publications

Publication – Dr Masahiro Ono is a T-cell expert and the inventor of the innovative Timer-of-Cell-Kinetics-and-Activity (Tocky) technology.

Key publications by Masahiro Ono, showcasing innovative approaches in immunological research and beyond.

2024

  1. A multidimensional toolkit for elucidating temporal trajectories in cell development in vivo
    Masahiro Ono, and Tessa Crompton
    Development, Nov 2024
  2. TockyLocus: Quantitative Analysis Methods for Flow Cytometric Fluorescent Timer Data
    Masahiro Ono
    Nov 2024
  3. TockyPrep: Data Preprocessing Methods for Flow Cytometric Fluorescent Timer Analysis
    Masahiro Ono
    Nov 2024
  4. GatingTree: Pathfinding Analysis of Group-Specific Effects in Cytometry Data
    Masahiro Ono
    Nov 2024
  5. Spectrum of Treg and self-reactive T cells: single cell perspectives from old friend HTLV-1
    Masahiro Ono, and Yorifumi Satou
    Discovery Immunology, May 2024
  6. HIV-Tocky system to visualize proviral expression dynamics
    Omnia Reda , Kazuaki Monde , Kenji Sugata , Akhinur Rahman , Wajihah Sakhor , Samiul Alam Rajib , Sharmin Nahar Sithi , Benjy Jek Yang Tan , Koki Niimura , Chihiro Motozono , Kenji Maeda , Masahiro Ono, Hiroaki Takeuchi , and Yorifumi Satou
    Communications Biology, May 2024
  7. Unraveling T-cell dynamics using fluorescent timer: Insights from the Tocky system
    Masahiro Ono
    Biophysics and Physicobiology, May 2024

2023

  1. Single-Cell Transcriptome Analysis of Treg
    B. J. Y. Tan , M. Ono , and Y. Satou
    Methods Mol Biol, May 2023
  2. Masahiro Ono
    Methods Mol Biol, May 2023
    Editor

2022

  1. CD4 T cell dynamics shape the immune response to combination oncolytic herpes virus and BRAF inhibitor therapy for melanoma
    Galabina Bozhanova , Jehanne Hassan , Lizzie Appleton , Victoria Jennings , Shane Foo , Martin McLaughlin , Charleen ML Chan Wah Hak , Emmanuel C Patin , Eva Crespo-Rodriguez , Gabby Baker , Edward Armstrong , Matthew Chiu , Hardev Pandha , Adel Samson , Victoria Roulstone , Joan Kyula , Richard Vile , Fiona Errington-Mais , Malin Pedersen , Kevin Harrington , Masahiro Ono, and Alan Melcher
    Journal for ImmunoTherapy of Cancer, May 2022
  2. HTLV-1 persistence and leukemogenesis: A game of hide-and-seek with the host immune system
    B. J. Y. Tan , K. Sugata , M. Ono , and Y. Satou
    Front Immunol, May 2022
  3. Single-cell level temporal profiling of tumour-reactive T cells under immune checkpoint blockade
    Jehanne Hassan , Elizabeth Appleton , Bahire Kalfaoglu , Malin Pedersen , José Almeida-Santos , Hisashi Kanemaru , Nobuko Irie , Shane Foo , Omnia Reda , Benjy J.Y. Tan , Il-mi Okazaki , Taku Okazaki , Yorifumi Satou , Kevin Harrington , Alan Melcher , and Masahiro Ono
    bioRxiv, May 2022
  4. Nur77-Tempo mice reveal T cell steady state antigen recognition
    T. A. E. Elliot , E. K. Jennings , D. A. J. Lecky , S. Rouvray , G. M. Mackie , L. Scarfe , L. Sheriff , M. Ono , K. M. Maslowski , and D. Bending
    Discov Immunol, May 2022
  5. Temporal profiling of CD4 T-cell activation and differentiation upon SARS-CoV-2 spike protein immunisation
    José Almeida-Santos , Rita Berkachy , Chanidapa Adele Tye , Jehanne Hassan , Bahire Kalfaoglu , Murray E. Selkirk , and Masahiro Ono
    bioRxiv, May 2022
  6. Context-dependent effects of IL-2 rewire immunity into distinct cellular circuits
    Carly E. Whyte , Kailash Singh , Oliver T. Burton , Meryem Aloulou , Lubna Kouser , Rafael Valente Veiga , Amy Dashwood , Hanneke Okkenhaug , Samira Benadda , Alena Moudra , Orian Bricard , Stephanie Lienart , Pascal Bielefeld , Carlos P. Roca , Francisco José Naranjo-Galindo , Félix Lombard-Vadnais , Steffie Junius , David Bending , Masahiro Ono, Tino Hochepied , Timotheus Y.F. Halim , Susan Schlenner , Sylvie Lesage , James Dooley , and Adrian Liston
    Journal of Experimental Medicine, Jun 2022

2021

  1. HTLV-1 infection promotes excessive T cell activation and transformation into adult T cell leukemia/lymphoma
    Benjy J. Y. Tan , Kenji Sugata , Omnia Reda , Misaki Matsuo , Kyosuke Uchiyama , Paola Miyazato , Vincent Hahaut , Makoto Yamagishi , Kaoru Uchimaru , Yutaka Suzuki , Takamasa Ueno , Hitoshi Suzushima , Hiroo Katsuya , Masahito Tokunaga , Yoshikazu Uchiyama , Hideaki Nakamura , Eisaburo Sueoka , Atae Utsunomiya , Masahiro Ono, and Yorifumi Satou
    The Journal of Clinical Investigation, Jun 2021
  2. Retrovirus-induced leukemia–hijack of T-cell activation mechanisms revealed by single-cell analysis
    Benjy Jek Yang Tan , Kenji Sugata , Omnia Reda , Misaki Matsuo , Kyosuke Uchiyama , Paola Miyazato , Vincent Hahaut , Makoto Yamagishi , Kaoru Uchimaru , and Yutaka Suzuki
    bioRxiv, Jun 2021
  3. HTLV-1 infection promotes excessive T cell activation and transformation into adult T cell leukemia/lymphoma
    Benjy JY Tan , Kenji Sugata , Omnia Reda , Misaki Matsuo , Kyosuke Uchiyama , Paola Miyazato , Vincent Hahaut , Makoto Yamagishi , Kaoru Uchimaru , and Yutaka Suzuki
    Journal of Clinical Investigation, Jun 2021
  4. Restoring control over autoimmunity by inducing Foxp3
    Masahiro Ono
    Nature Immunology, Jun 2021
  5. The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection
    Ching-In Lau , Jasmine Rowell , Diana C Yanez , Anisha Solanki , Susan Ross , Masahiro Ono, and Tessa Crompton
    Development, Jun 2021
  6. T-cell dysregulation in COVID-19
    Bahire Kalfaoglu , José Almeida-Santos , Chanidapa Adele Tye , Yorifumi Satou , and Masahiro Ono
    Biochemical and biophysical research communications, Jun 2021
  7. Application of dual Nr4a1-GFP Nr4a3-Tocky reporter mice to study T cell receptor signaling by flow cytometry
    Emma K Jennings , David AJ Lecky , Masahiro Ono, and David Bending
    STAR protocols, Jun 2021
  8. Brief homogeneous TCR signals instruct common iNKT progenitors whose effector diversification is characterized by subsequent cytokine signaling
    Sabrina Bortoluzzi , Nyambayar Dashtsoodol , Thomas Engleitner , Christoph Drees , Sabine Helmrath , Jonas Mir , Albulena Toska , Michael Flossdorf , Rupert Öllinger , and Maria Solovey
    Immunity, Jun 2021
  9. Kickstarting immunity in cold tumours: localised tumour therapy combinations with immune checkpoint blockade
    Elizabeth Appleton , Jehanne Hassan , Charleen Chan Wah Hak , Nanna Sivamanoharan , Anna Wilkins , Adel Samson , Masahiro Ono, Kevin J Harrington , Alan Melcher , and Erik Wennerberg
    Frontiers in Immunology, Jun 2021
  10. NF-κB activation in cardiac fibroblasts results in the recruitment of inflammatory Ly6Chi monocytes in pressure-overloaded hearts
    Hajime Abe , Yohei Tanada , Shigemiki Omiya , Mihai-Nicolae Podaru , Tomokazu Murakawa , Jumpei Ito , Ajay M Shah , Simon J Conway , Masahiro Ono, and Kinya Otsu
    Science Signaling, Jun 2021

2020

  1. Regulatory T cells restrain interleukin-2-and Blimp-1-dependent acquisition of cytotoxic function by CD4+ T cells
    Anna Śledzińska , Maria Vila Mucha , Katharina Bergerhoff , Alastair Hotblack , Dafne Franz Demane , Ehsan Ghorani , Ayse U Akarca , Maria AV Marzolini , Isabelle Solomon , and Frederick Arce Vargas
    Immunity, Jun 2020
  2. Control of regulatory T-cell differentiation and function by T-cell receptor signalling and Foxp3 transcription factor complexes
    Masahiro Ono
    Immunology, Jun 2020
  3. T-cell hyperactivation and paralysis in severe COVID-19 infection revealed by single-cell analysis
    Bahire Kalfaoglu , José Almeida-Santos , Chanidapa Adele Tye , Yorifumi Satou , and Masahiro Ono
    Frontiers in immunology, Jun 2020
  4. Nr4a1 and Nr4a3 reporter mice are differentially sensitive to T cell receptor signal strength and duration
    Emma Jennings , Thomas AE Elliot , Natasha Thawait , Shivani Kanabar , Juan Carlos Yam-Puc , Masahiro Ono, Kai-Michael Toellner , David C Wraith , Graham Anderson , and David Bending
    Cell reports, Jun 2020
  5. Mutant BRAF small molecule inhibition enhances oncolytic herpes virus immunotherapy through increased immune cell recruitment and activation in melanoma
    Galabina Bozhanova , Victoria Jennings , Malin Pedersen , Joan Kyula , Emmanuel Patin , Jehanne Hassan , Masahiro Ono, Kevin Harrington , and Alan Melcher
    Cancer Research, Jun 2020

2019

  1. IFITM proteins drive type 2 T helper cell differentiation and exacerbate allergic airway inflammation
    Diana C Yánez , Hemant Sahni , Susan Ross , Anisha Solanki , Ching‐In Lau , Eleftheria Papaioannou , Alessandro Barbarulo , Rebecca Powell , Ulrike C Lange , and David J Adams
    European journal of immunology, Jun 2019
  2. Sonic Hedgehog signaling limits atopic dermatitis via Gli2-driven immune regulation
    Eleftheria Papaioannou , Diana C Yánez , Susan Ross , Ching-In Lau , Anisha Solanki , Mira Manilal Chawda , Alex Virasami , Ismael Ranz , Masahiro Ono, and Ryan FL O’Shaughnessy
    The Journal of clinical investigation, Jun 2019
  3. Sonic hedgehog is a determinant of γδ T-cell differentiation in the thymus
    Konstantinos Mengrelis , Ching-In Lau , Jasmine Rowell , Anisha Solanki , Sonia Norris , Susan Ross , Masahiro Ono, Susan Outram , and Tessa Crompton
    Frontiers in immunology, Jun 2019
  4. Distinct regulation of Nr4a receptors by NFAT and ERK signalling during T cell activation
    Emma Jennings , Shivani Kanabar , Masahiro Ono, David C Wraith , David Bending , and David Bending
    Jun 2019

2018

  1. From stability to dynamics: understanding molecular mechanisms of regulatory T cells through Foxp3 transcriptional dynamics
    David Bending , and Masahiro Ono
    Clinical and Experimental Immunology, Sep 2018
  2. Elucidating T Cell Activation-Dependent Mechanisms for Bifurcation of Regulatory and Effector T Cell Differentiation by Multidimensional and Single-Cell Analysis
    Alla Bradley , Tetsuo Hashimoto , and Masahiro Ono
    Frontiers in Immunology, Sep 2018
  3. A temporally dynamic Foxp3 autoregulatory transcriptional circuit controls the effector Treg programme
    David Bending , Alina Paduraru , Catherine B Ducker , Paz Prieto Martı́n , Tessa Crompton , and Masahiro Ono
    The EMBO journal, Sep 2018
    The second Tocky paper from the Ono lab uncovers the temporally dynamic regulation of Foxp3 transcription, offering new insights into T cell regulation.
  4. A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo
    David Bending , Paz Prieto Martı́n , Alina Paduraru , Catherine Ducker , Erik Marzaganov , Marie Laviron , Satsuki Kitano , Hitoshi Miyachi , Tessa Crompton , and Masahiro Ono
    Journal of Cell Biology, Sep 2018
    The foundational publication introducing Tocky technology by the Ono lab, marking a breakthrough in T cell and B cell studies.

2017

  1. Revealing the mechanism of regulatory T-cell generation in vivo by novel Fluorescent Timer reporter
    Masahiro Ono, David Bending , and Paz Prieto Martin
    Journal of Immunology, May 2017
  2. The impact of environmental enrichment on the murine inflammatory immune response
    Samuel Brod , Thomas Gobbetti , Beatrice Gittens , Masahiro Ono, Mauro Perretti , and Fulvio D’Acquisto
    JCI insight, May 2017
  3. FoxP3 partners up
    David Bending , and Masahiro Ono
    Nature Immunology, May 2017
  4. Interplay between the skin barrier and immune cells in patients with atopic dermatitis unraveled by means of mathematical modeling
    David Bending , and Masahiro Ono
    Journal of Allergy and Clinical Immunology, May 2017

2016

  1. Water resistance profile as a marker of skin barrier damage in atopic dermatitis patients
    Mark DA Logtestijn , Peter J Caspers , Sanja Kezic , Douglas R Hoffman , David W Koenig , Masahiro Ono, Georgios N Stamatas , and Reiko J Tanaka
    Journal of Dermatological Science, May 2016
  2. Sonic Hedgehog regulates thymic epithelial cell differentiation
    José Ignacio Saldaña , Anisha Solanki , Ching-In Lau , Hemant Sahni , Susan Ross , Anna L Furmanski , Masahiro Ono, Georg Holländer , and Tessa Crompton
    Journal of Autoimmunity, May 2016
  3. Impact of enriched environment on murine T cell differentiation and gene expression profile
    Lorenza Rattazzi , Giuseppa Piras , Samuel Brod , Koval Smith , Masahiro Ono, and Fulvio D’Acquisto
    Frontiers in Immunology, May 2016
  4. Controversies concerning thymus‐derived regulatory T cells: fundamental issues and a new perspective
    Masahiro Ono, and Reiko J Tanaka
    Immunology and cell biology, May 2016
    A landmark opinion piece challenging the reproducibility of a foundational Treg experiment, while introducing a groundbreaking dynamic view on Foxp3-mediated T cell regulation.
  5. Regulatory T cells in melanoma revisited by a computational clustering of FOXP3+ T cell subpopulations
    Hiroko Fujii , Julie Josse , Miki Tanioka , Yoshiki Miyachi , François Husson , and Masahiro Ono
    The Journal of Immunology, May 2016
    The pioneering study ntroduces a data-driven methodology to explore Treg subpopulations, employing Principal Component Analysis (PCA) for the first time.

2015

  1. A Zap70‐dependent feedback circuit is essential for efficient selection of CD4 lineage thymocytes
    Charles Sinclair , Masahiro Ono, and Benedict Seddon
    Immunology and Cell Biology, May 2015
  2. A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation
    Hemant Sahni , Susan Ross , Alessandro Barbarulo , Anisha Solanki , Ching-In Lau , Anna Furmanski , Jose Ignacio Saldana , Masahiro Ono, Mike Hubank , and Martino Barenco
    Oncotarget, May 2015
  3. Follicular helper T cell signature in type 1 diabetes
    Rupert Kenefeck , Chun Jing Wang , Tauseef Kapadi , Lukasz Wardzinski , Kesley Attridge , Louise E. Clough , Frank Heuts , Alexandros Kogimtzis , Sapna Patel , Miranda Rosenthal , Masahiro Ono, David M. Sansom , Parth Narendran , and Lucy S.K. Walker
    The Journal of Clinical Investigation, Jan 2015

2014

  1. Identifying a hyperkeratosis signature in autosomal recessive congenital ichthyosis: Mdm2 inhibition prevents hyperkeratosis in a rat ARCI model
    Gehad Youssef , Masahiro Ono, Stuart J Brown , Veronica A Kinsler , Neil J Sebire , John I Harper , and Ryan FL O’shaughnessy
    The Journal of Investigative Dermatology, Jan 2014
  2. Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes
    Masahiro Ono, Reiko Tanaka , and Manabu Kano
    BMC Genomics, Jan 2014
    This study establishes CCA as a vital quantitative tool for transcriptome analysis in immunological datasets.
  3. CD8+ tumor‐infiltrating lymphocytes at primary sites as a possible prognostic factor of cutaneous angiosarcoma
    Hiroko Fujii , Akiko Arakawa , Daisuke Utsumi , Shinji Sumiyoshi , Yosuke Yamamoto , Akihiko Kitoh , Masahiro Ono, Yumi Matsumura , Mayumi Kato , and Keisuke Konishi
    International journal of cancer, Jan 2014

2013

  1. Rab3Gap1 mediates exocytosis of Claudin-1 and tight junction formation during epidermal barrier acquisition
    G Youssef , L Gerner , AS Naeem , O Ralph , M Ono , CA O’neill , and RFL O’Shaughnessy
    Developmental biology, Jan 2013
  2. Skin disease modeling from a mathematical perspective
    Reiko J Tanaka , and Masahiro Ono
    Journal of Investigative Dermatology, Jan 2013
  3. CD4+ but not CD8+ T cells revert the impaired emotional behavior of immunocompromised RAG-1-deficient mice
    Lorenza Rattazzi , Giuseppa Piras , Mutsumi Ono , Robert Deacon , CM Pariante , and F D’acquisto
    Translational psychiatry, Jan 2013
  4. Visualising the cross-level relationships between pathological and physiological processes and gene expression: analyses of haematological diseases
    Masahiro Ono, Reiko Tanaka , Manabu Kano , and Toshio Sugiman
    PLoS One, Jan 2013
    The pioneering study developing Canonical Correspondence Analysis (CCA) as a genomics method, establishing a novel approach for transcriptome analysis.
  5. Tissue-Derived Hedgehog Proteins Modulate Th Differentiation and Disease
    Anna L Furmanski , Jose Ignacio Saldana , Masahiro Ono, Hemant Sahni , Nikolaos Paschalidis , Fulvio D’Acquisto , and Tessa Crompton
    The Journal of Immunology, Jan 2013
  6. Risk factor-dependent dynamics of atopic dermatitis: modelling multi-scale regulation of epithelium homeostasis
    Elisa Domı́nguez-Hüttinger , Masahiro Ono, Mauricio Barahona , and Reiko J Tanaka
    Interface Focus, Jan 2013

2011

  1. Differential effects of inhibition of bone morphogenic protein (BMP) signalling on T-cell activation and differentiation
    Y Yoshioka , M Ono , M Osaki , I Konishi , and S Sakaguchi
    Eur J Immunol, Jan 2011
  2. Skin barrier homeostasis in atopic dermatitis: feedback regulation of kallikrein activity
    Reiko J Tanaka , Masahiro Ono, and Heather A Harrington
    PLoS One, Jan 2011
  3. HTLV-1 bZIP Factor Induces T-Cell Lymphoma and Systemic Inflammation In Vivo
    Yorifumi Satou , Jun-ichirou Yasunaga , Tiejun Zhao , Mika Yoshida , Paola Miyazato , Ken Takai , Kei Shimizu , Koichi Ohshima , Patrick L. Green , Naganari Ohkura , Tomoyuki Yamaguchi , Masahiro Ono, Shimon Sakaguchi , and Masao Matsuoka
    PLOS Pathogens, Feb 2011
  4. Perturbations of both nonregulatory and regulatory FOXP3+ T cells in patients with malignant melanoma
    Hiroko Fujii , A Arakawa , A Kitoh , M Miyara , M Kato , S Kore‐Eda , S Sakaguchi , Y Miyachi , M Tanioka , and M Ono
    British Journal of Dermatology, Feb 2011

2009

  1. Functional Delineation and Differentiation Dynamics of Human CD4+ T Cells Expressing the FoxP3 Transcription Factor
    Makoto Miyara , Yumiko Yoshioka , Akihiko Kitoh , Tomoko Shima , Kajsa Wing , Akira Niwa , Christophe Parizot , Cécile Taflin , Toshio Heike , Dominique Valeyre , Alexis Mathian , Tatsutoshi Nakahata , Tomoyuki Yamaguchi , Takashi Nomura , Masahiro Ono, Zahir Amoura , Guy Gorochov , and Shimon Sakaguchi
    Immunity, Feb 2009
  2. Indispensable Role of the Runx1-Cbfβ Transcription Complex for In Vivo-Suppressive Function of FoxP3+ Regulatory T Cells
    Akihiko Kitoh , Masahiro Ono, Yoshinori Naoe , Naganari Ohkura , Tomoyuki Yamaguchi , Hiroko Yaguchi , Issay Kitabayashi , Toshihiko Tsukada , Takashi Nomura , Yoshiki Miyachi , Ichiro Taniuchi , and Shimon Sakaguchi
    Immunity, Feb 2009

2008

  1. Regulatory T Cells and Immune Tolerance
    Shimon Sakaguchi , Tomoyuki Yamaguchi , Takashi Nomura , and Masahiro Ono
    Cell, Feb 2008

2007

  1. Foxp3 controls regulatory T-cell function by interacting with AML1/Runx1
    Masahiro Ono, Hiroko Yaguchi , Naganari Ohkura , Issay Kitabayashi , Yuko Nagamura , Takashi Nomura , Yoshiki Miyachi , Toshihiko Tsukada , and Shimon Sakaguchi
    Nature, Feb 2007

2006

  1. Foxp3+ CD25+ CD4+ natural regulatory T cells in dominant self‐tolerance and autoimmune disease
    Shimon Sakaguchi , Masahiro Ono, Ruka Setoguchi , Haruhiko Yagi , Shohei Hori , Zoltan Fehervari , Jun Shimizu , Takeshi Takahashi , and Takashi Nomura
    Immunological Reviews, Feb 2006
  2. Control of autoimmune myocarditis and multiorgan inflammation by glucocorticoid-induced TNF receptor family-related proteinhigh, Foxp3-expressing CD25+ and CD25− regulatory T cells
    Masahiro Ono, Jun Shimizu , Yoshiki Miyachi , and Shimon Sakaguchi
    The Journal of Immunology, Feb 2006

2004

  1. Cutaneous alternariosis in an immunocompetent patient: analysis of the internal transcribed spacer region of rDNA and Brm2 of isolated Alternaria alternata
    M Ono , C Nishigori , C Tanaka , S Tanaka , M Tsuda , and Y Miyachi
    British Journal of Dermatology, Feb 2004