C)

    KOHDA Takashi

      More details

    Mouse Peg3 is an imprinted gene exclusively express from paternal allele. This gene encodes C2H2 type zinc finger motif containing protein and known to have important roles in nursing behavior in mice, tumor progression in and cell apoptosis.
    To elucidate the biochemical function of Peg3, we have screened the Peg3 binding proteins using yeast two-hybrid system. Through the screening of mouse brain cDNAs by GAL4 fused Peg3 as bait, 10 candidate gene were isolated from 4x16^6 cDNA clones. These candidate cDNAs were fused with Flag-tag and expressed with Myc-tagged Peg3 in HeLa cells. One of the candidates was proved to bind in vivo with Peg3 by immuno-precipitation followed by western blotting. The cDNA clone encodes near full-length coding region of adopter protein 14-3-3 eta.
    Re-examining the amino acids sequence of the Peg3, we found a consensus motif for 14-3-3 binding in the N-terminal part of Peg3 protein. It is also proved that the binding activity was destroyed when the serine residue within the motif changed to alanine by site directed mutagenesis.
    Until now, we couldn't proof the Peg3 binding activity of other candidate cDNA clones in vivo because of the insulubility of the protein in Hela cells.

  • Biological significance of genomic Imprinting

    Grant number:08458216  1996 - 1998

    Japan Society for the Promotion of Science  TOKYO INSTITUTE OF TECHNOLOGY  Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

    ISHINO Fumitoshi, KOHDA Takashi

      More details

    Genomic imprinting plays an essential role on mammalian development, growth and behavior. Functional difference between paternal and maternal genomes are thought to be attributable to two kinds of imprinted genes, Peg (paternally expressed genes) and Meg (maternally expressed genes).
    We have isolated novel Pegs and Megs systematically using a newly developed subtraction-hybridization method. Pegs have been screened by subtraction between normal fertilized embryos and parthenogenetic embryos that have only maternal genomes and Megs by subtraction between normal embryos and androgenetic embryos that have only paternal genomes. So far 13 imprinted genes including 9 novel ones have been obtained. Mapping of these imprinted genes demonstrated that they all located in the previously estimated imprinted regions in the mouse predicted by genetical study, indicating that varieties of imprinting effects including some human genetic diseases were caused by lack and/or overproduction of the imprinted genes, Pegs and Megs.
    Systematic analysis on expression sites of these genes revealed that all imprinted genes so far examined were commonly expressed in placental tissues including yolk sac tissues. We proposed a novel placenta hypothesis that genomic imprinting is the mechanism of gene expression that enabled a group of the imprinted genes to be expressed in the placental tissues. Thus, this mechanise plays an important role for mammalian development at present and also might be essential for evolution of mammalian group from, ancestor animals.

▼display all

Papers

  • Effect of microgravity on mammalian embryo development evaluated at the International Space Station Reviewed

    Sayaka Wakayama, Yasuyuki Kikuchi, Mariko Soejima, Erika Hayashi, Natsuki Ushigome, Chiaki Yamazaki, Tomomi Suzuki, Toru Shimazu, Tohru Yamamori, Ikuko Osada, Hiromi Sano, Masumi Umehara, Ayumi Hasegawa, Keiji Mochida, Li Ly Yang, Rina Emura, Kousuke Kazama, Kenta Imase, Yuna Kurokawa, Yoshimasa Sato, Akira Higashibata, Hitomi Matsunari, Hiroshi Nagashima, Atsuo Ogura, Takashi Kohda, Teruhiko Wakayama

    iScience   26 ( 11 )   108177 - 108177   2023.10

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Mammalian embryos differentiate into the inner cell mass (ICM) and trophectoderm at the 8-16 cell stage. The ICM forms a single cluster that develops into a single fetus. However, the factors that determine differentiation and single cluster formation are unknown. Here we investigated whether embryos could develop normally without gravity. As the embryos cannot be handled by an untrained astronaut, a new device was developed for this purpose. Using this device, two-cell frozen mouse embryos launched to the International Space Station were thawed and cultured by the astronauts under microgravity for 4 days. The embryos cultured under microgravity conditions developed into blastocysts with normal cell numbers, ICM, trophectoderm, and gene expression profiles similar to those cultured under artificial-1 g control on the International Space Station and ground-1 g control, which clearly demonstrated that gravity had no significant effect on the blastocyst formation and initial differentiation of mammalian embryos.

    DOI: 10.1016/j.isci.2023.108177

    PubMed

  • Paternally inherited H3K27me3 affects chromatin accessibility in mouse embryos produced by round spermatid injection Reviewed

    Mizuki Sakamoto, Daiyu Ito, Rei Inoue, Sayaka Wakayama, Yasuyuki Kikuchi, Li Yang, Erika Hayashi, Rina Emura, Hirosuke Shiura, Takashi Kohda, Satoshi H Namekawa, Takashi Ishiuchi, Teruhiko Wakayama, Masatoshi Ooga

    DEVELOPMENT   149 ( 18 )   dev200696   2022.9( ISSN:0950-1991 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

  • PEG10 viral aspartic protease domain is essential for the maintenance of fetal capillary structure in the mouse placenta. Reviewed

    Shiura H, Ono R, Tachibana S, Kohda T, Kaneko-Ishino T, Ishino F.

    DEVELOPMENT   148 ( 19 )   dev199564   2021.10( ISSN:0950-1991 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    The therian-specific gene paternally expressed 10 (Peg10) plays an essential role in placenta formation: Peg10 knockout mice exhibit early embryonic lethality as a result of severe placental defects. The PEG10 protein exhibits homology with long terminal repeat (LTR) retrotransposon GAG and POL proteins; therefore, we generated mice harboring a mutation in the highly conserved viral aspartic protease motif in the POL-like region of PEG10 because this motif is essential for the life cycle of LTR retrotransposons/retroviruses. Intriguingly, frequent perinatal lethality, not early embryonic lethality, was observed with fetal and placental growth retardation starting mid-gestation. In the mutant placentas, severe defects were observed in the fetal vasculature, where PEG10 is expressed in the three trophoblast cell layers that surround fetal capillary endothelial cells. Thus, Peg10 has essential roles, not only in early placenta formation, but also in placental vasculature maintenance from mid- to late-gestation. This implies that along the feto-maternal placenta interface an interaction occurs between two retrovirus-derived genes, Peg10 and retrotransposon Gag like 1 (Rtl1, also called Peg11), that is essential for the maintenance of fetal capillary endothelial cells.

    DOI: 10.1242/dev.199564

    PubMed

  • AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation. Reviewed

    Sekita Y, Sugiura Y, Matsumoto A, Kawasaki Y, Akasaka K, Konno R, Shimizu M, Ito T, Sugiyama E, Yamazaki T, Kanai E, Nakamura T, Suematsu M, Ishino F, Kodera Y, Kohda T, Kimura T.

    Stem Cell Research & Therapy   12 ( 1 )   510   2021.9

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1186/s13287-021-02578-1

  • Evaluating the long-term effect of space radiation on the reproductive normality of mammalian sperm preserved on the International Space Station. Reviewed

    Wakayama S, Ito D, Kamada Y, Shimazu T, Suzuki T, Nagamatsu A, Araki R, Ishikawa T, Kamimura S, Hirose N, Kazama K, Yang L, Inoue R, Kikuchi Y, Hayashi E, Emura R, Watanabe R, Nagatomo H, Suzuki H, Yamamori T, Tada MN, Osada I, Umehara M, Sano H, Kasahara H, Higashibata A, Yano S, Abe M, Kishigami S, Kohda T, Ooga M, Wakayama T.

    Science Advances   7 ( 24 )   eabg5554 - eabg5554   2021.6( ISSN:2375-2548  eISSN:2375-2548 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Association for the Advancement of Science (AAAS)  

    Space radiation may cause DNA damage to cells and concern for the inheritance of mutations in offspring after deep space exploration. However, there is no way to study the long-term effects of space radiation using biological materials. Here, we developed a method to evaluate the biological effect of space radiation and examined the reproductive potential of mouse freeze-dried spermatozoa stored on the International Space Station (ISS) for the longest period in biological research. The space radiation did not affect sperm DNA or fertility after preservation on ISS, and many genetically normal offspring were obtained without reducing the success rate compared to the ground-preserved control. The results of ground x-ray experiments showed that sperm can be stored for more than 200 years in space. These results suggest that the effect of deep space radiation on mammalian reproduction can be evaluated using spermatozoa, even without being monitored by astronauts in Gateway.

    DOI: 10.1126/sciadv.abg5554

  • Promoter CpG methylation inhibits Krüppel-like factor 2 (KLF2)-Mediated repression of hTERT gene expression in human T-cells Reviewed

    Mariko Mizuguchi, Toshifumi Hara, Manami Yoshita-Takahashi, Takashi Kohda, Yuetsu Tanaka, Masataka Nakamura

    Biochemistry and Biophysics Reports   26   100984 - 100984   2021.3( ISSN:2405-5808 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Elsevier BV  

    DOI: 10.1016/j.bbrep.2021.100984

  • Ascorbic acid during the suckling period is required for proper DNA demethylation in the liver Reviewed

    Kenichi Kawahori, Yoshitaka Kondo, Xunmei Yuan, Yuki Kawasaki, Nozomi Hanzawa, Kazutaka Tsujimoto, Fumiko Wada, Takashi Kohda, Akihito Ishigami, Tetsuya Yamada, Yoshihiro Ogawa, Koshi Hashimoto

    Scientific Reports   10 ( 1 )   21228 - 21228   2020.12( ISSN:2045-2322 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Ascorbic acid (AA, vitamin C) serves as a cofactor for ten-eleven translocation (TET) enzymes and induces DNA demethylation in vitro. However, its role in DNA demethylation in vivo remains unclear. We previously reported that DNA demethylation in the mouse liver was enhanced during the suckling period. Therefore, we hypothesized that DNA demethylation is enhanced in an AA-dependent manner during the suckling period. To examine our hypothesis, we employed wild-type (WT) mice, which synthesize AA, and senescence marker protein-30/gluconolactonase (SMP30/GNL) knockout (KO) mice, which cannot synthesize AA, and analyzed the DNA methylation status in the livers of offspring in both the suckling period and adulthood. SMP30/GNL KO offspring showed DNA hypermethylation in the liver possibly due to low plasma and hepatic AA levels during the suckling period despite the administration of rescue-dose AA to dams. Furthermore, DNA hypermethylation of the fibroblast growth factor 21 gene (Fgf21), a PPARα target gene, persisted into adulthood. In contrast, a high-dose AA administration to SMP30/GNL KO dams during the lactation period restored DNA demethylation in the livers of offspring. Even though a slight increase was observed in plasma AA levels with the administration of rescue-dose AA to WT dams during the gestation and lactation periods, DNA demethylation in the livers of offspring was minimally enhanced. The present results demonstrate that AA intake during the suckling period is required for proper DNA demethylation in the liver.

    DOI: 10.1038/s41598-020-77962-7

    PubMed

  • In vitro generation of functional murine heart organoids via FGF4 and extracellular matrix Reviewed

    Jiyoung Lee, Akito Sutani, Rin Kaneko, Jun Takeuchi, Tetsuo Sasano, Takashi Kohda, Kensuke Ihara, Kentaro Takahashi, Masahiro Yamazoe, Tomohiro Morio, Tetsushi Furukawa, Fumitoshi Ishino

    Nature Communications   11 ( 1 )   4283 - 4283   2020.9( ISSN:2041-1723 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Our understanding of the spatiotemporal regulation of cardiogenesis is hindered by the difficulties in modeling this complex organ currently by in vitro models. Here we develop a method to generate heart organoids from mouse embryonic stem cell-derived embryoid bodies. Consecutive morphological changes proceed in a self-organizing manner in the presence of the laminin-entactin (LN/ET) complex and fibroblast growth factor 4 (FGF4), and the resulting in vitro heart organoid possesses atrium- and ventricle-like parts containing cardiac muscle, conducting tissues, smooth muscle and endothelial cells that exhibited myocardial contraction and action potentials. The heart organoids exhibit ultrastructural, histochemical and gene expression characteristics of considerable similarity to those of developmental hearts in vivo. Our results demonstrate that this method not only provides a biomimetic model of the developing heart-like structure with simplified differentiation protocol, but also represents a promising research tool with a broad range of applications, including drug testing.

    DOI: 10.1038/s41467-020-18031-5

    PubMed

  • NELL2-mediated lumicrine signaling through OVCH2 is required for male fertility Reviewed

    Daiji Kiyozumi, Taichi Noda, Ryo Yamaguchi, Tomohiro Tobita , Takafumi Matsumura, Kentaro Shimada, Mayo Kodani, Takashi Kohda, Yoshitaka Fujihara, Manabu Ozawa, Zhifeng Yu, Gabriella Miklossy, Kurt M Bohren, Masato Horie, Masaru Okabe, Martin M Matzuk, Masahito Ikawa

    SCIENCE   368 ( 6495 )   1132 - 1135   2020.6( ISSN:0036-8075 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    The lumicrine system is a postulated signaling system in which testis-derived (upstream) secreted factors enter the male reproductive tract to regulate epididymal (downstream) pathways required for sperm maturation. Until now, no lumicrine factors have been identified. We demonstrate that a testicular germ-cell-secreted epidermal growth factor-like protein, neural epidermal growth factor-like-like 2 (NELL2), specifically binds to an orphan receptor tyrosine kinase, c-ros oncogene 1 (ROS1), and mediates the differentiation of the initial segment (IS) of the caput epididymis. Male mice in which Nell2 had been knocked out were infertile. The IS-specific secreted proteases, ovochymase 2 (OVCH2) and A disintegrin and metallopeptidase 28 (ADAM28), were expressed upon IS maturation, and OVCH2 was required for processing of the sperm surface protein ADAM3, which is required for sperm fertilizing ability. This work identifies a lumicrine system essential for testis-epididymis-spermatozoa (NELL2-ROS1-OVCH2-ADAM3) signaling and male fertility.

    DOI: 10.1126/science.aay5134

    PubMed

  • ELAVL2-directed RNA Regulatory Network Drives the Formation of Quiescent Primordial Follicles Reviewed

    Yuzuru Kato, Tokuko Iwamori, Youichirou Ninomiya, Takashi Kohda, Jyunko Miyashita, Mikiko Sato, Yumiko Saga

    EMBO REPORTS   20 ( 12 )   e48251   2019.12( ISSN:1469-221X )

     More details

    Language:English  

    DOI: 10.15252/embr.201948251

    PubMed

  • Paternal Knockout of Slc38a4/SNAT4 Causes Placental Hypoplasia Associated With Intrauterine Growth Restriction in Mice Reviewed

    Shogo Matoba, Shoko Nakamuta, Kento Miura, Michiko Hirose, Hirosuke Shiura, Takashi Kohda, Nobuaki Nakamuta, Atsuo Ogura

    PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   116 ( 42 )   21047 - 21053   2019.10( ISSN:0027-8424 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    The placenta is critical in mammalian embryonic development because the embryo's supply of nutrients, including amino acids, depends solely on mother-to-embryo transport through it. However, the molecular mechanisms underlying this amino acid supply are poorly understood. In this study, we focused on system A amino acid transporters Slc38a1/SNAT1, Slc38a2/SNAT2, and Slc38a4/SNAT4, which carry neutral, short-side-chain amino acids, to determine their involvement in placental or embryonic development. A triple-target CRISPR screen identified Slc38a4/SNAT4 as the critical amino acid transporter for placental development in mice. We established mouse lines from the CRISPR founders with large deletions in Slc38a4 and found that, consistent with the imprinted paternal expression of Slc38a4/SNAT4 in the placenta, paternal knockout (KO) but not maternal KO of Slc38a4/SNAT4 caused placental hypoplasia associated with reduced fetal weight. Immunostaining revealed that SNAT4 was widely expressed in differentiating cytotrophoblasts and maturing trophoblasts at the maternal-fetal interface. A blood metabolome analysis revealed that amino acid concentrations were globally reduced in Slc38a4/SNAT4 mutant embryos. These results indicated that SNAT4-mediated amino acid transport in mice plays a major role in placental and embryonic development. Given that expression of Slc38a4 in the placenta is conserved in other species, our Slc38a4/SNAT4 mutant mice could be a promising model for the analysis of placental defects leading to intrauterine growth restriction in mammals.

    DOI: 10.1073/pnas.1907884116

    PubMed

  • Cellulomonas algicola Sp. Nov., an Actinobacterium Isolated From a Freshwater Alga Reviewed

    Yamamura H, Hayashi T, Hamada M, Kohda T, Serisawa Y, Matsuyama-Serisawa K, Nakagawa Y, Otoguro M, Yanagida F, Tamura T, Hayakawa M.

    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY   69 ( 9 )   2723 - 2728   2019.9( ISSN:1466-5026 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1099/ijsem.0.003549.

  • Identification of genes and pathways, including the CXCL2 axis, altered by DNA methylation in hepatocellular carcinoma. Reviewed

    Subat S, Mogushi K, Yasen M, Kohda T, Ishikawa Y, Tanaka H.

    JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY   145 ( 3 )   675 - 684   2019.3( ISSN:0171-5216 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)  

    Recent genetic studies have suggested that tumor suppressor genes are often silenced during carcinogenesis via epigenetic modification caused by methylation of promoter CpG islands. Here, we characterized genes inactivated by DNA methylation in human hepatocellular carcinoma (HCC) to identify the genes and pathways involved in DNA methylation in hepatocellular carcinoma.
    We identified CXCL2, an immune-related chemokine, decreased in hepatocellular carcinoma and the regulation mechanism may be controlled by methylation. Further studies should be warranted to examine if and to what extent the gene is actually suppressed by methylation and if there is a possibility that the CXCL2 axis plays a role for diagnosis and treatment of hepatocellular carcinoma.

    DOI: 10.1007/s00432-018-2824-0

    PubMed

  • Female mice lacking Ftx lncRNA exhibit impaired X-chromosome inactivation and a microphthalmia-like phenotype. Reviewed

    Hosoi Y, Soma M, Shiura H, Sado T, Hasuwa H, Abe K, Kohda T, Ishino F, Kobayashi S.

    Nature Communications   9 ( 1 )   1 - 13   2018.10( ISSN:2041-1723 )

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Springer Nature America, Inc  

    X-chromosome inactivation (XCI) is an essential epigenetic process in female mammalian development. Although cell-based studies suggest the potential importance of the Ftx long non-protein-coding RNA (lncRNA) in XCI, its physiological roles in vivo remain unclear. Here we show that targeted deletion of X-linked mouse Ftx lncRNA causes eye abnormalities resembling human microphthalmia in a subset of females but rarely in males. This inheritance pattern cannot be explained by X-linked dominant or recessive inheritance, where males typically show a more severe phenotype than females. In Ftx-deficient mice, some X-linked genes remain active on the inactive X, suggesting that defects in random XCI in somatic cells cause a substantially female-specific phenotype. The expression level of Xist, a master regulator of XCI, is diminished in females homozygous or heterozygous for Ftx deficiency. We propose that loss-of-Ftx lncRNA abolishes gene silencing on the inactive X chromosome, leading to a female microphthalmia-like phenotype.

    DOI: 10.1038/s41467-018-06327-6

    Web of Science

  • Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice. Reviewed

    Sasaki N, Katagiri S, Komazaki R, Watanabe K, Maekawa S, Shiba T, Udagawa S, Takeuchi Y, Ohtsu A, Kohda T, Tohara H, Miyasaka N, Hirota T, Tamari M, Izumi Y.

    Frontiers in Microbiology   24 ( 9 )   1 - 16   2018.10( ISSN:1664-302X )

     More details

    Language:English   Publishing type:Research paper (scientific journal)   Publisher:FRONTIERS MEDIA SA  

    Many risk factors related to the development of non-alcoholic fatty liver disease (NAFLD) have been proposed, including the most well-known of diabetes and obesity as well as periodontitis. As periodontal pathogenic bacteria produce endotoxins, periodontal treatment can result in endotoxemia. The aim of this study was to investigate the effects of intravenous, sonicated Porphyromonas gingivalis (Pg) injection on glucose/lipid metabolism, liver steatosis, and gut microbiota in mice. Endotoxemia was induced in C57BL/6J mice (8 weeks old) by intravenous injection of sonicated Pg; Pg was deactivated but its endotoxin remained. The mice were fed a high-fat diet and administered sonicated Pg (HFPg) or saline (HFco) injections for 12 weeks. Liver steatosis, glucose metabolism, and gene expression in the liver were evaluated. 16S rRNA gene sequencing with metagenome prediction was performed on the gut microbiota. Overall, intravenous injection of sonicated Pg caused impaired glucose tolerance, insulin resistance, and liver steatosis in mice fed high-fat diets. Thus, blood infusion of Pg contributes to NAFLD and alters the gut microbiota.

    DOI: 10.3389/fmicb.2018.02470

    Web of Science

▼display all

Presentations

  • Simultaneous analysis of hydroxymethylcytosine and methylcytosine.

    Takashi Kohda

    MBSJ2021  2021.12 

     More details

    Event date: 2021.12

    Language:Japanese   Presentation type:Poster presentation  

  • ooperative interaction between two retrovirus-derived genes, Peg10 and Peg11/Rtl1, in the feto-materal interface of placenta.

    MBSJ2021  2021.12 

     More details

    Event date: 2021.12

    Language:Japanese   Presentation type:Oral presentation(general)  

  • Involvement of retrotransposon/virus-derived PEG10 gene in mammalian development and evolution.

    MBSJ2021  2021.12 

     More details

    Event date: 2021.12

    Language:Japanese   Presentation type:Poster presentation  

  • LTRレトロトランスポゾン由来の真獣類特異的Sirh3/Ldoc1l遺伝子は行動性を制御する(2)

    金児-石野 知子、入江 将仁、伊東 丈夫、高安 直子、立花 沙織、石田 紗恵子、田中 光一、幸田 尚、石野 史敏

    第42回日本分子生物学会年会  2019.12 

     More details

    Event date: 2019.12

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • マウスES細胞を用いた心臓オルガノイド作製

    李 知英、酢谷 明人、金子 凜、笹野 哲郎、幸田 尚、古川 哲史、石野 史敏

    第42回日本分子生物学会年会  2019.12 

     More details

    Event date: 2019.12

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • iPS細胞誘導過程での、Aktシグナルによるエピジェネティックリプログラミングの促進

    関田 洋一、杉浦 悠毅、松元 愛香里、川崎 佑季、伊藤 駿瑛、赤坂 和哉、山崎 瑛司、紺野 亮、中村 肇伸、石野 史敏、小寺 義男、幸田 尚、木村 透

    第42回日本分子生物学会年会  2019.12 

     More details

    Event date: 2019.12

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • ヒドロキシメチルシトシンとメチルシトシンのゲノムワイド解析

    幸田 尚、渡邉 裕貴、志浦 寛相

    第42回日本分子生物学会年会  2019.12 

     More details

    Event date: 2019.12

    Language:Japanese   Presentation type:Poster presentation  

    Venue:福岡  

  • Aktシグナルは、 iPS細胞誘導過程で、転写と代謝のシフトを介してエピジェネティックリプログラミングを促進する

    関田 洋一、杉浦 悠毅、松元 愛香里、川崎 佑季、伊藤 駿瑛、赤坂 和哉、山崎 瑛司、紺野 亮、中村 肇伸 、石野 史敏、小寺 義男、幸田 尚、木村 透

    第41回日本分子生物学会年会  2018.11 

     More details

    Event date: 2018.11

    Language:Japanese   Presentation type:Poster presentation  

    Venue:パシフィコ横浜  

  • 両親年齢が配偶子形成から受精後の遺伝子発現調節に及ぼす影響 Invited

    幸田 尚

    第41回日本分子生物学会年会  2018.11 

     More details

    Event date: 2018.11

    Language:Japanese   Presentation type:Symposium workshop panel(nominated)  

    Venue:パシフィコ横浜  

    受精から着床までの初期発生の時期はゲノムのエピジェネティックな状態がダイナミックに変化するステージである。配偶子の成熟過程において年齢をはじめとする両親の生理的な条件がゲノムのエピジェネティック修飾に影響を及ぼし、世代を超えて受精後もその影響を残すのかということも重要な問題である。そこで我々はヒト胚盤胞期胚の遺伝子発現を、単一胚ごとにRNA-seqによって解析を行ってきた。その結果多くの遺伝子の発現変動と相関を示したのは母親年齢・父親年齢であった。特に、母親年齢の上昇に従って発現が低下する遺伝子の中に、PTTG1、AURKC、SMC1B、CENPW、MEIKINといった減数分裂時の染色体分配に重要な遺伝子が含まれていることが明らかとなった。このことは、胚盤胞期の遺伝子発現が生殖細胞の成立時期の親の生理的状態の影響をエピジェネティックな調節を介して強く受け、その変化が受精を経て次の世代に伝わる可能性を示唆している。

▼display all

Teaching Experience (On-campus)

  • Seminar on Bioscience A

    2023Year

  • Research on Bioscience A

    2023Year

  • Bioinformatics Major achievement

    2023Year

  • Technical English I Major achievement

    2023Year

  • Advanced Lecture on Genome Science Major achievement

    2023Year

  • Bioengineering Experiment II

    2023Year

  • Experiments in Molecular Biology Major achievement

    2023Year

▼display all

Teaching Experience

  • Bioinformatics

    2018.4
    Institution:University of Yamanashi

Guidance results

  • 2023

    Type:Master's (Major B course)dissertations guidance

    Number of people receiving guidance :2people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :2people  (Overseas students):0people

    Number of teachers:2people

  • 2023

    Type:Undergraduate (Major A course)graduation thesis guidance

    Number of people receiving guidance :4people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :4people 

    Number of teachers:2people

  • 2022

    Type:Undergraduate (Major A course)graduation thesis guidance  Period:12months

    Number of people receiving guidance :1people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :0people  (Overseas students):0people

    Number of teachers:2people

  • 2022

    Type:Master's (Major B course)dissertations guidance

    Number of people receiving guidance :4people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :0people  (Overseas students):0people

    Number of teachers:2people

  • 2021

    Type:Undergraduate (Major A course)graduation thesis guidance

    Number of people receiving guidance :4people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :3people  (Overseas students):0people

    Number of teachers:2people

  • 2021

    Type:Master's (Major B course)dissertations guidance

    Number of people receiving guidance :2people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :0people  (Overseas students):0people

    Number of teachers:2people

  • 2020

    Type:Undergraduate (Major A course)graduation thesis guidance

    Number of people receiving guidance :3people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :1people  (Overseas students):0people

    Number of teachers:2people

  • 2020

    Type:Master's (Major B course)dissertations guidance

    Number of people receiving guidance :3people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :1people  (Overseas students):0people

    Number of teachers:2people

  • 2019

    Type:Undergraduate (Major A course)graduation thesis guidance

    Number of people receiving guidance :3people 

  • 2019

    Type:Master's (Major B course)dissertations guidance

    Number of people receiving guidance :1people 

  • 2018

    Type:Undergraduate (Major A course)graduation thesis guidance

    Number of people receiving guidance :2people  (Overseas students):0people

    Graduation / pass / number of people awarded degrees :2people  (Overseas students):0people

    Number of teachers:2people

▼display all

Teaching achievements

  • 令和元年度第3回生命環境学域FD研修会
    Moodleの利用について‐実例紹介‐

    2020.02.13

Review of master's and doctoral thesis

  • 2022

    Examiner classification:Chief examiner

    Master :1people  (Overseas student):0people

    Doctoral :0people  (Overseas student):0people

    Thesis Dr. :0people  (Overseas student):0people

  • 2022

    Examiner classification:Second reader

    Master :3people  (Overseas student):0people

    Doctoral :1people  (Overseas student):0people

    Thesis Dr. :0people  (Overseas student):0people

  • 2021

    Examiner classification:Second reader

    Doctoral :1people 

  • 2021

    Examiner classification:Second reader

    Master :5people 

  • 2020

    Examiner classification:Second reader

    Master :5people  (Overseas student):0people

    Doctoral :2people  (Overseas student):0people

    Thesis Dr. :0people  (Overseas student):0people

  • 2019

    Examiner classification:Second reader

    Master :2people 

    Doctoral :0people 

    Thesis Dr. :0people 

  • 2018

    Examiner classification:Second reader

    Master :2people  (Overseas student):0people

    Doctoral :0people  (Overseas student):0people

    Thesis Dr. :0people  (Overseas student):0people

▼display all

Social Activities

  • ゲノムインプリンティングの機構と個体発生

    Role(s): Lecturer

    農林水産省生産局  中央畜産技術研修会(畜産新技術A・B)  2022.10

  • ゲノムインプリンティングの機構と個体発生

    Role(s): Lecturer

    農林水産省生産局  中央畜産技術研修会(畜産新技術A・B)  2021.10

     More details

    Audience: Researchesrs

    Type:Lecture

  • ゲノムインプリンティングの機構と個体発生

    Role(s): Lecturer

    農林水産省生産局  中央畜産技術研修会 畜産新技術A・B  2020.10

     More details

    Audience: Researchesrs

    Type:Lecture

  • ゲノムインプリンティングの機構と個体発生

    Role(s): Lecturer

    農林水産省生産局  中央畜産技術研修会 畜産新技術A・B  2019.10

     More details

    Audience: Researchesrs

    Type:Lecture

  • 第 10 回山梨大学教育学部附属中学校「若桐講座」

    Role(s): Lecturer

    山梨大学教育学部附属中学校  2019.8

     More details

    Audience: Junior students

    Type:Visiting lecture

  • 山梨大学FUTURE SEED <山梨大学生命環境学部>

    FM富士  FM-FUJI『GOOD DAY』山梨大学FUTURE SEED  2019.3

     More details

    Audience: General

    Type:TV or radio program

  • ゲノムインプリンティングの機構と個体発生

    Role(s): Lecturer

    農林水産省  独立行政法人家畜改良センター中央畜産研修施設  2018.10

     More details

    Audience: Researchesrs, Governmental agency

    Type:Seminar, workshop

▼display all