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Nishimura Yukako

Institute for Genetic Medicine PathophysiologyLecturer

Researcher basic information

■ Degree
  • 学術博士, 東京大学大学院 総合文化研究科
■ URL
researchmap URLホームページURL■ Various IDs
ORCID IDJ-Global ID■ Research Keywords and Fields
Research Field
  • Life Science, Cell biology, Mechanobiology
■ Educational Organization

Career

■ Career
Career
  • Nov. 2022 - Present
    Hokkaido University, Institute for Genetic Medicine, 講師
  • Jan. 2021 - Oct. 2022
    Hokkaido University, Institute for Genetic Medicine, 助教

Research activity information

■ Awards
  • Jun. 2021, 第14回 資生堂女性研究者サイエンスグラント
■ Papers
  • MARK2 regulates directed cell migration through modulation of myosin II contractility and focal adhesion organization.
    Ana M Pasapera; Sarah M Heissler; Masumi Eto; Yukako Nishimura; Robert S Fischer; Hawa R Thiam; Clare M Waterman
    Current biology : CB, 16 May 2022, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Cancer cell migration during metastasis is mediated by a highly polarized cytoskeleton. MARK2 and its invertebrate homolog Par1B are kinases that regulate the microtubule cytoskeleton to mediate polarization of neurons in mammals and embryos in invertebrates. However, the role of MARK2 in cancer cell migration is unclear. Using osteosarcoma cells, we found that in addition to its known localizations on microtubules and the plasma membrane, MARK2 also associates with the actomyosin cytoskeleton and focal adhesions. Cells depleted of MARK proteins demonstrated that MARK2 promotes phosphorylation of both myosin II and the myosin phosphatase targeting subunit MYPT1 to synergistically drive myosin II contractility and stress fiber formation in cells. Studies with isolated proteins showed that MARK2 directly phosphorylates myosin II regulatory light chain, while its effects on MYPT1 phosphorylation are indirect. Using a mutant lacking the membrane-binding domain, we found that membrane association is required for focal adhesion targeting of MARK2, where it specifically enhances cell protrusion by promoting FAK phosphorylation and formation of focal adhesions oriented in the direction of migration to mediate directionally persistent cell motility. Together, our results define MARK2 as a master regulator of the actomyosin and microtubule cytoskeletal systems and focal adhesions to mediate directional cancer cell migration.
  • Crosstalk between myosin II and formin functions in the regulation of force generation and actomyosin dynamics in stress fibers
    Yukako Nishimura; Shidong Shi; Qingsen Li; Alexander D. Bershadsky; Virgile Viasnoff
    Cells & Development, 203736, 203736, Elsevier BV, Aug. 2021, [Peer-reviewed], [Lead author]
    Scientific journal
  • The Formin Inhibitor, SMIFH2, Inhibits Members of the Myosin Superfamily.
    Yukako Nishimura; Shidong Shi; Fang Zhang; Rong Liu; Yasuharu Takagi; Alexander D Bershadsky; Virgile Viasnoff; James R Sellers
    Journal of cell science, 23 Feb. 2021, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, The small molecular inhibitor of formin FH2 domains, SMIFH2, is widely used in cell biological studies. It inhibits formin-driven actin polymerization in vitro, but not polymerization of pure actin. It is active against several types of formins from different species (Rizvi et al., 2009). Here, we found that SMIFH2 inhibits retrograde flow of myosin 2 filaments and contraction of stress fibers. We further checked the effect of SMIFH2 on non-muscle myosin 2A and skeletal muscle myosin 2 in vitro and found that SMIFH2 inhibits myosin ATPase activity and ability to translocate actin filaments in the in vitro motility assay. The inhibition of non-muscle myosin 2A in vitro required a higher concentration of SMIFH2 than for the inhibition of retrograde flow and stress fiber contraction in cells. We also found that SMIFH2 inhibits several other non-muscle myosin types, e.g. mammalian myosin 10, Drosophila myosin 7a and Drosophila myosin 5, more efficient than inhibition of formins. These off-target inhibitions demand additional careful analysis in each case when solely SMIFH2 is used to probe formin functions.
  • mDia1/3-dependent actin polymerization spatiotemporally controls LAT phosphorylation by Zap70 at the immune synapse
    D. Thumkeo; Y. Katsura; Y. Nishimura; P. Kanchanawong; K. Tohyama; T. Ishizaki; S. Kitajima; C. Takahashi; T. Hirata; N. Watanabe; M. F. Krummel; S. Narumiya
    Science Advances, 6, 1, American Association for the Advancement of Science ({AAAS}), 03 Jan. 2020, [Peer-reviewed]
    Scientific journal
  • A mechano-signalling network linking microtubules, myosin IIA filaments and integrin-based adhesions.
    Nisha Bte Mohd Rafiq; Yukako Nishimura; Sergey V Plotnikov; Visalatchi Thiagarajan; Zhen Zhang; Shidong Shi; Meenubharathi Natarajan; Virgile Viasnoff; Pakorn Kanchanawong; Gareth E Jones; Alexander D Bershadsky
    Nature materials, 18, 6, 638, 649, Jun. 2019, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, The interrelationship between microtubules and the actin cytoskeleton in mechanoregulation of integrin-mediated adhesions is poorly understood. Here, we show that the effects of microtubules on two major types of cell-matrix adhesion, focal adhesions and podosomes, are mediated by KANK family proteins connecting the adhesion protein talin with microtubule tips. Both total microtubule disruption and microtubule uncoupling from adhesions by manipulations with KANKs trigger a massive assembly of myosin IIA filaments, augmenting focal adhesions and disrupting podosomes. Myosin IIA filaments are indispensable effectors in the microtubule-driven regulation of integrin-mediated adhesions. Myosin IIA filament assembly depends on Rho activation by the RhoGEF GEF-H1, which is trapped by microtubules when they are connected with integrin-mediated adhesions via KANK proteins but released after their disconnection. Thus, microtubule capture by integrin-mediated adhesions modulates the GEF-H1-dependent effect of microtubules on the assembly of myosin IIA filaments. Subsequent actomyosin reorganization then remodels the focal adhesions and podosomes, closing the regulatory loop.
  • Cortical forces and CDC-42 control clustering of PAR proteins for Caenorhabditis elegans embryonic polarization.
    Shyi-Chyi Wang; Tricia Yu Feng Low; Yukako Nishimura; Laurent Gole; Weimiao Yu; Fumio Motegi
    Nature cell biology, 19, 8, 988, 995, Aug. 2017, [Peer-reviewed], [International Magazine]
    English, Scientific journal, Cell polarization enables zygotes to acquire spatial asymmetry, which in turn patterns cellular and tissue axes during development. Local modification in the actomyosin cytoskeleton mediates spatial segregation of partitioning-defective (PAR) proteins at the cortex, but how mechanical changes in the cytoskeleton are transmitted to PAR proteins remains elusive. Here we uncover a role of actomyosin contractility in the remodelling of PAR proteins through cortical clustering. During embryonic polarization in Caenorhabditis elegans, actomyosin contractility and the resultant cortical tension stimulate clustering of PAR-3 at the cortex. Clustering of atypical protein kinase C (aPKC) is supported by PAR-3 clusters and is antagonized by activation of CDC-42. Cortical clustering is associated with retardation of PAR protein exchange at the cortex and with effective entrainment of advective cortical flows. Our findings delineate how cytoskeleton contractility couples the cortical clustering and long-range displacement of PAR proteins during polarization. The principles described here would apply to other pattern formation processes that rely on local modification of cortical actomyosin and PAR proteins.
  • Extracting microtubule networks from superresolution single-molecule localization microscopy data.
    Zhen Zhang; Yukako Nishimura; Pakorn Kanchanawong
    Molecular biology of the cell, 28, 2, 333, 345, 15 Jan. 2017, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, Microtubule filaments form ubiquitous networks that specify spatial organization in cells. However, quantitative analysis of microtubule networks is hampered by their complex architecture, limiting insights into the interplay between their organization and cellular functions. Although superresolution microscopy has greatly facilitated high-resolution imaging of microtubule filaments, extraction of complete filament networks from such data sets is challenging. Here we describe a computational tool for automated retrieval of microtubule filaments from single-molecule-localization-based superresolution microscopy images. We present a user-friendly, graphically interfaced implementation and a quantitative analysis of microtubule network architecture phenotypes in fibroblasts.
  • Automated screening of microtubule growth dynamics identifies MARK2 as a regulator of leading edge microtubules downstream of Rac1 in migrating cells.
    Yukako Nishimura; Kathryn Applegate; Michael W Davidson; Gaudenz Danuser; Clare M Waterman
    PloS one, 7, 7, e41413, 2012, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, Polarized microtubule (MT) growth in the leading edge is critical to directed cell migration, and is mediated by Rac1 GTPase. To find downstream targets of Rac1 that affect MT assembly dynamics, we performed an RNAi screen of 23 MT binding and regulatory factors and identified RNAi treatments that suppressed changes in MT dynamics induced by constitutively activated Rac1. By analyzing fluorescent EB3 dynamics with automated tracking, we found that RNAi treatments targeting p150(glued), APC2, spastin, EB1, Op18, or MARK2 blocked Rac1-mediated MT growth in lamellipodia. MARK2 was the only protein whose RNAi targeting additionally suppressed Rac1 effects on MT orientation in lamellipodia, and thus became the focus of further study. We show that GFP-MARK2 rescued effects of MARK2 depletion on MT growth lifetime and orientation, and GFP-MARK2 localized in lamellipodia in a Rac1-activity-dependent manner. In a wound-edge motility assay, MARK2-depleted cells failed to polarize their centrosomes or exhibit oriented MT growth in the leading edge, and displayed defects in directional cell migration. Thus, automated image analysis of MT assembly dynamics identified MARK2 as a target regulated downstream of Rac1 that promotes oriented MT growth in the leading edge to mediate directed cell migration.
  • Centralspindlin regulates ECT2 and RhoA accumulation at the equatorial cortex during cytokinesis.
    Yukako Nishimura; Shigenobu Yonemura
    Journal of cell science, 119, Pt 1, 104, 14, 01 Jan. 2006, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, During determination of the cell division plane, an actomyosin contractile ring is induced at the equatorial cell cortex by signals from the mitotic apparatus and contracts to cause cleavage furrow progression. Although the small GTPase RhoA is known to regulate the progression, probably by controlling actin filament assembly and enhancing actomyosin interaction, any involvement of RhoA in division plane determination is unknown. In this study, using a trichloroacetic acid (TCA) fixation protocol we recently developed, we show that RhoA accumulates at the equatorial cortex before furrow initiation and continues to concentrate at the cleavage furrow during cytokinesis. We also demonstrate that both Rho activity and microtubule organization are required for RhoA localization and proper furrowing. Selective disruption of microtubule organization revealed that both astral and central spindle microtubules can recruit RhoA at the equatorial cortex. We find that centralspindlin and ECT2 are required for RhoA localization and furrowing. Centralspindlin is localized both to central spindle microtubules and at the tips of astral microtubules near the equatorial cortex and recruits ECT2. Positional information for division plane determination from microtubules is transmitted to the cell cortex to organize actin cytoskeleton through a mechanism involving these proteins.
  • Rho localization in cells and tissues.
    Shigenobu Yonemura; Kazuyo Hirao-Minakuchi; Yukako Nishimura
    Experimental cell research, 295, 2, 300, 14, 01 May 2004, [International Magazine]
    English, Scientific journal, Rho family small GTPases regulate cytoskeletal organization. Although their spatiotemporal activities appear to be important for cellular morphogenesis, there has been little characterization of the localization of Rho family GTPases in cells and tissues. Here we show precise localization of Rho subfamily proteins in mammalian cultured cells and tissues through evaluation of anti-Rho antibodies and fixation protocols. Although Rho is not a structural protein but functions as a switching molecule, it often localizes at several distinct domains or structures of cells. In cultured epithelial cells, Rho was highly accumulated at lateral membranes. However, in fibroblastic cells, Rho appeared to be distributed evenly in the cytoplasm. Rho concentration at the cleavage furrow at cytokinesis was generally observed. In A431 cells, Rho translocation from the cytoplasm to elongating microvilli at the apical membrane within 30 s after EGF stimulation was clearly demonstrated. Also, Myc- or GFP-tagged RhoA did not always reflect the localization of endogenous Rho, indicating a drawback of protein-tagging methods for localization research. In mouse tissues, Rho localization differed depending on cell type, probably reflecting the functional differences of each cell type.
  • An IQGAP-like protein is involved in actin assembly together with Cdc42 in the sea urchin egg.
    Yukako Nishimura; Issei Mabuchi
    Cell motility and the cytoskeleton, 56, 4, 207, 18, Dec. 2003, [Peer-reviewed], [Lead author], [International Magazine]
    English, Scientific journal, We isolated a gene homologous to human cdc42 (ucdc42) from a sea urchin cDNA library. The GTPgammaS-bound UCdc42 induced actin assembly in sea urchin egg extract. Proteins that are involved in this actin assembly system were searched using UCdc42-bound agarose beads. A 180-kDa protein (p180), which showed a homology to human IQGAPs, bound to the GTPgammaS-UCdc42 beads. Immunodepletion of p180 from the sea urchin egg extract abolished this actin assembly on the UCdc42 beads. Immunofluorescent localization of p180 was similar to that of the actin cytoskeleton in the egg cortex and it was concentrated in the cleavage furrow during cytokinesis. A possible role of p180 in actin assembly is discussed.
  • Localization of Rho GTPase in sea urchin eggs
    Yukako Nishimura; Kentaro Nakano; Issei Mabuchi
    FEBS Letters, 441, 1, 121, 126, Wiley, 11 Dec. 1998, [Peer-reviewed], [Lead author]
    Scientific journal
■ Other Activities and Achievements
■ Lectures, oral presentations, etc.
  • Mechano-chemical signaling induced by microtubules in directed cell migration
    Yukako Nishimura; Kaori Kuribayashi-Sigetomi; Satoru Kidoaki; Fumio Motegi
    第47回日本分子生物学会年会, 28 Nov. 2024, Invited oral presentation
    27 Nov. 2024 - 29 Nov. 2024, [Invited]
  • Spatio-temporal control of cellular mechanics during cell migration
    Yukako Nishimura
    理化学研究所 生命機能科学研究センター, 21 Nov. 2023, Public discourse
    [Invited]
  • Mechano-chemical signaling induced by microtubules in directed cell migration
    Yukako Nishimura; Thasaneeya Kuboki; Satoru Kidoaki; Fumio Motegi
    第61回 日本生物物理学会年会, 14 Nov. 2023, English, Invited oral presentation
    [Invited]
  • 微小管によるアクチン細胞骨格再編成の時空間的制御メカニズム
    西村有香子; 久保木タッサニーニャ; 中畑和美; 栗林-繁富 香織; 木戸秋悟; 茂木文夫
    第32回 日本バイオイメージング学会, 03 Nov. 2023, Japanese, Invited oral presentation
    [Invited]
  • Cross-talk between focal adhesions and microtubules in directed cell migration
    Yukako Nishimura; Thasaneeya Kuboki; Satoru Kidoaki; Fumio Motegi
    第75回 日本細胞生物学会年会, 30 Jun. 2023, English, Invited oral presentation
    [Invited]
  • Crosstalk between myosin II and formin in the regulation of force generation and actomyosin dynamics in stress fibers
    Yukako Nishimura; Shidong Shi; Virgile Viasnoff; Alexander D. Bershadsky
    第60回日本生物物理学会年会, 01 Sep. 2022, Nominated symposium
    [Invited]
  • The Formin Inhibitor, SMIFH2, Inhibits Members of the Myosin Superfamily
    Yukako Nishimura; Shidong Shi; Fang Zhang; Rong Liu; Yasuharu Takagi; Alexander D. Bershadsky; Virgile Viasnoff; James R. Sellers
    第44回日本分子生物学会年会, 01 Dec. 2021, Nominated symposium
  • イメージングを基盤としたメカニクス計測:力によるアクチン繊維の動態制御
    西村有香子
    光塾シンポジウム, 27 Sep. 2021, Public discourse
    [Invited]
■ Research Themes
  • 走硬性を司る細胞間コミュニケーション機構の解明
    科学研究費助成事業
    01 Apr. 2024 - 31 Mar. 2026
    西村 有香子
    日本学術振興会, 学術変革領域研究(A), 北海道大学, 24H01918
  • 細胞外環境の機械的加工による接着斑メカノセンシング機構の解明
    科学研究費助成事業 基盤研究(C)
    01 Apr. 2022 - 31 Mar. 2025
    西村 有香子
    日本学術振興会, 基盤研究(C), 北海道大学, 22K06196
  • 微小管メカニクスが誘導する細胞極性パターニング
    科学研究費助成事業 国際共同研究加速基金(国際共同研究強化(B))
    Oct. 2021 - Mar. 2025
    茂木 文夫; 西村 有香子; 木戸秋 悟; 柴田 達夫; 多羅間 允輔
    生体内の細胞は、細胞内外に作用する機械的力を利用して、細胞極性の非対称パターンを獲得することが示されたが、この過程で力刺激を感知・応答する分子機構は未だに不明な点が多い。本研究は、細胞骨格である「微小管」のメカニクスを中心とするメカノトランスダクション機構が、細胞極性の非対称パターンを誘導する機構を包括的に理解することを目標とする。
    本提案研究では、線虫初期胚とヒト培養細胞を対象とし、細胞内微小管の構造と機能を人為操作する実験手法を確立し、この微小管メカニクスの変動が細胞極性パターンの誘導と維持に及ぼす影響を高解像度ライブイメージングにより解析する。線虫初期胚では、細胞内温度変化によって微小管(チューブリン)、微小管形成中心(中心体)、または微小管モーター(ダイニン複合体)の機能を操作する株を作成し、温度変化と同時にライブイメージングを可能な実験系を確立した。ヒト培養細胞では、メカノトランスダクション構造である細胞接着斑と微小管の相互作用を操作する化学遺伝学手法を確立し、更にこの技術を改変した光遺伝学的手法を開発している。更に、細胞接着斑のメカノトランスダクション機能を操作するために、細胞外基質の機械的性質を微細加工する技術を構築している。今後はこれらの手法を組み合わせて、微小管と細胞外環境のメカニクスを人為操作する技術を確立し、微小管の高速高解像度ライブイメージングと画像解析・数理解析を融合した学際的研究戦略によって、細胞極性化における微小管メカニクスの生理的意義を解明する。
    日本学術振興会, 国際共同研究加速基金(国際共同研究強化(B)), 北海道大学, 21KK0127
  • 細胞メカノセンシングにおける微小管を中心としたシグナル伝達機構の役割
    2023年度 女性研究者リーダー育成共同研究助成
    Aug. 2023 - Mar. 2024
    繁富香織; Jennifer Young
    北海道大学, 北海道大学, Principal investigator
  • 腫瘍化メカノセンシング転換が引き起こす細胞移動の解明
    Apr. 2023 - Mar. 2024
    西村有香子
    一般財団法人 北海道B型肝炎訴訟オレンジ基金, Principal investigator
  • ガン細胞における力学刺激感知応答メカニズムの生理的意義
    Mar. 2023 - Mar. 2024
    西村有香子
    公益財団法人寿原記念財団, Principal investigator
  • 微小管が制御する力学-化学情報の変換メカニズム
    科学研究費助成事業 新学術領域研究(研究領域提案型)
    Apr. 2022 - Mar. 2024
    西村 有香子
    日本学術振興会, 新学術領域研究(研究領域提案型), 北海道大学, Principal investigator, 22H04825
  • 接着斑メカノセンシングにおける細胞骨格微小管の役割
    Jul. 2022 - Jun. 2023
    西村有香子
    公益財団法人 秋山記念生命科学振興財団, Principal investigator
  • 細胞メカノセンシング機構における微小管情報伝達の役割
    科学研究費助成事業 研究活動スタート支援
    30 Aug. 2021 - 31 Mar. 2023
    西村 有香子
    近年の研究により、細胞には外環境の機械的性質や力作用を感知し応答するメカノセンシング機構があることが示されている。これらの力学刺激が、細胞メカノセンシングの中核を担う「細胞接着斑」の構造と機能を制御するメカニズムの理解は未だに不足している。これまでの研究により、細胞骨格の微小管が接着斑と相互作用し、接着斑の形成と崩壊を制御することを明らかにしてきた。本研究では、この微小管-接着斑クロストークのメカノセンシングにおける役割解明を目指す。
    初年度は、微小管と接着斑の連結を人為的に阻害・誘導するための光遺伝学技術を導入したツールを作製した。このツールを実際に細胞内に導入し、顕微鏡下の光照射によって細胞内局所で微小管と接着斑の相互作用を操作できるか検討している。それに加え、細胞外基質の微細加工によって「メカノセンシングに依存した細胞移動」を誘導できる実験系を構築し、メカノセンシング移動中における微小管と接着斑のダイナミクスを高解像度で観察するための条件検討を行なっている。また、微小管-接着斑連結の下流で作用するシグナル伝達経路を同定する目的で、微小管結合能を持つRhoA活性化因子GEF-H1の活性化メカニズムについて解析している。微小管上におけるGEF-H1の局在を詳細に観察するため、一分子レベルでの計測を行ったところ、GEF-H1が微小管から結合・解離する様子に加えて、微小管上を滑る様子が観測できた。今後は、GEF-H1分子の動態を、外部から機械的刺激を与えた細胞内でも観察することで、メカノセンシングとGEF-H1の連携における時空間制御機構を明らかにする。
    日本学術振興会, 研究活動スタート支援, 北海道大学, 21K20620
  • 細胞運動メカノセンシングにおける微小管制御システム
    Aug. 2021 - Jul. 2022
    西村有香子
    公益信託 成茂動物科学振興基金, Principal investigator
  • 細胞運動メカノセンシングにおける微小管情報伝達機構
    Jul. 2021 - Jun. 2022
    西村有香子
    資生堂 女性研究者サイエンスグラント, Principal investigator
  • Rhoファミリータンパク質の正確な細胞内局在の決定とがん化に伴う変化の解析
    科学研究費助成事業 特定領域研究
    2003 - 2003
    米村 重信; 木下 暢暁; 西村 有香子
    本研究は、低分子量Gタンパク質、Rhoファミリーの細胞、組織における局在の信頼性高い解析を可能にする、特異抗体、固定法を確立し、それを利用して、形態形成時におけるRhoファミリータンパク質の正確な挙動、各組織における局在の情報から機能との関連を探り、がん化にともなう変化の有無を調べることを目的としている。本年度は、Rhoに関しての基礎的な研究が終了し、Rac,Cdc42に関しては足がかりができた。
    1
    すでに確立した抗体(RhoA特異的なものとRhoA,RhoCに特異的なもの)、固定法を用いて、各組織における局在の詳細を決定した。また、培養細胞を用いて、Rhoの活性化時にRhoの細胞質から細胞膜への移行を明瞭に可視化することができた。また、細胞周期を通じてのRhoの局在変化を詳細に解析した。その結果細胞質分裂時の分裂面決定の時期に、Rhoが分裂溝域に濃縮することがわかった。この濃縮は、分裂面決定に必要な微小管に依存しており、またRhoの活性が細胞質分裂に必要であるという報告と考え合わせると、Rhoの濃縮は分裂面決定における重要なステップであると考えられた。RhoA,B,Cそれぞれに特異的な抗体の作製を試みているが、ウェスタンブロット、免疫染色が共に可能な抗体の作製は今のところ成功していない。
    2
    Rac,Cdc42に関しては、市販されている抗体の中に、ウェスタンブロット、免疫染色が共に可能な抗体があることが判明した。また、そのために必要な固定条件も決定することができた。しかし、Rhoと比較すると、培養細胞、ほ乳類組織などで特徴的な分布を示さなかった。非常にドラスティックな形態形成運動が起こる、胚発生に焦点を当てて、局在を検討したところ、上皮の管形成時にはその頂端部に強い濃縮が見られ、現在、その場所での機能を解析している。
    日本学術振興会, 特定領域研究, 独立行政法人理化学研究所, 15024267