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From pseudo to real-time dynamics of T cell thymic differentiation

Gavish, Avishai; Chain, Benny; Salame, Tomer M; Antebi, Yaron E; Nevo, Shir; Reich-Zeliger, Shlomit; Friedman, Nir; (2023) From pseudo to real-time dynamics of T cell thymic differentiation. iScience , 26 (1) , Article 105826. 10.1016/j.isci.2022.105826. Green open access

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Abstract

Numerous methods have recently emerged for ordering single cells along developmental trajectories. However, accurate depiction of developmental dynamics can only be achieved after rescaling the trajectory according to the relative time spent at each developmental point. We formulate a model which estimates local cell densities and fluxes, and incorporates cell division and apoptosis rates, to infer the real-time dimension of the developmental trajectory. We validate the model using mathematical simulations and apply it to experimental high dimensional cytometry data obtained from the mouse thymus to construct the true time profile of the thymocyte developmental process. Our method can easily be implemented in any of the existing tools for trajectory inference.

Type: Article
Title: From pseudo to real-time dynamics of T cell thymic differentiation
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.isci.2022.105826
Publisher version: https://doi.org/10.1016/j.isci.2022.105826
Language: English
Additional information: © 2022 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Keywords: Bioinformatics, Developmental biology, Stem cells research
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity
URI: https://discovery.ucl.ac.uk/id/eprint/10163321
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