Dr. Yoshibumi UEDA

Research and Professional Experience

1994-1997  The University of Tokyo, Natural sciences II
Obtain a bachelor's degree of science (1998, Mar)
1998-2003 Department of Chemistry, School of Science, the University of Tokyo
Obtain a doctorate of science (2004, Mar)
2004-2007 Lipid biology laboratory, RIKEN, Japan,
Postdoctoral fellow (Head of laboratory: Dr. Toshihide Kobayashi)
The Picower Institute for Learning and Memory,
Massachusetts Institute of Technology (MIT), USA and
Laboratory for Memory mechanisms, Brain Science Institute, RIKEN, Japan
Postdoctoral fellow (Head of laboratory: Dr. Yasunori Hayashi)
2013-2015 Department of Hematology and Immunology, Kanazawa Medical University, Japan
Assistant professor (Head of laboratory: Dr. Toshiro Okazaki)
2016-2018 Graduate School of Arts and Sciences, College of Arts and Sciences, The University of Tokyo.
AMED-PRIME researcher (Head of laboratory: Dr. Moritoshi Sato)
2019-current Analytical chemistry, School of science, The University of Tokyo
Postdoctoral fellow (Head of laboratory: Dr. Takeaki Ozawa)

Research Interests
My interest is lipid biology. Lipids play important roles in a variety of cellular functions such as learning and memory, and cancer growth and metastasis. However, how lipids work for these functions remains unknown. I have revealed the mechanisms using brand-new techniques such as förester resonance energy transfer (FRET) and fluorescence lifetime (FLIM) and two-photon microscopy. I have been through a broad spectrum of experiences including chemistry (The University of Tokyo), cell biology (RIKEN), brain science (Picower institute in Massachusetts Institute of Technology), medical science (Kanazawa medical University), and optogenetics (The University of Tokyo). Currently, I especially focus on the study using optogenetics how lipids regulate cancer metastasis, and mental disorder.


 Original Papers

  • Mechanistic insights into cancer drug resistance through optogenetic PI3K signaling hyperactivation.
    Y. Ueda*, Y. Miura, N. Tomishige, N. Sugimoto, M. Murase, G. Kawamura, N. Sasaki, T. Ishiwata, and T. Ozawa*,
    Cell Chem. Biol., in press

  • Increased spine PIP3 is sequestered from dendritic shafts.
    Y. Ueda, N. Sugimoto and T. Ozawa,
    Mol. Brain, 15, 59 (2022). doi: 10.1186/s13041-022-00944-5.

  • Sphingomyelin localization in the intestinal crypt surface.
    Y. Ueda, M. Abe, T. Ishiwata and T. Ozawa,
    Biochem. Biophys. Res. Commun.., 611, 14–18 (2022). doi: 10.1016/j.bbrc.2022.03.128

  • Deficiency of sphingomyelin synthase 2 prolongs survival by inhibition of lymphoma infiltration through ICAM-1 reduction
    Taniguchi M, Ueda Y, Matsushita M, Nagaya S, Hashizume C, Arai K, Kabayama K, Fukase K, Watanabe K, Hayashi K, Okazaki T.,
    FASEB J., Accepted, 201901783RR(2019).

  • Establishment and characterization of a novel neuroendocrine carcinoma cell line derived from a human ascending colon tumor
    Shinji S, Sasaki N, Yamada T, Koizumi M, Ohta R. Matsuda A, Yokoyama Y, Takahashi G, Hotta M, Hara K, Takeda K, Ueda K, Kuriyama S, Ishiwata T, Ueda Y, Murakami T, Kanazawa Y, Yoshida H.,
    Cancer Sci, 110, 3708-3717(2019).

  • Corticosterone inhibits the expression of cannabinoid receptor-1 and cannabinoid receptor agonist-induced decrease in cell viability in glioblastoma cells.
    Sugimoto N, Ishibashi H, Ueda Y, Nakamura H, Yachie A, Ohno-Shosaku T.,
    Oncol Lett., 2019 Aug;18(2):1557-1563.

  • A split CRISPR-Cpf1 platform for inducible genome editing and gene activation.
    Nihongaki Y, Otabe T, Ueda Y, Sato M.,
    Nat Chem Biol., 2019 Sep;15(9):882-888.

  • Protein Engineering of Dual-Cys Cyanobacteriochrome AM1_1186g2 for Biliverdin Incorporation and Far-Red/Blue Reversible Photoconversion.
    Kuwasaki Y, Miyake K, Fushimi K, Takeda Y, Ueda Y, Nakajima T, Ikeuchi M, Sato M, Narikawa R.,
    Int J Mol Sci., 2019 Jun 15;20(12).

  • Rational conversion of chromophore selectivity of cyanobacteriochromes to accept mammalian intrinsic biliverdin.
    Fushimi K, Miyazaki T, Kuwasaki Y, Nakajima T, Yamamoto T, Suzuki K, Ueda Y, Miyake K, Takeda Y, Choi JH, Kawagishi H, Park EY, Ikeuchi M, Sato M, Narikawa R.,
    Proceedings of the National Academy of Sciences of the United States of America, 116, 8301-8309(2019).

  • Yamamoto S, Iwamaru Y, Shimizu Y, Ueda Y, Sato M, Yamaguchi K, Nakanishi J.
    Epidermal growth factor-nanoparticle conjugates change the activity from anti-apoptotic to pro-apoptotic at membrane rafts.
    Acta Biomater. 2019 Feb 19. pii: S1742-7061(19)30139-4.

  • Heat attenuates sensitivity of mammalian cells to capsaicin.
    Sugimoto N, Matsuzaki K, Katakura M, Nakamura H, Ueda Y, Yachie A, Shido O.
    J Biochem Mol Toxicol. 2019 Jan 23:e22288.

  • Ueda Y (Corresponding author), Ii T, Aono Y, Sugimoto N, Shinji S, Yoshida H, Sato M.
    Membrane dynamics induced by a PIP3 optogenetic tool.
    Anal Sci. 2018 Nov 2. doi: 10.2116/analsci.

  • Shinji S, Ueda Y † (†Co-first author, Co-corresponding author), Yamada T, Koizumi M, Yokoyama Y, Takahashi G, Hotta M, Iwai T, Hara K, Takeda K, Okusa M, Kan H, Uchida E, Yoshida H.
    Male sex and history of ischemic heart disease are major risk factors for anastomotic leakage after laparoscopic anterior resection in patients with rectal cancer
    BMC Gastroenterol. 2018 Jul 17;18(1):117.

  • Ueda Y*, Ishiwata T, Shinji S, Arai T, Matsuda Y, Aida J, Sugimoto N, Okazaki T, Kikuta J, Ishii M, Sato M. (*Corresponding author)
    In vivo imaging of T cell lymphoma infiltration process at the colon
    Scientific Reports, (2018) Mar 5;8(1):3978.

  • Shinji S, Ueda Y, Yamada T, Koizumi M, Yokoyama Y, Takahashi G, Hotta M, Iwai T, Hara K, Takeda K, Okusa M, Kan H, Uchida E.
    Combined use of preoperative lymphocyte counts and the post/preoperative lymphocyte count ratio as a prognostic marker of recurrence after curative resection of stage II colon cancer
    Oncotarget., (2017) Dec 20;9(2):2553-2564.

  • Furuya A, Kawano F, Nakajima T, Ueda Y, Sato M.
    Assembly domain-based optogenetic system for the efficient control of cellular signaling.
    ACS Synthetic Biology, (2017) doi: 10.1021/acssynbio.7b00022.

  • Taniguchi M, Tasaki T, Ninomiya H, Ueda Y, Kuremoto KI, Mitsutake S, Igarashi Y, Okazaki T, Takegami T.
    Sphingomyelin generated by sphingomyelin synthase 1 is involved in attachment and infection with Japanese encephalitis virus.
    Scientific Reports, 6:37829 (2016)

  • Yu G, Onodera H, Aono Y, Kawano F, Ueda Y, Furuya A, Suzuki H, Sato M.
    Optical manipulation of the alpha subunits of heterotrimeric G proteins using photoswitchable dimerization systems
    Scientific Reports, 6:35777 (2016)

  • Ueda Y, Ogiso H, Sato M, Umezawa Y, Okazaki T, Kobayashi T.
    Asymmetrical diacylglycerol dynamics at the cytosolic and lumenal sides of a single endomembrane in living cells
    Scientific Reports, 5:12960 (2015)

  • Takagishi T, Oda M, Kabura M, Kurosawa M, Tominaga K, Urano S, Ueda Y, Kobayashi K, Kobayashi T, Sakurai J, Terao Y, Nagahama M.
    Clostridium perfringens Alpha-Toxin Induces Gm1a Clustering and Trka Phosphorylation in the Host Cell Membrane.
    PLoS One, 10(4):e0120497 (2015)

  • Ogiso H, Taniguchi M, Araya S, Aoki S, Wardhani LO, Yamashita Y, Ueda Y, Okazaki T.
    Comparative Analysis of Biological Sphingolipids with Glycerophospholipids and Diacylglycerol by LC-MS/MS
    Metabolites, 4, 98-114 (2014)

  • Ueda Y* (*Corresponding author) and Hayashi Y.
    PIP3 Regulates Spinule Formation in Dendritic Spines during Structural Long-Term Potentiation.
    Journal of Neuroscience, Vol.33, No.27, 11040-7 (2013).

  • Ueda Y, Makino A, Murase-Tamada K, Sakai S, Inaba T, Hullin-Matsuda F, Kobayashi T.
    Sphingomyelin regulates the transbilayer movement of diacylglycerol in the plasma membrane of Madin-Darby canine kidney cells.
    FASEB Journal, Vol.27, No.8, 3284-3297. (2013).

  • Sato M†, Ueda Y† (†Co-first author), Umezawa Y.
    Imaging diacylglycerol dynamics at organelle membranes.
    Nature Methods, vol3, No 10, 797 - 799. (2006).

  • Sato M, Ueda Y, Shibuya M and Umezawa Y.
    Locating Inositol 1,4,5-Triphosphate in the Nucleus and Neuronal Dendrites with
    Genetically Encoded Fluorescent Indicators.
    Analytical Chemistry, 77, No.15, 4751-4758. (2005)

  • Sato M†, Ueda Y† (†Co-first author), Takagi T, Umezawa Y.
    Production of PtdInsP3 at endomembranes is triggered by receptor endocytosis.
    Nature Cell Biology, 5, 1016 - 1022. (2003).



  • Ueda Y, Sato M.
    Induction of signal transduction using non-channelrhodopsin-type optogenetic tools
    Chembiochem., (2018) doi: 10.1002/cbic.201700635.

  • Ueda Y, Sato M.
    Cell membrane dynamics induction using optogenetic tools.
    Biochem Biophys Res Commun., (2017) Nov 16. pii: S0006-291X(17)32269-6.

  • Ueda Y, Ishitsuka R, Hullin-Matsuda F, Kobayashi T.
    Regulation of the transbilayer movement of diacylglycerol in the plasma membrane 
    Biochimie, 107 Pt A:43-50. (2014)

  • Ueda Y*(*Corresponding author).
    The role of phosphoinositides in synapse function
    Molecular Neurobiology, 50(3):821-38. (2014)

  • Ueda Y, Kwok S. and Hayashi Y.
    Application of FRET probes in the analysis of neuronal plasticity.
    Frontiers in Neural Circuits, Vol.7, No.163, 1-19 (2013).



  • Ueda Y. and Sato M.
    Spatiotemporal Dynamics of Cellular Signaling Processes
    Royal Society of Chemistry
    Optogenetics: Light-driven Actuators and Light-emitting Sensors in Cell Biology_chapter 5

  • 佐藤守俊,上田善文,梅澤喜夫
    PIP3 の可視化動態分析 実験医学 (2004) Vol22, 2141-2146.


 Invited talk

  • 3rd International symposium on Nanoarchitectonics for Mechanobiology
    Lipid control by optogenetics
    Yoshibumi Ueda

  • JCBL: 第60回 日本脂質生化学会
    シンポジウム2 「脂質テクノロジー」
    2018年5月31日 (木)、6月1日 (金)  京王プラザホテル八王子 東京