{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T21:10:29Z","timestamp":1773695429953,"version":"3.50.1"},"reference-count":50,"publisher":"The Company of Biologists","issue":"24","license":[{"start":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T00:00:00Z","timestamp":1734480000000},"content-version":"vor","delay-in-days":3,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"Medical Research Council","award":["MR\/S000208\/1"],"award-info":[{"award-number":["MR\/S000208\/1"]}]},{"name":"Medical Research Council","award":["MR\/S037764\/1"],"award-info":[{"award-number":["MR\/S037764\/1"]}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/T020970\/1"],"award-info":[{"award-number":["BB\/T020970\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"crossref","award":["BB\/J013951\/2"],"award-info":[{"award-number":["BB\/J013951\/2"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n               <jats:p>Progenitor cells initiate development upon receiving key signals, dynamically altering gene and protein expression to diverge into various lineages and fates. Despite the use of several experimental approaches, including the Fluorescent Timer-based method Timer-of-cell-kinetics-and-activity (Tocky), analysing time-dependent processes at the single-cell level in vivo remains challenging. This study introduces a novel integrated experimental and computational approach, using an advanced multidimensional toolkit. This toolkit facilitates the simultaneous examination of temporal progression and T-cell profiles using high-dimensional flow cytometric data. Employing novel algorithms based on canonical correspondence analysis and network analysis, our toolkit identifies developmental trajectories and analyses dynamic changes in developing cells. The efficacy of this approach is demonstrated by analysing thymic T cells from Nr4a3-Tocky mice, which monitor activities downstream of the T-cell receptor (TCR) signal. Further validation was achieved by deleting the proapoptotic gene Bcl2l11 in Nr4a3-Tocky mice. This revealed dynamic changes in thymic T cells during cellular development and negative selection following TCR signalling. Overall, this study establishes a new method for analysing the temporal dynamics of individual developing cells in response to in vivo signalling cues.<\/jats:p>","DOI":"10.1242\/dev.204255","type":"journal-article","created":{"date-parts":[[2024,11,29]],"date-time":"2024-11-29T14:45:47Z","timestamp":1732891547000},"source":"Crossref","is-referenced-by-count":4,"title":["A multidimensional toolkit for elucidating temporal trajectories in cell development <i>in vivo<\/i>"],"prefix":"10.1242","volume":"151","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9284-7326","authenticated-orcid":false,"given":"Masahiro","family":"Ono","sequence":"first","affiliation":[{"name":"Imperial College London, London SW7 2AZ 1 Department of Life Sciences , ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8973-4021","authenticated-orcid":false,"given":"Tessa","family":"Crompton","sequence":"additional","affiliation":[{"name":"Great Ormond Street Institute of Child Health, University College London 2 , London WC1N 1EH ,","place":["UK"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"237","published-online":{"date-parts":[[2024,12,18]]},"reference":[{"key":"2024121811452315500_DEV204255C1","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1038\/ni.2918","article-title":"Quantitative and temporal requirements revealed for Zap70 catalytic activity during T cell development","volume":"15","author":"Au-Yeung","year":"2014","journal-title":"Nat. Immunol."},{"key":"2024121811452315500_DEV204255C2","doi-asserted-by":"publisher","first-page":"e8024","DOI":"10.15252\/msb.20178024","article-title":"Timing of gene expression in a cell-fate decision system","volume":"14","author":"Aymoz","year":"2018","journal-title":"Mol. Syst. Biol."},{"key":"2024121811452315500_DEV204255C3","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2024121811452315500_DEV204255C4","doi-asserted-by":"publisher","first-page":"2931","DOI":"10.1083\/jcb.201711048","article-title":"A timer for analyzing temporally dynamic changes in transcription during differentiation in vivo","volume":"217","author":"Bending","year":"2018","journal-title":"J. Cell Biol."},{"key":"2024121811452315500_DEV204255C5","doi-asserted-by":"publisher","first-page":"e99013","DOI":"10.15252\/embj.201899013","article-title":"A temporally dynamic Foxp3 autoregulatory transcriptional circuit controls the effector Treg programme","volume":"37","author":"Bending","year":"2018","journal-title":"EMBO J."},{"key":"2024121811452315500_DEV204255C6","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B Methodol."},{"key":"2024121811452315500_DEV204255C7","doi-asserted-by":"publisher","first-page":"1444","DOI":"10.3389\/fimmu.2018.01444","article-title":"Elucidating T cell activation-dependent mechanisms for bifurcation of regulatory and effector T cell differentiation by multidimensional and single-cell analysis","volume":"9","author":"Bradley","year":"2018","journal-title":"Front. Immunol."},{"key":"2024121811452315500_DEV204255C8","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"Int. J. Complex Syst."},{"key":"2024121811452315500_DEV204255C9","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1007\/BF01386390","article-title":"A note on two problems in connexion with graphs","volume":"1","author":"Dijkstra","year":"1959","journal-title":"Numer. Math."},{"key":"2024121811452315500_DEV204255C10","doi-asserted-by":"publisher","first-page":"2885","DOI":"10.4049\/jimmunol.1402695","article-title":"Regulatory T cells in melanoma revisited by a computational clustering of FOXP3+ T cell subpopulations","volume":"196","author":"Fujii","year":"2016","journal-title":"J. Immunol."},{"key":"2024121811452315500_DEV204255C11","doi-asserted-by":"publisher","first-page":"2641","DOI":"10.4049\/jimmunol.1202541","article-title":"Tissue-derived Hedgehog proteins modulate Th differentiation and disease","volume":"190","author":"Furmanski","year":"2013","journal-title":"J. Immunol."},{"key":"2024121811452315500_DEV204255C12","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1016\/j.immuni.2016.08.015","article-title":"Unsupervised high-dimensional analysis aligns dendritic cells across tissues and species","volume":"45","author":"Guilliams","year":"2016","journal-title":"Immunity"},{"key":"2024121811452315500_DEV204255C13","doi-asserted-by":"publisher","first-page":"2603","DOI":"10.1038\/s41467-019-10525-1","article-title":"Identification of a genomic enhancer that enforces proper apoptosis induction in thymic negative selection","volume":"10","author":"Hojo","year":"2019","journal-title":"Nat. Commun."},{"key":"2024121811452315500_DEV204255C14","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1126\/science.aas9435","article-title":"Neuronal specification in space and time","volume":"362","author":"Holguera","year":"2018","journal-title":"Science"},{"key":"2024121811452315500_DEV204255C15","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1002\/cyto.b.20485","article-title":"Considerations for the control of background fluorescence in clinical flow cytometry","volume":"76","author":"Hulspas","year":"2009","journal-title":"Cytometry B Clin. Cytom"},{"key":"2024121811452315500_DEV204255C16","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1146\/annurev-immunol-101320-022432","article-title":"Instructive cues of thymic T cell selection","volume":"40","author":"Irla","year":"2022","journal-title":"Annu. Rev. Immunol."},{"key":"2024121811452315500_DEV204255C17","doi-asserted-by":"publisher","first-page":"589380","DOI":"10.3389\/fimmu.2020.589380","article-title":"T-cell hyperactivation and paralysis in severe COVID-19 infection revealed by single-cell analysis","volume":"11","author":"Kalfaoglu","year":"2020","journal-title":"Front. Immunol."},{"key":"2024121811452315500_DEV204255C18","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1172\/JCI76238","article-title":"Follicular helper T cell signature in type 1 diabetes","volume":"125","author":"Kenefeck","year":"2015","journal-title":"J. Clin. Invest."},{"key":"2024121811452315500_DEV204255C20","doi-asserted-by":"publisher","first-page":"29","DOI":"10.32614\/RJ-2013-003","article-title":"Multiple factor analysis for contingency tables in the FactoMineR Package","volume":"5","author":"Kostov","year":"2013","journal-title":"R J."},{"key":"2024121811452315500_DEV204255C21","doi-asserted-by":"publisher","first-page":"2220","DOI":"10.1038\/s41467-019-09727-4","article-title":"Live-cell imaging reveals the relative contributions of antigen-presenting cell subsets to thymic central tolerance","volume":"10","author":"Lancaster","year":"2019","journal-title":"Nat. Commun."},{"key":"2024121811452315500_DEV204255C22","doi-asserted-by":"publisher","first-page":"dev199754","DOI":"10.1242\/dev.199754","article-title":"The pioneer transcription factors Foxa1 and Foxa2 regulate alternative RNA splicing during thymocyte positive selection","volume":"148","author":"Lau","year":"2021","journal-title":"Development"},{"key":"2024121811452315500_DEV204255C23","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/j.immuni.2012.07.009","article-title":"A broad range of self-reactivity drives thymic regulatory T cell selection to limit responses to self","volume":"37","author":"Lee","year":"2012","journal-title":"Immunity"},{"key":"2024121811452315500_DEV204255C24","doi-asserted-by":"publisher","first-page":"1037","DOI":"10.1002\/cyto.a.20333","article-title":"Flow cytometry controls, instrument setup, and the determination of positivity","volume":"69A","author":"Maecker","year":"2006","journal-title":"Cytometry A"},{"key":"2024121811452315500_DEV204255C25","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1016\/j.immuni.2015.09.009","article-title":"Crossreactive \u03b1\u03b2 T cell receptors are the predominant targets of thymocyte negative selection","volume":"43","author":"McDonald","year":"2015","journal-title":"Immunity"},{"key":"2024121811452315500_DEV204255C26","doi-asserted-by":"publisher","first-page":"1629","DOI":"10.3389\/fimmu.2019.01629","article-title":"Sonic hedgehog is a determinant of \u03b3\u03b4 T-cell differentiation in the thymus","volume":"10","author":"Mengrelis","year":"2019","journal-title":"Front. Immunol."},{"key":"2024121811452315500_DEV204255C27","doi-asserted-by":"publisher","first-page":"4740","DOI":"10.1128\/AEM.68.10.4740-4750.2002","article-title":"Relationship between bacterial community composition and bottom-up versus top-down variables in four eutrophic shallow lakes","volume":"68","author":"Muylaert","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"2024121811452315500_DEV204255C30","doi-asserted-by":"publisher","first-page":"4748","DOI":"10.4049\/jimmunol.176.8.4748","article-title":"Control of autoimmune myocarditis and multiorgan inflammation by glucocorticoid-induced TNF receptor family-related protein(high), Foxp3-expressing CD25+ and CD25- regulatory T cells","volume":"176","author":"Ono","year":"2006","journal-title":"J. Immunol."},{"key":"2024121811452315500_DEV204255C31","doi-asserted-by":"publisher","first-page":"e53544","DOI":"10.1371\/journal.pone.0053544","article-title":"Visualising the cross-level relationships between pathological and physiological processes and gene expression: analyses of haematological diseases","volume":"8","author":"Ono","year":"2013","journal-title":"PLoS ONE"},{"key":"2024121811452315500_DEV204255C32","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.1186\/1471-2164-15-1028","article-title":"Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes","volume":"15","author":"Ono","year":"2014","journal-title":"BMC Genomics"},{"key":"2024121811452315500_DEV204255C33","doi-asserted-by":"publisher","first-page":"eaay3224","DOI":"10.1126\/science.aay3224","article-title":"A cell atlas of human thymic development defines T cell repertoire formation","volume":"367","author":"Park","year":"2020","journal-title":"Science"},{"key":"2024121811452315500_DEV204255C34","doi-asserted-by":"publisher","first-page":"e1004486","DOI":"10.1371\/journal.pgen.1004486","article-title":"LIN-42, the Caenorhabditis elegans PERIOD homolog, negatively regulates microRNA transcription","volume":"10","author":"Perales","year":"2014","journal-title":"PLoS Genet."},{"key":"2024121811452315500_DEV204255C35","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1101\/gad.350486.123","article-title":"How do genomes encode developmental time?","volume":"37","author":"Raimundo","year":"2023","journal-title":"Genes Dev."},{"key":"2024121811452315500_DEV204255C29","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1038\/s42003-024-06025-8","article-title":"HIV-Tocky system to visualize proviral expression dynamics","volume":"7","author":"Reda","year":"2024","journal-title":"Commun. Biol."},{"key":"2024121811452315500_DEV204255C36","doi-asserted-by":"publisher","first-page":"28646","DOI":"10.18632\/oncotarget.5796","article-title":"A genome wide transcriptional model of the complex response to pre-TCR signalling during thymocyte differentiation","volume":"6","author":"Sahni","year":"2015","journal-title":"Oncotarget"},{"key":"2024121811452315500_DEV204255C37","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.jaut.2015.12.004","article-title":"Sonic Hedgehog regulates thymic epithelial cell differentiation","volume":"68","author":"Salda\u00f1a","year":"2016","journal-title":"J. Autoimmun."},{"key":"2024121811452315500_DEV204255C38","doi-asserted-by":"publisher","first-page":"406","DOI":"10.1038\/icb.2014.107","article-title":"A Zap70-dependent feedback circuit is essential for efficient selection of CD4 lineage thymocytes","volume":"93","author":"Sinclair","year":"2015","journal-title":"Immunol. Cell Biol."},{"key":"2024121811452315500_DEV204255C39","doi-asserted-by":"publisher","first-page":"dev146910","DOI":"10.1242\/dev.146910","article-title":"Gli3 in fetal thymic epithelial cells promotes thymocyte positive selection and differentiation by repression of Shh","volume":"145","author":"Solanki","year":"2018","journal-title":"Development"},{"key":"2024121811452315500_DEV204255C40","doi-asserted-by":"publisher","first-page":"dev192203","DOI":"10.1242\/dev.192203","article-title":"The transcriptional repressor Bcl6 promotes pre-TCR-induced thymocyte differentiation and attenuates Notch1 activation","volume":"147","author":"Solanki","year":"2020","journal-title":"Development"},{"key":"2024121811452315500_DEV204255C41","doi-asserted-by":"publisher","first-page":"1579","DOI":"10.1038\/s41590-023-01584-0","article-title":"Single-cell multiomic analysis of thymocyte development reveals drivers of CD4(+) T cell and CD8(+) T cell lineage commitment","volume":"24","author":"Steier","year":"2023","journal-title":"Nat. Immunol."},{"key":"2024121811452315500_DEV204255C42","doi-asserted-by":"publisher","first-page":"4679","DOI":"10.1073\/pnas.1217532110","article-title":"Murine thymic selection quantified using a unique method to capture deleted T cells","volume":"110","author":"Stritesky","year":"2013","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2024121811452315500_DEV204255C43","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1038\/nchembio.138","article-title":"Monomeric fluorescent timers that change color from blue to red report on cellular trafficking","volume":"5","author":"Subach","year":"2009","journal-title":"Nat. Chem. Biol."},{"key":"2024121811452315500_DEV204255C44","doi-asserted-by":"publisher","first-page":"e150472","DOI":"10.1172\/JCI150472","article-title":"HTLV-1 infection promotes excessive T cell activation and transformation into adult T cell leukemia\/lymphoma","volume":"131","author":"Tan","year":"2021","journal-title":"J. Clin. Invest."},{"key":"2024121811452315500_DEV204255C45","doi-asserted-by":"publisher","first-page":"1167","DOI":"10.2307\/1938672","article-title":"Canonical correspondence analysis: a new eigenvector technique for multivariate direct gradient analysis","volume":"67","author":"ter Braak","year":"1986","journal-title":"Ecology"},{"key":"2024121811452315500_DEV204255C46","doi-asserted-by":"publisher","first-page":"8926","DOI":"10.1038\/s41598-021-87971-9","article-title":"Correspondence analysis, spectral clustering and graph embedding: applications to ecology and economic complexity","volume":"11","author":"Van Dam","year":"2021","journal-title":"Sci. Rep."},{"key":"2024121811452315500_DEV204255C47","doi-asserted-by":"publisher","first-page":"380","DOI":"10.3389\/fimmu.2015.00380","article-title":"An introduction to automated flow cytometry gating tools and their implementation","volume":"6","author":"Verschoor","year":"2015","journal-title":"Front. Immunol."},{"key":"2024121811452315500_DEV204255C48","doi-asserted-by":"publisher","first-page":"1817","DOI":"10.1016\/j.devcel.2022.06.016","article-title":"Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies","volume":"57","author":"Voortman","year":"2022","journal-title":"Dev. Cell"},{"key":"2024121811452315500_DEV204255C49","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1038\/nbt.3711","article-title":"Revealing the vectors of cellular identity with single-cell genomics","volume":"34","author":"Wagner","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"2024121811452315500_DEV204255C50","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"2024121811452315500_DEV204255C52","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1038\/ni.3522","article-title":"Affinity for self antigen selects Treg cells with distinct functional properties","volume":"17","author":"Wyss","year":"2016","journal-title":"Nat. Immunol."},{"key":"2024121811452315500_DEV204255C53","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1038\/s42003-023-04662-z","article-title":"Structure-preserving visualization for single-cell RNA-Seq profiles using deep manifold transformation with batch-correction","volume":"6","author":"Xu","year":"2023","journal-title":"Commun. Biol."}],"container-title":["Development"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.biologists.com\/dev\/article-pdf\/doi\/10.1242\/dev.204255\/3584850\/dev204255.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/journals.biologists.com\/dev\/article-pdf\/doi\/10.1242\/dev.204255\/3607694\/dev204255.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/journals.biologists.com\/dev\/article-pdf\/doi\/10.1242\/dev.204255\/3607694\/dev204255.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T11:46:03Z","timestamp":1734522363000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.biologists.com\/dev\/article\/151\/24\/dev204255\/363483\/A-multidimensional-toolkit-for-elucidating"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,15]]},"references-count":50,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2024,12,15]]}},"URL":"https:\/\/doi.org\/10.1242\/dev.204255","relation":{},"ISSN":["0950-1991","1477-9129"],"issn-type":[{"value":"0950-1991","type":"print"},{"value":"1477-9129","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,15]]},"article-number":"dev204255"}}