Updated on 2024/03/28

写真a

 
KOBAYASHI Daiki
 
Organization
Academic Assembly Institute of Medicine and Dentistry IGAKU KEIRETU Assistant Professor
Graduate School of Medical and Dental Sciences Molecular and Cellular Medicine Molecular Genetics Assistant Professor
Title
Assistant Professor
External link

Degree

  • 博士(農学) ( 2006.3   九州大学 )

Research Interests

  • プロテオミクス

  • 分子生物学

  • 生化学

Research Areas

  • Life Science / Pathological biochemistry

  • Life Science / Applied biochemistry

  • Life Science / Molecular biology

  • Life Science / Functional biochemistry

Research History (researchmap)

  • 新潟大学医歯学系   システム生化学分野   助教

    2020.1

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    Country:Japan

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  • Kumamoto University   Faculty of Life Sciences   Specially Appointed Assistant Professor

    2015.9 - 2019.12

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  • Kumamoto University   Faculty of Life Sciences

    2010.1 - 2015.8

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  • 熊本大学大学院医学薬学研究部   博士研究員

    2006.4 - 2009.12

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Research History

  • Niigata University   Graduate School of Medical and Dental Sciences Molecular and Cellular Medicine Molecular Genetics   Assistant Professor

    2020.1

Education

  • Kyushu University   生物資源環境科学研究科   博士過程

    2003.4 - 2006.3

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  • Kyushu University   生物資源環境科学研究科   修士課程

    2001.4 - 2003.3

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    Country: Japan

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  • Kyushu University   School of Agriculture   農芸化学科

    1997.4 - 2001.3

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    Country: Japan

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Professional Memberships

Committee Memberships

  • 日本プロテオーム学会   理事  

    2021.1   

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  •   Journal of Proteome Data and Methods, Editorial Broad Member  

    2021.1   

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  •   Proteome letters, 編集委員  

    2021.1   

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Papers

  • Chondroitin sulfate modification of CSPG4 regulates the maintenance and differentiation of glioma-initiating cells via integrin-associated signaling Reviewed

    Akiko Niibori-Nambu, Yoshimune Yamasaki, Daiki Kobayashi, Kiyohiko Angata, Atsushi Kuno, Orasa Panawan, Atit Silsirivanit, Hisashi Narimatsu, Norie Araki

    Journal of Biological Chemistry   300 ( 3 )   105706 - 105706   2024.3

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

    DOI: 10.1016/j.jbc.2024.105706

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  • AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells. Reviewed International journal

    Takao Kitagawa, Daiki Kobayashi, Byron Baron, Hajime Okita, Tatsuo Miyamoto, Rie Takai, Durga Paudel, Tohru Ohta, Yoichi Asaoka, Masayuki Tokunaga, Koji Nakagawa, Makoto Furutani-Seiki, Norie Araki, Yasuhiro Kuramitsu, Masanobu Kobayashi

    PloS one   17 ( 10 )   e0269077   2022.10

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

    Ewing's sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewing's sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.

    DOI: 10.1371/journal.pone.0269077

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  • SPP1 Derived from Macrophages Is Associated with a Worse Clinical Course and Chemo-Resistance in Lung Adenocarcinoma Reviewed

    Eri Matsubara, Yoshihiro Komohara, Shigeyuki Esumi, Yusuke Shinchi, Shiho Ishizuka, Remi Mito, Cheng Pan, Hiromu Yano, Daiki Kobayashi, Yukio Fujiwara, Koei Ikeda, Takuro Sakagami, Makoto Suzuki

    Cancers   14 ( 18 )   4374 - 4374   2022.9

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    Publishing type:Research paper (scientific journal)   Publisher:MDPI AG  

    Osteopontin, also called secreted phosphoprotein 1 (SPP1), is a multifunctional secreted phosphorylated glycoprotein. SPP1 is also expressed in tumor cells, and many studies demonstrated that a high level of circulating SPP1 is correlated with a poor prognosis in various cancers. SPP1 is expressed not only by tumor cells but also by stromal cells, such as macrophages. However, there have been no studies distinguishing the SPP1 expression of cancer cells and tumor-associated macrophages (TAMs). Thus, in this study, we tried to accurately evaluate the SPP1 expression status on cancer cells and TAMs separately in patients with non-small cell lung cancer by using double immunohistochemistry. We demonstrated that high SPP1 expression on TAMs predicted a poor prognosis in lung adenocarcinoma patients. Additionally, we investigated the expression mechanisms related to SPP1 using human-monocyte-derived macrophages and revealed that the SPP1 expression level increased in macrophage differentiation mediated by granulocyte-macrophage colony-stimulating factor. Furthermore, SPP1 contributed to anti-cancer drug resistance in lung cancer cell lines. In conclusion, SPP1 production on TAMs predicted a poor prognosis in lung adenocarcinoma patients, and TAM-derived SPP1′s involvement in the chemo-resistance of cancer cells was suggested.

    DOI: 10.3390/cancers14184374

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  • Water Droplet-in-Oil Digestion Method for Single-Cell Proteomics Reviewed International journal

    Takeshi Masuda, Yuma Inamori, Arisu Furukawa, Maki Yamahiro, Kazuki Momosaki, Chih-Hsiang Chang, Daiki Kobayashi, Hiroto Ohguchi, Yawara Kawano, Shingo Ito, Norie Araki, Shao-En Ong, Sumio Ohtsuki

    Analytical Chemistry   94 ( 29 )   10329 - 10336   2022.7

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:American Chemical Society (ACS)  

    Recent advances in single-cell proteomics highlight the promise of sensitive analyses in limited cell populations. However, technical challenges remain for sample recovery, throughput, and versatility. Here, we first report a water droplet-in-oil digestion (WinO) method based on carboxyl-coated beads and phase transfer surfactants for proteomic analysis using limited sample amounts. This method was developed to minimize the contact area between the sample solution and the container to reduce the loss of proteins and peptides by adsorption. This method increased protein and peptide recovery 10-fold. The proteome profiles obtained from 100 cells using the WinO method highly correlated with those from 10,000 cells using the in-solution digestion method. We successfully applied the WinO method to single-cell proteomics and quantified 462 proteins. Using the WinO method, samples can be easily prepared in a multi-well plate, making it a widely applicable and suitable method for single-cell proteomics.

    DOI: 10.1021/acs.analchem.1c05487

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  • AT-hook DNA-binding motif-containing protein one knockdown downregulates EWS-FLI1 transcriptional activity in Ewing's sarcoma cells. International journal

    Takao Kitagawa, Daiki Kobayashi, Byron Baron, Hajime Okita, Tatsuo Miyamoto, Rie Takai, Durga Paudel, Tohru Ohta, Yoichi Asaoka, Masayuki Tokunaga, Koji Nakagawa, Makoto Furutani-Seiki, Norie Araki, Yasuhiro Kuramitsu, Masanobu Kobayashi

    PloS one   17 ( 10 )   e0269077   2022.5

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

    Ewing's sarcoma is the second most common bone malignancy in children or young adults and is caused by an oncogenic transcription factor by a chromosomal translocation between the EWSR1 gene and the ETS transcription factor family. However, the transcriptional mechanism of EWS-ETS fusion proteins is still unclear. To identify the transcriptional complexes of EWS-ETS fusion transcription factors, we applied a proximal labeling system called BioID in Ewing's sarcoma cells. We identified AHDC1 as a proximal protein of EWS-ETS fusion proteins. AHDC1 knockdown showed a reduced cell growth and transcriptional activity of EWS-FLI1. AHDC1 knockdown also reduced BRD4 and BRG1 protein levels, both known as interacting proteins of EWS-FLI1. Our results suggest that AHDC1 supports cell growth through EWS-FLI1.

    DOI: 10.1101/2022.05.16.492174

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  • Water droplet-in-oil digestion method for single-cell proteomics

    Takeshi Masuda, Yuma Inamori, Arisu Furukawa, Kazuki Momosaki, Chih-Hsiang Chang, Daiki Kobayashi, Hiroto Ohguchi, Yawara Kawano, Shingo Ito, Norie Araki, Shao-En Ong, Sumio Ohtsuki

    bioRxiv   2021.12

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    Publisher:Cold Spring Harbor Laboratory  

    <title>Abstract</title>Recent advances in single-cell proteomics highlight the promise of sensitive analyses in limited cell populations. However, technical challenges remain for sample recovery, throughput, and versatility. Here, we first report a water droplet-in-oil digestion (WinO) method based on carboxyl-coated beads and phase transfer surfactants for proteomic analysis using limited sample amounts. This method was developed to minimize the contact area between the sample solution and the container to reduce the loss of proteins and peptides by adsorption. This method increased protein and peptide recovery 10-fold as well as the number of quantified transmembrane proteins compared to an in-solution digestion (ISD) method. The proteome profiles obtained from 100 cells using the WinO method highly correlated with those from 10000 cells using the ISD method. We successfully applied the WinO method to single-cell proteomics and quantified 462 proteins. Using the WinO method, samples can be easily prepared in a multi-well plate, making it a widely applicable and suitable method for single-cell proteomics.

    DOI: 10.1101/2021.12.13.472378

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  • TCTP interactomics in NF1-associated malignant tumor cells by affinity-purification and SWATH-MS Reviewed

    Daiki Kobayashi, Norie Araki

    Journal of Proteome Data and Methods   3   2   2021.10

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    Authorship:Lead author, Corresponding author   Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.14889/jpdm.2021.0002

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  • Data for quantitative proteome analyses of NF1-deficient PC12 cells during NGF induced neural differentiation using iTRAQ Reviewed

    Daiki Kobayashi, Norie Araki

    Journal of Proteome Data and Methods   2   2   2020.11

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    DOI: 10.14889/jpdm.2020.0002

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  • FTO Demethylates Cyclin D1 mRNA and Controls Cell-Cycle Progression. Reviewed International journal

    Mayumi Hirayama, Fan-Yan Wei, Takeshi Chujo, Shinya Oki, Maya Yakita, Daiki Kobayashi, Norie Araki, Nozomu Takahashi, Ryoji Yoshida, Hideki Nakayama, Kazuhito Tomizawa

    Cell reports   31 ( 1 )   107464 - 107464   2020.4

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    N6-Methyladenosine (m6A) modification is the major chemical modification in mRNA that controls fundamental biological processes, including cell proliferation. Herein, we demonstrate that fat mass and obesity-associated (FTO) demethylates m6A modification of cyclin D1, the key regulator for G1 phase progression and controls cell proliferation in vitro and in vivo. FTO depletion upregulates cyclin D1 m6A modification, which in turn accelerates the degradation of cyclin D1 mRNA, leading to the impairment of G1 progression. m6A modification of cyclin D1 oscillates in a cell-cycle-dependent manner; m6A levels are suppressed during the G1 phase and enhanced during other phases. Low m6A levels during G1 are associated with the nuclear translocation of FTO from the cytosol. Furthermore, nucleocytoplasmic shuttling of FTO is regulated by casein kinase II-mediated phosphorylation of FTO. Our results highlight the role of m6A in regulating cyclin D1 mRNA stability and add another layer of complexity to cell-cycle regulation.

    DOI: 10.1016/j.celrep.2020.03.028

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  • Identification of a Specific Translational Machinery via TCTP-EF1A2 Interaction Regulating NF1-associated Tumor Growth by Affinity Purification and Data-independent Mass Spectrometry Acquisition (AP-DIA). Reviewed International journal

    Daiki Kobayashi, Takaho Tokuda, Kyosuke Sato, Hiroki Okanishi, Megumi Nagayama, Mio Hirayama-Kurogi, Sumio Ohtsuki, Norie Araki

    Molecular & cellular proteomics : MCP   18 ( 2 )   245 - 262   2019.2

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    Authorship:Lead author   Language:English  

    Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that predisposes individuals to developing benign neurofibromas and malignant peripheral nerve sheath tumors (MPNST). The mechanism of NF1-tumorigenesis or the curatives have not been established. Using unique trascriptome and proteome integration method, iPEACH (1), we previously identified translationally controlled tumor protein (TCTP) as a novel biological target for NF1-associated tumors (2). Here, we identified specific TCTP-interacting proteins by sequential affinity purification and data-independent mass spectrometry acquisition (AP-DIA/SWATH) to investigate the role of TCTP in NF1-associated malignant tumors. TCTP mainly interacts with proteins related to protein synthesis and especially to elongation factor complex components, including EF1A2, EF1B, EF1D, EF1G, and valyl-tRNA synthetase (VARS), in NF1-deficient malignant tumor cells. Interestingly, TCTP preferentially binds to EF1A2 (normally found only in neural and skeletal-muscle cells and several cancer cells), rather than EF1A1 despite the high homologies (98%) in their sequences. The docking simulation and further validations to study the interaction between TCTP and EF1A2 revealed that TCTP directly binds with EF1A2 via the contact areas of EF1A2 dimerization. Using unique and common sequences between EF1A2 and EF1A1 in AP-DIA/SWATH, we quantitatively validated the interaction of EF1A2 and TCTP/other elongation factors and found that TCTP coordinates the translational machinery of elongation factors via the association with EF1A2. These data suggest that TCTP activates EF1A2-dependent translation by mediating complex formation with other elongation factors. Inhibiting the TCTP-EF1A2 interaction with EF1A2 siRNAs or a TCTP inhibitor, artesunate, significantly down-regulated the factors related to protein translation and caused dramatic suppression of growth/translation in NF1-associated tumors. Our findings demonstrate that a specific protein translation machinery related to the TCTP-EF1A2 interaction is functionally implicated in the tumorigenesis and progression of NF1-associated tumors and could represent a therapeutic target.

    DOI: 10.1074/mcp.RA118.001014

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  • The jPOST environment: an integrated proteomics data repository and database Reviewed

    Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Yoshinori Yamanouchi, Norie Araki, Akiyasu C Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama

    Nucleic Acids Research   47 ( D1 )   D1218 - D1224   2019.1

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    DOI: 10.1093/nar/gky899

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  • Isocitrate dehydrogenase gene mutations and 2-hydroxyglutarate accumulation in esophageal squamous cell carcinoma Reviewed

    Keisuke Miyake, Yoshifumi Baba, Takatsugu Ishimoto, Yukiharu Hiyoshi, Masaaki Iwatsuki, Yuji Miyamoto, Naoya Yoshida, Masayuki Watanabe, Yoko Ogata, Megumi Nagayama, Atit Silsirivanit, Daiki Kobayashi, Norie Araki, Hideo Baba

    Medical Oncology   36 ( 1 )   11:1 - 9   2019.1

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    Publishing type:Research paper (scientific journal)   Publisher:Springer Science and Business Media LLC  

    DOI: 10.1007/s12032-018-1229-x

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    Other Link: http://link.springer.com/content/pdf/10.1007/s12032-018-1229-x.pdf

  • SIRT7 has a critical role in bone formation by regulating lysine acylation of SP7/Osterix. Reviewed International journal

    Masatoshi Fukuda, Tatsuya Yoshizawa, Md Fazlul Karim, Shihab U Sobuz, Wataru Korogi, Daiki Kobayasi, Hiroki Okanishi, Masayoshi Tasaki, Katsuhiko Ono, Tomohiro Sawa, Yoshifumi Sato, Mami Chirifu, Takeshi Masuda, Teruya Nakamura, Hironori Tanoue, Kazuhisa Nakashima, Yoshihiro Kobashigawa, Hiroshi Morioka, Eva Bober, Sumio Ohtsuki, Yuriko Yamagata, Yukio Ando, Yuichi Oike, Norie Araki, Shu Takeda, Hiroshi Mizuta, Kazuya Yamagata

    Nature communications   9 ( 1 )   2833 - 2833   2018.7

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    SP7/Osterix (OSX) is a master regulatory transcription factor that activates a variety of genes during differentiation of osteoblasts. However, the influence of post-translational modifications on the regulation of its transactivation activity is largely unknown. Here, we report that sirtuins, which are NAD(+)-dependent deacylases, regulate lysine deacylation-mediated transactivation of OSX. Germline Sirt7 knockout mice develop severe osteopenia characterized by decreased bone formation and an increase of osteoclasts. Similarly, osteoblast-specific Sirt7 knockout mice showed attenuated bone formation. Interaction of SIRT7 with OSX leads to the activation of transactivation by OSX without altering its protein expression. Deacylation of lysine (K) 368 in the C-terminal region of OSX by SIRT7 promote its N-terminal transactivation activity. In addition, SIRT7-mediated deacylation of K368 also facilitates depropionylation of OSX by SIRT1, thereby increasing OSX transactivation activity. In conclusion, our findings suggest that SIRT7 has a critical role in bone formation by regulating acylation of OSX.

    DOI: 10.1038/s41467-018-05187-4

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  • Ribosome Incorporation into Somatic Cells Promotes Lineage Transdifferentiation towards Multipotency Reviewed

    Naofumi Ito, Kaoru Katoh, Hiroko Kushige, Yutaka Saito, Terumasa Umemoto, Yu Matsuzaki, Hiroshi Kiyonari, Daiki Kobayashi, Minami Soga, Takumi Era, Norie Araki, Yasuhide Furuta, Toshio Suda, Yasuyuki Kida, Kunimasa Ohta

    SCIENTIFIC REPORTS   8 ( 1 )   1634   2018.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:NATURE PUBLISHING GROUP  

    Recently, we reported that bacterial incorporation induces cellular transdifferentiation of human fibroblasts. However, the bacterium-intrinsic cellular-transdifferentiation factor remained unknown. Here, we found that cellular transdifferentiation is caused by ribosomes. Ribosomes, isolated from both prokaryotic and eukaryotic cells, induce the formation of embryoid body-like cell clusters. Numerous ribosomes are incorporated into both the cytoplasm and nucleus through trypsin-activated endocytosis, which leads to cell-cluster formation. Although ribosome-induced cell clusters (RICs) express several stemness markers and differentiate into derivatives of all three germ layers in heterogeneous cell populations, RICs fail to proliferate, alter the methylation states of pluripotent genes, or contribute to teratoma or chimera formation. However, RICs express markers of epithelial-mesenchymal transition without altering the cell cycle, despite their proliferation obstruction. These findings demonstrate that incorporation of ribosomes into host cells induces cell transdifferentiation and alters cellular plasticity.

    DOI: 10.1038/s41598-018-20057-1

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  • Artesunate and chloroquine induce cytotoxic activity on cholangiocarcinoma cells via different cell death mechanisms Reviewed

    Diwakar Guragain, Wunchana Seubwai, Daiki Kobayashi, Atit Silsinivanit, Kulthida Vaeteewoottacharn, Kanlayanee Sawanyawisuth, Chaisiri Wongkham, Sopit Wongkham, Norie Araki, Ubon Cha'on

    CELLULAR AND MOLECULAR BIOLOGY   64 ( 10 )   113 - 118   2018

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:C M B ASSOC  

    Chemotherapy for cholangiocarcinoma (CCA) is not quite successful. In this study, we revisited the possibility of artesunate (ART) and chloroquine (CQ), the antimalarial drugs, as therapeutic agents against CCA. The possible mechanisms of these drugs to exert cytotoxicity on CCA cells were also explored. The effects of ART and CQ on proliferation and death patterns of two CCA cell lines, KKU-214 and its highly metastatic subtype KKU-214L5, were examined using water soluble tetrazolium (WST) assay and time-lapse photometry, respectively. To differentiate and verify the death patterns between necrosis and apoptosis, lactate dehydrogenase (LDH) release, and caspase 3 activity were measured. CellROX (TM) green reagent staining method was used to assess reactive oxygen species (ROS) production in ART-and CQ-treated cells. ART and CQ significantly inhibited proliferation of CCA cells. Both drugs kill malarial parasites via similar mechanism depending on ROS formation, however, ART induced necrotic cell death and CQ induced apoptotic cell death in CCA cells. ART induced LDH release, whereas CQ activated caspase 3, confirming induction of necrotic and apoptotic cell deaths by ART and CQ, respectively. ART treatment induced higher ROS production than CQ. ART and CQ induce CCA cells death via different death pathways. ART should be suitable for necrosis-sensitive CCA, whereas CQ is more suitable for apoptosis-sensitive CCA.

    DOI: 10.14715/cmb/2018.64.10.18

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  • JPOSTrepo: An international standard data repository for proteomes Reviewed

    Shujiro Okuda, Yu Watanabe, Yuki Moriya, Shin Kawano, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Naoyuki Sugiyama, Susumu Goto, Yasushi Ishihama

    Nucleic Acids Research   45 ( 1 )   D1107 - D1111   2017.1

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:Oxford University Press  

    Major advancements have recently been made in mass spectrometry-based proteomics, yielding an increasing number of datasets from various proteomics projects worldwide. In order to facilitate the sharing and reuse of promising datasets, it is important to construct appropriate, high-quality public data repositories. jPOSTrepo (https://repository. jpostdb.org/) has successfully implemented several unique features, including high-speed file uploading, flexible file management and easy-to-use interfaces. This repository has been launched as a public repository containing various proteomic datasets and is available for researchers worldwide. In addition, our repository has joined the ProteomeXchange consortium, which includes the most popular public repositories such as PRIDE in Europe for MS/MS datasets and PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the USA and accepted into the ProteomeXchange, as was our repository in July 2016, providing important datasets from Asia/Oceania. Accordingly, this repository thus contributes to a global alliance to share and store all datasets from a wide variety of proteomics experiments. Thus, the repository is expected to become a major repository, particularly for data collected in the Asia/Oceania region.

    DOI: 10.1093/nar/gkw1080

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  • Cellular Biological Validations of Proteomics Data Invited Reviewed

    Kobayashi Daiki, Araki Norie

    Proteome Letters   1 ( 1 )   37 - 43   2016

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    Authorship:Lead author, Corresponding author   Language:Japanese   Publisher:Japanese Proteomics Society  

    <p>Cellular biological validations of novel candidate molecules which are extracted from proteomics data are needed to uncover their functions. For examples, the molecules are inhibited or activated to validate their biological functions by using siRNA/shRNA, antibodies, chemical compounds, or expression plasmids, followed by the observations with microscope and analyses using the various assay systems. However, it takes much effort to biologically validate the candidate molecules because the approaches depend on their various functions. Therefore, the precise processes to extract the novel molecules of biological interest using the gene ontology or network analyses, as well as the strict sample preparations and the reliable proteome data, need to facilitate their validations. In this paper, we explained how the novel candidates of interest, especially related to the neurofibromatosis type I (NF1) pathogenesis, were validated biologically.</p>

    DOI: 10.14889/jpros.1.1_37

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  • Up-regulation of DRP-3 long isoform during the induction of neural progenitor cells by glutamate treatment in the ex vivo rat retina Reviewed

    Kazuhiro Tokuda, Yasuhiro Kuramitsu, Baron Byron, Takao Kitagawa, Nobuko Tokuda, Daiki Kobayashi, Megumi Nagayama, Norie Araki, Koh-Hei Sonoda, Kazuyuki Nakamura

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   463 ( 4 )   593 - 599   2015.8

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    Language:English   Publishing type:Research paper (scientific journal)   Publisher:ACADEMIC PRESS INC ELSEVIER SCIENCE  

    Glutamate has been shown to induce neural progenitor cells in the adult vertebrate retina. However, protein dynamics during progenitor cell induction by glutamate are not fully understood. To identify specific proteins involved in the process, we employed two-dimensional electrophoresis-based proteomics on glutamate untreated and treated retinal ex vivo sections. Rat retinal tissues were incubated with 1 mM glutamate for 1 h, followed by incubation in glutamate-free media for a total of 24 h. Consistent with prior reports, it was found that mitotic cells appeared in the outer nuclear layer without any histological damage. Immunohistological evaluations and immunoblotting confirmed the emergence of neuronal progenitor cells in the mature retina treated with glutamate. Proteomic analysis revealed the up-regulation of dihydropyrimidinase-related protein 3 (DRP-3), DRP-2 and stress-induced-phosphoprotein 1 (STIP1) during neural progenitor cell induction by glutamate. Moreover, mRNA expression of DRP-3, especially, its long isoform, robustly increased in the treated retina compared to that in the untreated retina. These results may indicate that glutamate induces neural progenitor cells in the mature rat retina by up-regulating the proteins which mediate cell mitosis and neurite growth. (C) 2015 Elsevier Inc. All rights reserved.

    DOI: 10.1016/j.bbrc.2015.05.102

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  • Analysis of neural tumors and related diseases by integrated proteomics Invited Reviewed

    Daiki Kobayashi, Norie Araki

    Journal of Clinical and Experimental Medicine   251 ( 10 )   939 - 947   2014.12

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    Language:Japanese   Publisher:医歯薬出版  

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  • Translationally Controlled Tumor Protein Is a Novel Biological Target for Neurofibromatosis Type 1-associated Tumors Reviewed

    Daiki Kobayashi, Mio Hirayama, Yoshihiro Komohara, Souhei Mizuguchi, Masayo Wilson Morifuji, Hironobu Ihn, Motohiro Takeya, Akira Kuramochi, Norie Araki

    JOURNAL OF BIOLOGICAL CHEMISTRY   289 ( 38 )   26314 - 26326   2014.9

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    Authorship:Lead author   Language:English   Publishing type:Research paper (scientific journal)   Publisher:AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC  

    Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that predisposes individuals to develop benign neurofibromas and malignant peripheral nerve sheath tumors (MPNSTs). Due to the lack of information on the molecular mechanism of NF1-associated tumor pathogenesis or biomarkers/therapeutic targets, an effective treatment for NF1 tumors has not been established. In this study, the novel NF1-associated protein, translationally controlled tumor protein (TCTP), was identified by integrated proteomics and found to be up-regulated via activated MAPK/PI3K-AKT signaling in response to growth factors in NF1-deficient Schwann cells. Immunohistochemical analysis of NF1-associated tumors revealed that the TCTP expression level correlated with tumorigenicity. In NF1-deficient MPNST cells, TCTP protein but not mRNA was down-regulated by NF1 GTPase-activating protein-related domain or MAPK/PI3K inhibitors, and this correlated with suppression of mammalian target of rapamycin (mTOR) signaling. mTOR inhibition by rapamycin also down-regulated TCTP protein expression, whereas knockdown or overexpression of TCTP suppressed or activated mTOR signaling, respectively, and affected cell viability. These results suggest that a positive feedback loop between TCTP and mTOR contributes to NF1-associated tumor formation. Last, the anti-tumor effect of artesunate, which binds to and degrades TCTP, was evaluated. Artesunate significantly suppressed the viability of MPNST cells but not normal Schwann cells, and the TCTP level inversely correlated with artesunate sensitivity. Moreover, combinational use of artesunate and rapamycin enhanced the cytotoxic effect on MPNST cells. These findings suggest that TCTP is functionally implicated in the progression of NF1-associated tumors and could serve as a biological target for their therapy.

    DOI: 10.1074/jbc.M114.568253

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  • Development of a fully automated two-dimensional electrophoresis device, Auto-2D, and its application for the integrated proteomics Reviewed

    Araki Norie, Niibori Nambu Akiko, Nishimura Munenori, Midorikawa Uichi, Kobayashi Daiki

    SEIBUTSU BUTSURI KAGAKU   58 ( 2 )   39 - 42   2014

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    Authorship:Last author   Language:Japanese   Publisher:Japanese Electrophoresis Society  

    DOI: 10.2198/sbk.58.39

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  • Analysis of specific cellular proteins in nervous systems tumors by integrated proteomics

    Kobayashi Daiki

    Abstracts for Annual Meeting of Japanese Proteomics Society   2014   6 - 6   2014

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    Language:Japanese   Publisher:Japanese Proteomics Society (Japan Human Proteome Organisation)  

    DOI: 10.14889/jhupo.2014.0.6.0

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  • Integrated Proteomics Identified Novel Activation of Dynein IC2-GR-COX-1 Signaling in Neurofibromatosis Type I (NF1) Disease Model Cells Reviewed

    Mio Hirayama, Daiki Kobayashi, Souhei Mizuguchi, Takashi Morikawa, Megumi Nagayama, Uichi Midorikawa, Masayo M. Wilson, Akiko N. Nambu, Akiyasu C. Yoshizawa, Shin Kawano, Norie Araki

    MOLECULAR & CELLULAR PROTEOMICS   12 ( 5 )   1377 - 1394   2013.5

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    Neurofibromatosis type 1 (NF1) tumor suppressor gene product, neurofibromin, functions in part as a Ras-GAP, and though its loss is implicated in the neuronal abnormality of NF1 patients, its precise cellular function remains unclear. To study the molecular mechanism of NF1 pathogenesis, we prepared NF1 gene knockdown (KD) PC12 cells, as a NF1 disease model, and analyzed their molecular (gene and protein) expression profiles with a unique integrated proteomics approach, comprising iTRAQ, 2D-DIGE, and DNA microarrays, using an integrated protein and gene expression analysis chart (iPEACH). In NF1-KD PC12 cells showing abnormal neuronal differentiation after NGF treatment, of 3198 molecules quantitatively identified and listed in iPEACH, 97 molecules continuously up-or down-regulated over time were extracted. Pathway and network analysis further revealed overrepresentation of calcium signaling and transcriptional regulation by glucocorticoid receptor (GR) in the up-regulated protein set, whereas nerve system development was overrepresented in the down-regulated protein set. The novel up-regulated network we discovered, "dynein IC2-GR-COX-1 signaling," was then examined in NF1-KD cells. Validation studies confirmed that NF1 knockdown induces altered splicing and phosphorylation patterns of dynein IC2 isomers, up-regulation and accumulation of nuclear GR, and increased COX-1 expression in NGF-treated cells. Moreover, the neurite retraction phenotype observed in NF1-KD cells was significantly recovered by knockdown of the dynein IC2-C isoform and COX-1. In addition, dynein IC2 siRNA significantly inhibited nuclear translocation and accumulation of GR and up-regulation of COX-1 expression. These results suggest that dynein IC2 up-regulates GR nuclear translocation and accumulation, and subsequently causes increased COX-1 expression, in this NF1 disease model. Our integrated proteomics strategy, which combines multiple approaches, demonstrates that NF1-related neural abnormalities are, in part, caused by up-regulation of dynein IC2-GR-COX-1 signaling, which may be a novel therapeutic target for NF1.

    DOI: 10.1074/mcp.M112.024802

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  • Glioma Initiating Cells Form a Differentiation Niche Via the Induction of Extracellular Matrices and Integrin alpha V Reviewed

    Akiko Niibori-Nambu, Uichi Midorikawa, Souhei Mizuguchi, Takuichiro Hide, Minako Nagai, Yoshihiro Komohara, Megumi Nagayama, Mio Hirayama, Daiki Kobayashi, Nobuyuki Tsubota, Tatsuya Takezaki, Keishi Makino, Hideo Nakamura, Motohiro Takeya, Junichi Kuratsu, Norie Araki

    8 ( 5 )   e59558   2013.5

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    Glioma initiating cells (GICs) are considered responsible for the therapeutic resistance and recurrence of malignant glioma. To clarify the molecular mechanism of GIC maintenance/differentiation, we established GIC clones having the potential to differentiate into malignant gliomas, and subjected to DNA microarray/iTRAQ based integrated proteomics. 21,857 mRNAs and 8,471 proteins were identified and integrated into a gene/protein expression analysis chart. Gene Ontology analysis revealed that the expression of cell adhesion molecules, including integrin subfamilies, such as alpha 2 and alpha, and extracellular matrices (ECMs), such as collagen IV (COL4), laminin alpha 2 (LAMA2), and fibronectin 1 (FN), was significantly upregulated during serum-induced GIC differentiation. This differentiation process, accompanied by the upregulation of MAPK as well as glioma specific proteins in GICs, was dramatically accelerated in these ECM (especially FN)-coated dishes. Integrin alpha V blocking antibody and RGD peptide significantly suppressed early events in GIC differentiation, suggesting that the coupling of ECMs to integrin alpha V is necessary for GIC differentiation. In addition, the expression of integrin alpha V and its strong ligand FN was prominently increased in glioblastomas developed from mouse intracranial GIC xenografts. Interestingly, during the initial phase of GIC differentiation, the RGD treatment significantly inhibited GIC proliferation and raised their sensitivity against anti-cancer drug temozolomide (TMZ). We also found that combination treatments of TMZ and RGD inhibit glioma progression and lead the longer survival of mouse intracranial GIC xenograft model. These results indicate that GICs induce/secrete ECMs to develop microenvironments with serum factors, namely differentiation niches that further stimulate GIC differentiation and proliferation via the integrin recognition motif RGD. A combination of RGD treatment with TMZ could have the higher inhibitory potential against the glioma recurrence that may be regulated by the GICs in the differentiation niche. This study provides a new perspective for developing therapeutic strategies against the early onset of GIC-associated glioma.

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  • An Integrated Approach of Differential Mass Spectrometry and Gene Ontology Analysis Identified Novel Proteins Regulating Neuronal Differentiation and Survival Reviewed

    Daiki Kobayashi, Jiro Kumagai, Takashi Morikawa, Masayo Wilson-Morifuji, Anthony Wilson, Atsushi Irie, Norie Araki

    MOLECULAR & CELLULAR PROTEOMICS   8 ( 10 )   2350 - 2367   2009.10

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    MS-based quantitative proteomics is widely used for large scale identification of proteins. However, an integrated approach that offers comprehensive proteome coverage, a tool for the quick categorization of the identified proteins, and a standardized biological study method is needed for helping the researcher focus on investigating the proteins with biologically important functions. In this study, we utilized isobaric tagging for relative and absolute quantification (iTRAQ)-based quantitative differential LC/MS/MS, functional annotation with a proprietary gene ontology tool (Molecular Annotation by Gene Ontology (MANGO)), and standard biochemical methods to identify proteins related to neuronal differentiation in nerve growth factor-treated rat pheochromocytoma (PC12) cells, which serve as a representative model system for studying neuronal biological processes. We performed MS analysis by using both nano-LC-MALDI-MS/MS and nano-LC-ESI-MS/MS for maximal proteome coverage. Of 1,482 non-redundant proteins semiquantitatively identified, 72 were differentially expressed with 39 up-and 33 down-regulated, including 64 novel nerve growth factor-responsive PC12 proteins. Gene ontology analysis of the differentially expressed proteins by MANGO indicated with statistical significance that the up-regulated proteins were mostly related to the biological processes of cell morphogenesis, apoptosis/survival, and cell differentiation. Some of the up-regulated proteins of unknown function, such as PAIRBP1, translationally controlled tumor protein, prothymosin alpha, and MAGED1, were further analyzed to validate their significant functions in neuronal differentiation by immunoblotting and immunocytochemistry using each antibody combined with a specific short interfering RNA technique. Knockdown of these proteins caused abnormal cell morphological changes, inhibition of neurite formation, and cell death during each course of the differentiation, confirming their important roles in neurite formation and survival of PC12 cells. These results show that our iTRAQ-MANGO-biological analysis framework, which integrates a number of standard proteomics strategies, is effective for targeting and elucidating the functions of proteins involved in the cellular biological process being studied. Molecular & Cellular Proteomics 8: 2350-2367, 2009.

    DOI: 10.1074/mcp.M900179-MCP200

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  • Neurofibromatosis type 1 (NF1) tumor suppressor, neurofibromin, regulates the neuronal differentiation of PC12 cells via its associating protein, CRMP-2 Reviewed

    Siriporn Patrakitkomjorn, Daiki Kobayashi, Takashi Morikawa, Masayo Morifuji Wilson, Nobuyuki Tsubota, Atsushi Irie, Tatsuya Ozawa, Masashi Aoki, Nariko Arimura, Kozo Kaibuchi, Hideyuki Saya, Norie Araki

    JOURNAL OF BIOLOGICAL CHEMISTRY   283 ( 14 )   9399 - 9413   2008.4

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    Neurofibromatosis type 1 (NF1) tumor suppressor gene product, neurofibromin, functions in part as a Ras-GAP, a negative regulator of Ras. Neurofibromin is implicated in the neuronal abnormality of NF1 patients; however, the precise cellular function of neurofibromin has yet to be clarified. Using proteomic strategies, we identified a set of neurofibromin-associating cellular proteins, including axon regulator CRMP-2 (Collapsin response mediator protein-2). CRMP-2 directly bound to the C-terminal domain of neurofibromin, and this association was regulated by the manner of CRMP-2 phosphorylation. In nerve growth factor-stimulated PC12 cells, neurofibromin and CRMP-2 co-localized particularly on the distal tips and branches of extended neurites. Suppression of neurofibromin using NF1 small interfering RNA significantly inhibited this neurite outgrowth and up-regulated a series of CRMP-2 phosphorylations by kinases identified as CDK5, GSK-3b, and Rho kinase. Overexpression of the NF1-RAS-GAP-related domain rescued these NF1 small interfering RNA-induced events. Our results suggest that neurofibromin regulates neuronal differentiation by performing one or more complementary roles. First, neurofibromin directly regulates CRMP-2 phosphorylation accessibility through the complex formation. Also, neurofibromin appears to indirectly regulate CRMP-2 activity by suppressing CRMP-2-phosphorylating kinase cascades via its Ras-GAP function. Our study demonstrates that the functional association of neurofibromin and CRMP-2 is essential for neuronal cell differentiation and that lack of expression or abnormal regulation of neurofibromin can result in impaired function of neuronal cells, which is likely a factor in NF1-related pathogenesis.

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  • Genomic cloning of ribonucleases in Nicotiana glutinosa leaves, as induced in response to wounding or to TMV-infection, and characterization of their promoters Reviewed

    T Hayashi, D Kobayashi, T Kariu, M Tahara, K Hada, Y Kouzuma, M Kimura

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   67 ( 12 )   2574 - 2583   2003.12

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    We previously cloned two distinct cDNA clones, NGR1 and NGR3, encoding S-like ribonucleases (RNases) induced by wounding and tobacco mosaic virus (TNIV) infection, respectively, in Nicotiana glutinosa leaves. To gain insight into the regulatory mechanism of the RNase genes, we analyzed nucleotide sequences of the genes ngr1 (4.1 kbp) and ngr3 (5.3 kbp), containing their structural genes as well as 5'-flanking regions. The ngr1 gene is organized in three exons with two intervening introns, and ngr3 has four exons interrupted by three introns. Primer extension analyses localized single transcription initiation sites at - 32 and - 99 upstream of the translation initiation codons ATG in the genes ngr1 and ngr3, respectively. The beta-glucuronidase (GUS) reporter gene analysis with serial 5'-deletion mutants as well as a gel shift assay defined the wound-responsive region at residues - 509 to - 288 in gene ngr1 and a TMV-responsive region at the residues - 401 to - 174 in ngr3, respectively. Sequence search using PLACE and PlantCARE data bases showed that a wound-responsive element: the WUN-motif, occurs within the wound-responsive region in ngr1, while ngr3 contains several potential cis-regulating elements, such as the elicitor responsiveness element: the W-box, a TNIV responsive element: GT1, and the WUN-motif at positions between - 401 and - 174. These findings suggested that some of these cis-elements may be involved in inducible expressions of ngr1 and ngr3. Furthermore, the gel shift assay suggested that the dissociation of protein factor(s) upon TMV-infection from the regulatory region may cause an inducible expression of ngr3.

    DOI: 10.1271/bbb.67.2574

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  • Protein engineering of novel proteinase inhibitors and their effects on the growth of Spodoptera exigua larvae Reviewed

    H Inanaga, D Kobayasi, Y Kouzuma, C Aoki-Yasunaga, K Iiyama, M Kimura

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   65 ( 10 )   2259 - 2264   2001.10

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    Novel types of proteinase inhibitors with multi-inhibitory activities were generated by replacement of phytocystatin domains in sunflower multi-cystatin (SMC) by the serine proteinase inhibitor BGIT from bitter gourd seeds. Two chimeric inhibitors SMC-T3 and SMC-T23, in which the third domain in SMC and the second and third domains in SMC were replaced by BGIT, acquired trypsin inhibitory activity (Ki: 1.46 x 10(-7) m and 1.75 x 10(-7) m), retaining inhibitory activity toward papain (Ki: 4.5 x 10(-8) m and 1.52 x 10(-7) M), respectively. We compared the chimeric inhibitors and the recombinant SMC (r-SMC) in relation to their effects on the growth of larval Spodoptera exigua. When the second instar larvae were reared on a diet containing rSMC, SMC-T3, or SMC-T23 for ten days, a significant reduction in weight gain was observed. Mean weights for rSMC, SMC-T3, and SMC-T23 were 43 mg, 32 mg, and 43 mg, respectively, as compared with that (60 mg) for the absence of the inhibitor. In contrast, BGIT had little effect on the growth of the S. exigua larvae. This result indicated that the chimeric inhibitor SMC-T3 with two phytocystatin domains and one serine proteinase inhibitor domain is an efficient inhibitor of proteinases in the S. exigua larvae. Therefore, this novel type of proteinase inhibitor with multi-inhibitory activities may represent a promising protein for successful application to a transgenic plant with insect resistance.

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MISC

  • Elucidation of the interaction between NF1-associated factor TCTPand translation elongation factors by cross-linking MassSpectrometry (XL-MS)

    Mukugi K, Kobayashi D, Tokuda T, Araki N

    Abstracts for Annual Meeting of Japanese Proteomics Society   2019   200 - 200   2019

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    DOI: 10.14889/jhupo.2019.0.200.0

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  • Integrated phospho-glyco-proteogenomics identified the potential clinical target signals against glioma stem cells

    Norie Araki, Akiko Namubu Niibori, Daiki Kobayashi, Takuichiro Hide, Hideo Nakamura, Junichi Kuratsu

    CANCER SCIENCE   109   656 - 656   2018.12

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  • Studies of key signals related to the maintenance and differentiation of glioma initiating cells by integrated-omics

    Norie Araki, Akiko N. Nambu, Atit Silsirivanit, Hiroki Okanishi, Daiki Kobayashi, Takuichiro Hide, Hideo Nakamura

    CANCER SCIENCE   109   630 - 630   2018.1

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  • jPOSTプロジェクトが提供するプロテオミクスデータとその解析ツール

    五斗進, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 松本雅記, 高見知代, 小林大樹, 山ノ内祥訓, 荒木令江, 吉沢明康, 田畑剛, 岩崎未央, 杉山直幸, 田中聡, 石濱泰

    第41回日本分子生物学会   41st   2018

  • Metadata Curation for fully utilizing raw MS data in jPOST repository

    Kobayashi, D, Araki, N, Okuda, S, Watanabe, Y, Moriya, Y, Kawano, S, Yamamoto, T, Matsumoto, T, Takami, T, Yoshizawa, A.C, Tabata, T, Iwasaki, M, Sugiyama, N, Tanaka, S, Goto, S, Ishihama, Y

    Mass Spectrometry and Proteomics 2018 (MSP2018)(日本質量分析学会・日本プロテオーム学会 2018年合同大会)   2018

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  • プロテオーム統合データベースの機能深化

    守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 松本雅記, 高見知代, 小林大樹, 山ノ内祥訓, 荒木令江, 吉沢明康, 田畑剛, 岩崎未央, 杉山直幸, 田中聡, 五斗進, 石濱泰

    第41回日本分子生物学会   41st   2018

  • jPOST統合環境の開発

    奥田修二郎, 渡辺由, 守屋勇樹, 河野信, 松本雅記, 高見知代, 小林大樹, 山ノ内祥訓, 荒木令江, 吉沢明康, 田畑剛, 岩崎未央, 杉山直幸, 田中聡, 五斗進, 石濱泰

    トーゴ―の日2018シンポジウム   2018

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  • プロテオミクスを基盤としたプロテオゲノム情報の疾患研究への橋渡しとその応用

    荒木令江, 南部(新堀)晶子, 山崎義宗, 山ノ内祥訓, 當房浩一, 小林大樹

    日本分子生物学会年会プログラム・要旨集(Web)   41st   ROMBUNNO.1PW1‐02‐4 (WEB ONLY)   2018

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  • jPOST:プロテオームデータベースの開発

    守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本生化学会大会(Web)   2017年度   [3P - 0173]   2017.12

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  • TCTP-EF1A2-翻訳伸長因子複合体を介した神経線維腫症1型腫瘍特異的な翻訳機構の解析

    小林 大樹, 徳田 高穂, 岡西 広樹, 大槻 純男, 荒木 令江

    生命科学系学会合同年次大会   2017年度   [3LBA - 029]   2017.12

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  • jPOST:プロテオーム統合データベースプロジェクト

    奥田修二郎, 渡辺由, 守屋勇樹, 河野信, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本生化学会大会(Web)   2017年度   [3P - 0171]   2017.12

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  • jPOST:同定結果のFDR改善を目指す再解析プロトコルの開発

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本生化学会大会(Web)   2017年度   [3P - 0172]   2017.12

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  • 融合オミクスによるグリオーマ幹細胞の分化と維持に関わる鍵分子群の同定と機能制御の解析

    荒木 令江, 南部 晶子, 堀, シルシリバニット・アチト, 岡西 広樹, 小林 大樹, 秀 拓一郎, 中村 英夫

    日本癌学会総会記事   76回   P - 2117   2017.9

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  • プロテオミクスデータ解析/演習

    石濱泰, 小林大樹, 吉沢明康

    BMSコンファレンス講演要旨集   44th   127‐132   2017.7

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  • Controlling false discovery rate in accumulated public proteome dataset

    Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama

    American Society for Mass Spectrometry Annual Conference   65th   MP321   2017.6

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  • データベース検索エンジンを用いたタンパク質同定における特異性向上

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 杉山直幸, 田中聡, 五斗進, 石濱泰

    質量分析総合討論会講演要旨集   65th   107   2017.5

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  • Reducing false positive identifications for proteome datasets accumulated in jPOST repository

    Yoshizawa A, Tabata T, Moriya Y, Kawano S, Okuda S, Watanabe Y, Yamamoto T, Matsumoto M, Takami T, Kobayashi D, Araki N, Sugiyama N, Tanaka S, Goto S, Ishihama Y

    16th Human Proteome Organization World Congress (HUPO2017)   2017

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  • jPOST:再解析プロトコルによる同定結果の質的向上

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 杉山直幸, 田中聡, 五斗進, 石濱泰

    トーゴ―の日シンポジウム2017   2017

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  • jPOST: Development of reanalysis protocol toward control of false discovery rate in peptide identification

    Akiyasu C. Yoshizawa, Tsuyoshi Tabata, Mio Iwasaki, Yuki Moriya, Shin Kawano, Shujiro Okuda, Yu Watanabe, Tadashi Yamamoto, Masaki Matsumoto, Tomoyo Takami, Daiki Kobayashi, Norie Araki, Naoyuki Sugiyama, Satoshi Tanaka, Susumu Goto, Yasushi Ishihama

    ConBio2017   2017

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  • プロテオーム統合データベースjPOST:質量分析データ・リポジトリ

    奥田修二郎, 渡辺由, 守屋勇樹, 河野信, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本プロテオーム学会大会プログラム・抄録集   2017   114   2017

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  • プロテオームデータにある生物学的な重要性を見出すための“Computational”ツール

    小林大樹, 荒木令江

    日本プロテオーム学会大会プログラム・抄録集   2017   117   2017

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  • グリオーマ幹細胞における翻訳後修飾アセチル化の分化変動プロテオミクス

    岡西広樹, 鷲頭朋之, 南部晶子, 小林大樹, 荒木令江

    日本プロテオーム学会大会プログラム・抄録集   2017   194   2017

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  • jPOST:プロテオーム統合データベースの開発

    守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 田中聡, 五斗進, 石澤泰

    日本プロテオーム学会大会プログラム・抄録集   2017   116   2017

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  • jPOST再解析プロトコル:偽陽性と偽陰性の同時減少を目指す

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 杉山直幸, 田中聡, 五斗進, 石濱泰

    日本プロテオーム学会大会プログラム・抄録集   2017   115   2017

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  • 融合的オミクス解析とシステムズバイオロジーによるNF1腫瘍の新規治療ターゲットシグナルの同定と機能解析

    荒木 令江, 小林 大樹, 新堀 晶子[南部], 中村 英夫, 尹 浩信, 倉津 純一

    日本癌学会総会記事   75回   E - 3038   2016.10

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  • 質量スペクトルはデータベース検索“グレーゾーン”を明瞭化するか

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 山本格, 松本雅記, 小林大樹, 荒木令江, 杉山直幸, 五斗進, 石濱泰

    質量分析総合討論会講演要旨集   64th   15   2016.5

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  • プロテオーム統合データベースjPOST:再解析プロトコルの開発

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知世, 小林大樹, 荒木令江, 杉山直幸, 五斗進, 石濱泰

    日本分子生物学会年会プログラム・要旨集(Web)   39th   ROMBUNNO.3P‐0880 (WEB ONLY)   2016

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  • バクテリアにおける翻訳後修飾アシル化プロテオミクス

    岡西広樹, 岡西広樹, 岡西広樹, 小林大樹, 荒木令江, 増井良治, 倉光成紀

    日本分子生物学会年会プログラム・要旨集(Web)   39th   ROMBUNNO.1P‐0069 (WEB ONLY)   2016

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  • プロテオーム統合データベースjPOST:再解析プロトコルの開発

    吉沢明康, 田畑剛, 守屋勇樹, 河野信, 奥田修二郎, 渡邉由, 山本格, 松本雅記, 高見知世, 小林大樹, 荒木令江, 杉山直幸, 五斗進, 石濱泰

    日本プロテオーム学会大会プログラム・抄録集   2016   177   2016

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  • 生物に広く存在するアシル化修飾の働き:アセチル化,プロピオニル化,スクシニル化

    岡西広樹, 岡西広樹, 岡西広樹, 小林大樹, 荒木令江, 増井良治, 倉光成紀

    日本プロテオーム学会大会プログラム・抄録集   2016   110   2016

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  • ヒト表皮AGEs化修飾タンパク質の解析

    井上敬文, 川端慶吾, 長山慈, 小林大樹, 大槻純男, 荒木令江

    日本プロテオーム学会大会プログラム・抄録集   2016   150   2016

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  • プロテオーム統合データベースjPOSTの開発

    五斗進, 奥田修二郎, 渡邉由, 守屋勇樹, 河野信, 山本格, 松本雅記, 高見知代, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 石濱泰

    日本プロテオーム学会大会プログラム・抄録集   2016   88   2016

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  • jPOST:プロテオームデータベースプロジェクト

    守屋勇樹, 河野信, 奥田修二郎, 渡辺由, 山本格, 松本雅記, 高見知世, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 五斗進, 石濱泰

    日本分子生物学会年会プログラム・要旨集(Web)   39th   ROMBUNNO.1P‐0076 (WEB ONLY)   2016

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  • グリオーマ幹細胞の維持・分化に関わる新規マーカー分子群の探索

    當房浩一, 南部晶子, SILSIRIVANIT Atit, 山崎義宗, 小林大樹, 荒木令江

    日本プロテオーム学会大会プログラム・抄録集   2016   132   2016

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  • 生物に広く存在するアシル化修飾の働き:アセチル化,プロピオニル化,スクシニル化

    岡西広樹, 岡西広樹, 岡西広樹, 小林大樹, 荒木令江, 増井良治, 倉光成紀

    日本プロテオーム学会大会プログラム・抄録集   2016   152   2016

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  • プロテオーム統合データベースjPOST:質量分析データ・リポジトリの公開

    奥田修二郎, 渡辺由, 守屋勇樹, 河野信, 山本格, 松本雅記, 高見知世, 小林大樹, 荒木令江, 吉沢明康, 田畑剛, 杉山直幸, 五斗進, 石濱泰

    日本分子生物学会年会プログラム・要旨集(Web)   39th   ROMBUNNO.1PS7‐4(2P‐0039) (WEB ONLY)   2016

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  • Interactome解析によるNF1腫瘍内のTCTP‐翻訳伸長因子複合体の機能解明

    小林大樹, 徳田高穂, 長山慈, 佐藤恭介, 平山未央, 大槻純男, 荒木令江

    日本プロテオーム学会大会プログラム・抄録集   2016   133 - 77   2016

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    DOI: 10.14889/jhupo.2016.0.77.0

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  • jPOST:プロテオーム解析ワークフローの標準化

    守屋勇樹, 河野信, 奥田修二郎, 山本格, 松本雅記, 小林大樹, 荒木令江, 吉沢明康, 五斗進, 田畑剛, 杉山直幸, 石濱泰

    日本生化学会大会(Web)   88th   3P0417 (WEB ONLY) - [3P0417]   2015

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  • Interactome analysis identified a novel interaction form of TCTP and translaton elongation factors in Neurofibromatosis-type 1-associated tumors.

    小林大樹, 徳田高穂, 長山慈, 平山未央, 大槻純男, 荒木令江

    日本生化学会大会(Web)   88th   3LBA121 (WEB ONLY)   2015

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  • 融合プロテオミクスによる神経線維腫I型(NF1)病態モデル細胞内で活性化する新規Dynein IC2‐GR‐COX‐1シグナルの同定

    平山未央, 小林大樹, 荒木令江

    日本薬学会年会要旨集(CD-ROM)   135th   ROMBUNNO.26PB-AM209   2015

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  • プロテオミクスを基盤とした統合オミクスによるがん組織細胞の異常シグナルネットワークの抽出と検証

    荒木(佐藤)令江, 南部(新堀)晶子, シルシリバニト アチト, 小林大樹

    日本生化学会大会(Web)   88th   1W19-1 (WEB ONLY)   2015

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  • jPOST: Japan Proteome Standard Repository/Database

    守屋勇樹, 河野信, 奥田修二郎, 山本格, 松本雅記, 小林大樹, 荒木令江, 吉沢明康, 五斗進, 田畑剛, 杉山直幸, 石濱泰

    日本プロテオーム学会大会プログラム・抄録集   2015 (Web)   2015

  • 融合プロテオミクスによって同定された神経線維腫症1型(NF1)新規病態関連因子TCTPのNF1腫瘍内における機能と役割

    小林 大樹, 荒木 令江

    日本臨床プロテオーム研究会要旨集   2015   19   2015

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    DOI: 10.14905/jscp.2015.0_19

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  • Functional proteomic analysis identified a novel interaction form of TCTP and translaton elongation factors in Neurofibromatosis-type 1-associated tumors

    Kobayashi Daiki, Tokuda Takaho, Nagayama Megumi, Hirayama Mio, Ohtsuki Sumio, Araki Norie

    Abstracts for Annual Meeting of Japanese Proteomics Society   2015   187 - 187   2015

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    DOI: 10.14889/jhupo.2015.0.187.0

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  • Cellular biological validation of proteomics data

    Kobayashi Daiki

    Abstracts for Annual Meeting of Japanese Proteomics Society   2015   107 - 107   2015

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    DOI: 10.14889/jhupo.2015.0.107.0

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  • グリオーマ幹細胞の維持と分化に関わるニッチ分子群の融合プロテオミクスによる解析(Integrated proteomics of niches related to the maintenance and differentiation of glioma initiating cells)

    荒木 令江, 南部 晶子, 堀, 緑川 宇一, 水口 惣平, 小林 大樹, ウイルソン森藤 政代, 秀 拓一郎, 中村 英夫, 倉津 純一

    日本癌学会総会記事   73回   E - 3030   2014.9

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  • 神経皮膚症候群に関する調査研究 神経系細胞増殖に関わる新規NF1関連シグナルTCTP‐mTORの相互調節機構の解析

    荒木令江, 小林大樹, 倉持朗

    神経皮膚症候群に関する調査研究 平成25年度 総括・分担研究報告書   25 - 30   2014

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  • 融合プロテオミクス:新規治療標的分子ネットワーク同定のためのマルチオミクス解析基盤

    小林大樹, 荒木令江

    日本生化学会大会(Web)   87th   2S05A-1 (WEB ONLY)   2014

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  • 融合プロテオミクスによるNF1遺伝子発現抑制細胞内異常シグナルの同定と治療への展望

    平山未央, 小林大樹, 荒木令江

    日本薬学会年会要旨集(CD-ROM)   134th   ROMBUNNO.S26-6   2014

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  • 全自動2次元電気泳動装置を用いた前立腺がんの特異的翻訳後修飾タンパク質群のプロファイリング

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    日本生化学会大会(Web)   87th   3P-372 (WEB ONLY) - 372]   2014

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  • A quick profiling system for cancer marker proteins with multiple post-translational modifications by a fully automated 2DE device, Auto-2D

    Nishimura Munenori, Unuma Yutaka, Araki Norie, Midorikawa Uichi, Nagayama Megumi, Kobayashi Daiki, Murakami Yoji, Sasao Akira, Kawano Yoshiaki, Imamura Takahisa, Wada Yoshihiro

    Abstracts for Annual Meeting of Japanese Proteomics Society   2014 ( 0 )   123 - 123   2014

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    DOI: 10.14889/jhupo.2014.0.123.0

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  • Functional proteomic analysis of novel Neurofibromatosis type 1 (NF1)-related protein TCTP

    Kobayashi Daiki, Nagayama Megumi, Hirayama Mio, Ohtsuki Sumio, Araki Norie

    Abstracts for Annual Meeting of Japanese Proteomics Society   2014   55 - 55   2014

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    DOI: 10.14889/jhupo.2014.0.55.0

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  • 融合プロテオミクスによるグリオーマ幹細胞の分化誘導機構と治療ターゲット分子の解析(Analysis of the differentiation mechanism of glioma initiating cells by the integrated proteomics)

    荒木 令江, 南部 晶子, 堀, 緑川 宇一, 水口 惣平, 秀 拓一郎, 小林 大樹, ウイルソン森藤 政代, 菰原 義弘, 中村 英夫, 竹屋 元裕, 倉津 純一

    日本癌学会総会記事   72回   136 - 136   2013.10

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  • 融合プロテオミクスによる神経線維腫症1型(NF1)病態モデル細胞内活性化シグナルDynein IC2‐GR‐COX‐1の同定

    小林大樹, 平山未央, 水口惣平, 森川崇, 長山慈, 緑川宇一, WILSON‐MORIFUJI Masayo, 南部(新堀)晶子, 吉沢明康, 河野信, 荒木令江

    日本生化学会大会(Web)   86th   1T14P-11(1P-314) (WEB ONLY)   2013

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  • 融合プロテオミクスによるグリオーマ幹細胞の分化ニッチと悪性化メカニズムの解析

    荒木令江, 南部(新堀)晶子, 緑川宇一, 小林大樹, 水口惣平, 永井美奈子, 秀拓一郎, 中村英夫, 倉津純一

    日本生化学会大会(Web)   86th   1T10P-14(2P-401) (WEB ONLY)   2013

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  • 神経皮膚症候群に関する調査研究 融合プロテオミクスによる神経系細胞分化に関わるNF1腫瘍抑制遺伝子関連タンパク質の解析

    荒木令江, 小林大樹, 平山未央, 倉持朗

    神経皮膚症候群に関する調査研究 平成24年度 総括・分担研究報告書   33 - 39   2013

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  • 融合プロテオミクスによる新規神経線維腫症1型(NF1)関連因子TCTPの同定と,そのNF1腫瘍における機能解析

    小林大樹, 平山未央, 菰原義弘, 水口惣平, ウィルソン(森藤, 政代, 尹浩信, 竹屋元裕, 倉持朗, 荒木令江

    日本生化学会大会(Web)   85回   2T01 - 07   2012.12

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  • 全自動2次元電気泳動装置を用いた腫瘍マーカータンパク質の解析

    西村 宗徳, 緑川 宇一, 長山 慈, 小林 大樹, 平山 未央, 廣田 由夏, 村上 洋嗣, 和田 孝浩, 今村 隆寿, 直江 秀昭, 佐々木 裕, 鵜沼 豊, 荒木 令江

    日本生化学会大会プログラム・講演要旨集   85回   2P - 667   2012.12

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  • 神経皮膚症候群に関する調査研究 融合プロテオミクスによる神経系細胞分化に関わるNF1腫瘍抑制遺伝子関連細胞内タンパク質ネットワークの解析

    荒木令江, 小林大樹, 平山未央

    神経皮膚症候群に関する調査研究 平成23年度 総括・分担研究報告書   61 - 66   2012

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  • Identification and functional analysis of translationally controlled tumor protein (TCTP) as a novel therapeutic target for Neurofibromatosis type 1 (NF1)-associated tumors by integrated proteomics.

    Kobayashi Daiki, Hirayama Mio, Komohara Yoshihiro, Mizuguchi Souhei, Wilson-Morifuji Masayo, Ihn Hironobu, Takeya Motohiro, Kuramochi Akira, Araki Norie

    Abstracts for Annual Meeting of Japanese Proteomics Society   2012 ( 0 )   172 - 172   2012

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    DOI: 10.14889/jhupo.2012.0.172.0

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  • 融合プロテオミクスによるグリオーマ幹細胞の分化誘導ニッチの解析

    荒木令江, 南部(新堀)晶子, 緑川宇一, 永井美奈子, 小林大樹, 水口惣平, 秀拓一郎, 中村英夫, 菰原義弘, 竹屋元裕, 倉津純一

    日本生化学会大会(Web)   85th   2T01-08 (WEB ONLY)   2012

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  • 融合プロテオミクスによる悪性脳腫瘍化学治療耐性に関わる分子ネットワークの解析

    荒木令江, 水口惣平, 森川崇, 坪田誠之, 小林大樹, 平山未央, 緑川宇一, 南部晶子, 中村英夫, 倉津純一

    生化学   ROMBUNNO.2T16P-15   2011

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  • 融合プロテオミクスによるNF1腫瘍抑制遺伝子産物Neurofibrominの機能欠損による神経系細胞内異常シグナルの解析

    平山未央, 小林大樹, 森川崇, 長山慈, 緑川宇一, 水口惣平, 荒木令江

    生化学   ROMBUNNO.3T14P-9   2011

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  • 神経皮膚症候群に関する調査研究 融合プロテオミクスによる神経系細胞分化に関わるNF1腫瘍抑制遺伝子関連タンパク質の解析

    荒木令江, 小林大樹, 平山未央, 尹浩信, 竹屋元裕, 菰原義弘, 倉持朗

    神経皮膚症候群に関する調査研究 平成22年度 総括・分担研究報告書   59 - 64   2011

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  • Analysis of abnormal cellular signals via silencing of NF1 tumor suppressor protein in neuronal cells by integrated proteomics

    Hirayama Mio, Kobayashi Daiki, Morikawa Takashi, Nagayama Megumi, Midorikawa Uichi, Mizuguchi Sohei, Araki Norie

    Abstracts for Annual Meeting of Japanese Proteomics Society   2011   104 - 104   2011

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    DOI: 10.14889/jhupo.2011.0.104.0

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  • 神経皮膚症候群に関する調査研究 融合プロテオミクスによる神経系細胞分化に関わるNF1腫瘍抑制遺伝子関連タンパク質の解析

    荒木令江, 小林大樹, 平山未央, 尹浩信

    神経皮膚症候群に関する調査研究 平成21年度 総括・分担研究報告書   53 - 58   2010

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  • 融合プロテオミクスによるNF1腫瘍抑制タンパク質の神経系細胞内発現抑制による異常シグナルの解析

    平山未央, 小林大樹, 森川崇, 長山慈, 緑川宇一, 水口惣平, 荒木令江

    生化学   ROMBUNNO.4P-0212   2010

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  • FUNCTIONAL ANALYSIS OF THE PROTEOME RELATED TO THE CHEMOTHERAPY SENSITIVITY IN ANAPLASTIC OLIGODENDROGLIOMA AND ANAPLASTIC OLIGOASTROCYTOMA

    Nobuyuki Tsubora, Takashi Morikawa, Uichi Midorikawa, Daiki Kobayashi, Hideo Nakamura, Junichi Kuratsu, Norie Araki

    NEURO-ONCOLOGY   11 ( 6 )   931 - 931   2009.12

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  • 統合プロテオミクスとバイオインフォマティクスの手法を用いた脳腫瘍の化学治療感受性に関するVimentinを介したネットワークの解析

    水口惣平, 森川崇, 坪田誠之, 緑川宇一, 長山慈, 小林大樹, WILSON Anthony, ウィルソン(森藤, 政代, 中村英夫, 倉津純一, 荒木令江

    生化学   ROMBUNNO.2T4A-3   2009.9

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  • 抗体カクテルとnatural protein chipを用いた簡便な病態関連分子群解析法の開発

    荒木令江, 森川崇, 坪田誠之, 緑川宇一, 水口惣平, 小林大樹, 新堀晶子, 中村英夫, 倉津純一

    生化学   ROMBUNNO.4T15A-9   2009.9

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  • プロテオミクス手法による神経系細胞分化に関わるNF1腫瘍抑制遺伝子関連タンパク質の同定とその役割

    小林大樹, 平山未央, ウィルソン(森藤, 政代, 水口惣平, 長山慈, 森川崇, 新堀晶子, 坪田誠之, 緑川宇一, 荒木令江

    生化学   ROMBUNNO.4P-790   2009.9

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  • Proteomic approach to investigate the mechanisms for acquired Imatinib resistance in chronic myeloid leukemia cell line K562 cells

    Takeru Nambu, Takashi Morikawa, Daiki Kobayashi, Akihiko Kuniyasu, Akinobu Hamada, Norie Araki, Hideyuki Saito

    CANCER RESEARCH   69   2009.5

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  • 退形成性乏突起膠腫(AOG)における化学療法感受性に関連する蛋白質群の機能プロテオーム解析

    森川崇, 坪田誠之, 緑川宇一, 長山慈, 小林大樹, WILSON Anthony, WILSON(森藤, 政代, 中村英夫, 倉津純一, 森安眞津子, 荒木令江

    日本蛋白質科学会年会プログラム・要旨集   9th   116   2009.4

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  • iTRAQ試薬を用いたLC‐ショットガンおよび2D‐DIGEによるPC12細胞分化のプロテオーム解析

    小林大樹, 森川崇, 熊谷次郎, WILSON Anthony, 長山慈, 南部健, WILSON‐MORIFUJI Masayo, 荒木令江

    日本蛋白質科学会年会プログラム・要旨集   8th   71   2008.5

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  • NGF刺激によるPC12細胞分化に関わる新規蛋白質のプロテオミクスによる同定とその役割

    小林大樹, 森川崇, 熊谷次郎, ウィルソン(森藤, 政代, WILSON Anthony, 長山慈, 坪田誠之, 荒木令江

    生化学   3P-0139   2008

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  • Proteomic analysis of phosophorylated proteins related to the chemosensitivity in glioma using 2D-DIGE combined with phospho-specific staining

    Takashi Morikawa, Nobuyuki Tsubota, Megumi Nagayama, Daiki Kobayashi, Anthony Wilson, Masayo Wilson, Hideo Nakamura, Junichi Kuratsu, Matsuko Moriyasu, Norie Araki

    JOURNAL OF PHARMACOLOGICAL SCIENCES   106   245P - 245P   2008

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  • Functional Analysis of Neuronal Cellular Tumor Suppressors by Assembled Proteomic Strategies

    Araki Norie, Kobayashi Daiki, Morikawa Takashi, Wilson Morifuji Masayo, Tsubota Nobuyuki, Wilson Anthony, Nagayama Megumi, Saya Hideyuki

    Abstracts for Annual Meeting of Japanese Proteomics Society   2008   97 - 97   2008

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    Language:Japanese   Publisher:Japanese Proteomics Society (Japan Human Proteome Organisation)  

    Under the assembled proteomic analysis system, we have been studying the role of tumor related gene functions in cancer cells with two quantitative proteomic strategies. In this study, we focused on the function of neuronal tumor suppressors in NGF induced neuronal model cell PC12. To obtain a new set of functional protein information related to the biological processes, we identified specific proteins in PC12 cells after treatment of NGF and a siRNA of NF1 neuronal tumor suppressor by assembled proteomic strategies, such as differential analysis with iTRAQ (4-Plex) methods and differential phospho-protein analysis with 2D-DIGE coupled with proQ Diamond methods. At the moment more than 5000 non redundant cellular proteins were identified from the combined data by both of LC-MALDI and ESI-MS/MS analysis, and out of about 1500 proteins semi-quantitatively identified, 72 proteins were uniquely identified as differentially expressed in response to NGF and NF1 siRNA stimulations in PC12 cells. Parallel analysis was performed with affinity cellular mapping to identify 58 NF1 specific associating proteins by iTRAQ analysis, and the data obtained from all of the analysis were merged together and the most interesting signal molecules being expected to be drug targets were extracted after several mining protocols. We focused the novel neuronal cell survival, motility, and differentiation related protein cascades. The biological validation was performed by the 2D-western blotting and Time laps and confocal fluorescent microscopic analysis with using the specific antibodies and their inhibitors. The results suggest that the proteins identified in this study are strongly related to neuronal cellular differentiation, survival, and pathogenesis of NF1 with a specific kinase cascade such as CDK5, GSK-3b and Rho kinase, and assembled proteomic analysis are useful for the comprehensive functional proteome analysis to understand cellular biological mechanisms.

    DOI: 10.14889/jhupo.2008.0.97.0

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  • 慢性骨髄性白血病細胞におけるメシル酸イマチニブ耐性獲得機序の解析

    南部健, 南部健, 森川崇, 小林大樹, 國安明彦, 中島麗子, 濱田哲暢, 渡邊博志, 川口辰哉, 荒木令江, 齋藤秀之

    生化学   2007

  • 融合プロテオミクスによるヒト舌癌細胞における高転移性癌細胞増殖の分子メカニズムの解析

    ウィルソン森藤, 田代康介, WILSON Anthony Wayne, 森川崇, 小林大樹, 坪田誠之, 荒木令江

    生化学   3P-0104   2007

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  • 2D‐DIGEによる脳腫瘍化学治療感受性に関連する蛋白質群の解析

    森川崇, 坪田誠之, 永山慈, 小林大樹, WILSON Anthony, ウィルソン(森藤, 政代, 中村英夫, 倉津純一, 森安眞津子, 荒木令江

    生化学   4P-0911   2007

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  • iTRAQ法を用いた神経突起伸長に関わる細胞内タンパク質群の網羅的同定と,データマイニングによるこれら分子群の細胞内機能解析

    小林大樹, 熊谷次郎, PATRAKITKOMJORN Siriporn, 森川崇, 南部健, ウィルソン(森藤, 政代, 林田美和, WILSON Anthony, 荒木令江

    生化学   2P-1478   2007

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  • Analysis of cellular signal proteins related to the neuronal differentiation via neurofibromatosis type I tumor suppressor gene product by iTRAQ diffrential display

    Kobayashi Daiki, Patrakitkomjorn Siriporn, Morikawa Takashi, Fujimura Yoshinori, Kobayashi Takayuki, Kubo Miwa, Saya Hideyuki, Araki Norie

    Abstracts for Annual Meeting of Japanese Proteomics Society   2006   47 - 47   2006

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    DOI: 10.14889/jhupo.2006.0.47.0

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  • Analysis of cellular signal transduction of neuronal tumor suppressor gene product by proteomic strategy

    Araki Norie, Patrakitkomjorn Siriporn, Kobayashi Daiki, Aoki Masashi, Cho Keiko, Morikawa Takashi, Kubo Miwa, Saya Hideyuki

    Abstracts for Annual Meeting of Japanese Proteomics Society   2006   45 - 45   2006

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    DOI: 10.14889/jhupo.2006.0.45.0

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  • 多機能プロテアーゼインヒビターの創製とその性質

    稲永英子, 小林大樹, 上妻由章, 木村誠, 山崎信行, 青木智佐, 河原畑勇

    日本農芸化学会誌   75 ( 2 )   252   2001.2

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  • 多機能プロテアーゼインヒビターの創製とその性質

    稲永英子, 小林大樹, 上妻由章, 木村誠, 山崎信行, 青木智佐, 河原畑勇

    日本農芸化学会西日本支部大会およびシンポジウム講演要旨集   2000   87   2000.10

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Presentations

  • NGF刺激によるPC12細胞分化に関わる新規蛋白質のプロテオミクスによる同定とその役割

    BMB2008(第31回日本分子生物学会年会・第80回日本生化学会大会 合同大会)  2008 

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Awards

  • 2014年度日本プロテオーム学会奨励賞

    日本プロテオーム学会  

    小林 大樹

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  • 令和2年度新潟大学優秀論文表彰

    小林 大樹

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Research Projects

  • 神経線維腫症の神経系細胞異常分化と腫瘍化の責任因子シグナルと治療標的の解明

    Grant number:22H03187

    2022.4 - 2025.3

    System name:科学研究費助成事業 基盤研究(B)

    Research category:基盤研究(B)

    Awarding organization:日本学術振興会

    荒木 令江, 武笠 晃丈, 江良 択実, 福島 聡, 藤田 美歌子, 小林 大樹, 北川 孝雄, 南部 晶子

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    Grant amount:\17550000 ( Direct Cost: \13500000 、 Indirect Cost:\4050000 )

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  • プロテオーム熱安定性評価法(TPP)によるがん細胞の酸化ストレス耐性機構の解明

    Grant number:22K07144

    2022.4 - 2025.3

    System name:科学研究費助成事業 基盤研究(C)

    Research category:基盤研究(C)

    Awarding organization:日本学術振興会

    小林 大樹

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    Grant amount:\4160000 ( Direct Cost: \3200000 、 Indirect Cost:\960000 )

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  • 質量分析によるアミノ酸配列de novo決定のための新規手法開発

    Grant number:20H03245

    2020.4 - 2023.3

    System name:科学研究費助成事業 基盤研究(B)

    Research category:基盤研究(B)

    Awarding organization:日本学術振興会

    河野 信, 岩崎 未央, 小林 大樹, 吉沢 明康

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    Grant amount:\17680000 ( Direct Cost: \13600000 、 Indirect Cost:\4080000 )

    本研究の目的は、アミノ酸配列の配列データベースを用いない同定(de novo sequencing)を行うにあたって、通常はアルゴリズムを用いて情報学的に行われてきた配列候補の絞り込み(枝刈り)を、新規の実験系から取得した物性情報を用いることによる実験情報に基づく枝刈りに代えることによって、既存手法の問題点を回避した新規手法を開発することである。ただし本年度は、「8.進捗状況」にも記載したようにCOVID-19蔓延の影響を受けて様々な点で研究遂行が妨げられた。このため、当初の計画に比べて達成できた内容が少ない。具体的には以下の項目を実施した。
    ・情報学的研究:de novo sequencingを行うための先行ソフトウェアであるPEAKS(商用ソフト)を用いたベンチマーク実験を実施し、特にsequencingに失敗するアミノ酸配列の特徴について調査した。
    ・情報学的研究:de novo sequencingを行うときに、アミノ酸配列の絞り込み(枝刈り)を行うのに有効と思われる物性情報を探索するために、仮想配列のデータベースを用いたde novo sequencing法のシミュレーションを行った。
    ・情報学的研究:本手法を実装して公開するためのオープンソース・ソフトウェア・プラットフォーム(Mass++ ver.4)の開発に着手した(本件は、本研究グループ以外との共同開発である)。
    ・実験的研究:ベンチマークに用いる予定の合成ペプチドの作成を行い、マススペクトルおよび液体クロマトグラフィーの保持時間の情報を質量分析計を用いて取得した。

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  • TCTP-EF1A2による翻訳制御を標的としたNF1腫瘍化機構の解析と治療法開発

    Grant number:19K07691

    2019.4 - 2022.3

    System name:科学研究費助成事業 基盤研究(C)

    Research category:基盤研究(C)

    Awarding organization:日本学術振興会

    小林 大樹, 荒木 令江

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    Grant amount:\4290000 ( Direct Cost: \3300000 、 Indirect Cost:\990000 )

    神経線維腫症Ⅰ型(NF1)は3000人に1人の割合で発症する遺伝性疾患で、悪性神経鞘腫瘍(MPNST)やグリオーマを発症することが知られている。本研究室の以前の研究結果から、NF1腫瘍細胞内ではTranslationally Controlled Tumor Protein (TCTP)の発現が上昇しており、悪性度の高いNF1腫瘍ではTCTPの発現量が高くなる傾向にあることを明らかにした1) 2)。加えて、TCTPはEF1A2を中心としたNF1腫瘍特異的な翻訳伸長因子群との相互作用によって、NF1腫瘍の悪性化に寄与することを明らかにした。本研究では、TCTPと相互作用するタンパク質の同定と、それらの相互作用部位の特定をクロスリンク質量分析法によって行い、TCTPの構造と機能を解明することでTCTPのNF1腫瘍治療ターゲットとしての有用性を検討した。その結果、TCTPは、EF1A2のホモ二量体構造を形成する部位と拮抗的に結合し、EF1A2の二量体化を阻害することで、EF1A2の翻訳機能を活性化することが考えられた。また、EF1A2のGTP結合領域で翻訳伸長因子群との複合体の形成を媒介することによって、TCTPはEF1A2の活性化に寄与することが示唆された。これらの情報をもとに、TCTPとNF1腫瘍特異的な翻訳伸長因子群の立体構造形成を阻害するような薬剤を選択的に用いることで、NF1に関連する腫瘍の治療の開発に応用できることが期待される。

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  • Metabolic adaptation of type 2 diabetes

    Grant number:17H06300

    2017.6 - 2022.3

    System name:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Research category:Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

    Awarding organization:Japan Society for the Promotion of Science

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    Grant amount:\237900000 ( Direct Cost: \183000000 、 Indirect Cost:\54900000 )

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  • Identification and fuctional analysis of a novel molecular signal network related to NF1 tumorigenesis via the activation of translation mediated by TCTP

    Grant number:16K07118

    2016.4 - 2020.3

    System name:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C)

    Research category:Grant-in-Aid for Scientific Research (C)

    Awarding organization:Japan Society for the Promotion of Science

    Kobayashi Daiki

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    Grant amount:\4940000 ( Direct Cost: \3800000 、 Indirect Cost:\1140000 )

    In order to elucidate the pathogenesis of neurofibromatosis type 1 (NF1), we investigated the role of TCTP-mediated translational control mechanism in NF1 tumor cells. TCTP significantly binds to the translation elongation factor complex, and in particular, TCTP forms a complex with the translation elongation factors including EF1A2, which promotes protein translation in NF1 tumor cells. Therefore, This study demonatrates that TCTP promotes the pathogenesis of NF1 tumor by activating the protein translation elongation by interacting with EF1A2.

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  • Elucidation of functional roles of a novel related protein, TCTP, in NF1 tumors

    Grant number:26830079

    2014 - 2015

    System name:Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)

    Research category:Grant-in-Aid for Young Scientists (B)

    Awarding organization:Japan Society for the Promotion of Science

    Kobayashi Daiki

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    Authorship:Principal investigator  Grant type:Competitive

    Grant amount:\4030000 ( Direct Cost: \3100000 、 Indirect Cost:\930000 )

    Neurofibromatosis type 1 (NF1) is an autosomal dominant disease that predisposes individuals to developing benign neurofibromas and malignant peripheral nerve sheath tumors (MPNSTs). Owing to the lack of information on the molecular mechanism of NF1-associated tumor pathogenesis, biomarkers, and therapeutic targets, a radical treatment for NF1 tumors has not been established. To analyze the function of a novel NF1-related protein, TCTP, in detail in NF1-associated tumor, we identified the TCTP-interacting proteins by proteomic approach. As a result, TCTP interacts with proteins related to protein translation mechinery and stress. Especially, TCTP specifically interacts with EF1A2, suggesting that the interaction between TCTP and EF1A2 contributes to the formation of NF1-tumor specific translational machinery. Our findings also suggest that the inhibition of TCTP-EF1A2 interaction is a therapeutic target for NF1-associated tumors.

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  • Analysis of the molecular mechanism and clinical targets for neural tumors via the loss of function of NF1/NF2 gene products

    Grant number:25293312

    2013.4 - 2016.3

    System name:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

    Araki Norie, KURATSU Junichi, NAKAMURA Hideo

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    Grant amount:\18200000 ( Direct Cost: \14000000 、 Indirect Cost:\4200000 )

    Neurofibromatosis type 1/2 (NF1/2) is an autosomal dominant disease that predisposes individuals to develop neural tumors including neurofibromas and malignant tumors etc. To identify novel biological targets for NF-associated tumors, a unique integrated-omics was performed, and a novel abnormal network, “Translationally controlled tumor protein (TCTP)-mTOR/EF signalings” was identified. This network activates the MAPK/PI3K-AKT-mTOR and specific EF1 complex associated translational signalings in NF1 tumors. In NF1-deficient MPNST cells, MAPK/PI3K/mTOR inhibitors downregulated TCTP associated cell expansions, and TCTP knockdown (or overexpression) suppressed (or activated) mTOR/EF1 signalings. Artesunate, a TCTP target, inhibited the TCTP-mTOR/EF1 signal cascade and suppressed the viability of MPNST cells significantly. These findings suggest that TCTP-mTOR/EF signaling is implicated in the progression of NF1-tumors and could serve as a biological target for the specific therapy.

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  • Elucidation of the pathogenic mechanism of, and construction of therapeutic strategy for, Neurofibromatosis type 1-associated tumors via TCTP

    Grant number:24700981

    2012.4 - 2014.3

    System name:Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B)

    Research category:Grant-in-Aid for Young Scientists (B)

    Awarding organization:Japan Society for the Promotion of Science

    KOBAYASHI Daiki

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    Grant amount:\4420000 ( Direct Cost: \3400000 、 Indirect Cost:\1020000 )

    Neurofibromatosis type-1 (NF1) is an inherited disorder that presents various pathological conditions including benign neurofibromas and malignant tumors. Due to the lack of information on the molecular mechanism of NF1-associated tumor pathogenesis or biomarkers/therapeutic targets, a radical treatment for NF1 tumors has not been established. In this study, we evaluated whether the novel NF1-associated protein, translationally controlled tumor protein (TCTP), could be a novel biomarker and therapeutic target for NF1-associated tumors. We found that TCTP expression level correlated with their malignancy and contributes to NF1-associated tumor cell growth. Collective to our findings, it is expected that a diagnostic method and therapeutic strategies targeting TCTP for NF1-associated tumors has been developed.

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  • Analysis of cellular signal transduction via Neurofibromatosis tumor suppressor gene products and development of their clinical targets

    Grant number:19390382

    2007 - 2009

    System name:Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)

    Research category:Grant-in-Aid for Scientific Research (B)

    Awarding organization:Japan Society for the Promotion of Science

    ARAKI Norie, SAYA Hideyuki, NAKAMURA Hideo, KOBAYASHI Daiki

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    Grant amount:\18590000 ( Direct Cost: \14300000 、 Indirect Cost:\4290000 )

    Neurofibromatosis (NF) tumor suppressor gene products, neurofibromin : NF1 and merlin : NF2, are though to be important regulators of cellular growth, differentiation, and apoptosis, and implicated in the neural abnormality of NF patients. However, the precise cellular function of NF proteins has yet to be clarified. In this study, we utilized proteomic strategies, functional annotation with a proprietary gene ontology (MANGO), and standard biochemical methods to identify proteins related to neuronal differentiation in PC12 cells, which serve as a representative model system for studying NF related neuronal biological processes. Of 1,600 non-redundant proteins quantitatively identified, 72 were novel nerve growth factor-responsive PC12 proteins mostly related to the biological processes of cell morphogenesis, apoptosis/survival, and cell differentiation. Using these proteomic strategies and database, we identified a set of NF-associating cellular proteins, including axon regulator CRMP-2. These associations were crucial for the axon formation in neuron and were regulated by a series of kinase activations by CDK5, GSK-3b, and Rho kinase being controlled by neurofibromin. Our study demonstrates that the functional association of NF proteins and their associating proteins are essential for neuronal cell differentiation and that lack of expression or abnormal regulation of NF proteins can result in impaired function of neural cells, which is likely a factor in NF-related pathogenesis.

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