Skip to main content

ORIGINAL RESEARCH article

Front. Cell Dev. Biol.
Sec. Nuclear Organization and Dynamics
Volume 13 - 2025 | doi: 10.3389/fcell.2025.1514627
This article is part of the Research Topic 10 years of Frontiers in Cell and Developmental Biology: Past Discoveries, Current Challenges and Future Perspectives View all 7 articles

Memory CD4+ T Cells Sequentially Restructure Their 3D Genome During Stepwise Activation

Provisionally accepted
Alex Ward Alex Ward 1*Jose De Las Heras Jose De Las Heras 2Eric C Schirmer Eric C Schirmer 2Ariberto Fassati Ariberto Fassati 1
  • 1 University College London, London, United Kingdom
  • 2 University of Edinburgh, Edinburgh, Scotland, United Kingdom

The final, formatted version of the article will be published soon.

    CD4+ T cells are a highly differentiated cell type that maintain enough transcriptomic plasticity to cycle between activated and memory statuses. How the 1D chromatin state and 3D chromatin architecture support this plasticity is under intensive investigation. Here, we wished to test a commercially available in situ Hi-C kit (Arima Genomics Inc) to establish whether published performance on limiting cell numbers from clonal cell lines copies across to a primary immune cell type. We were able to achieve comparable contact matrices from 50,000, 250,000 and 1,000,000 memory CD4+ T cell inputs. We generated multiple Hi-C and RNA-seq libraries from the same biological blood donors under three separate conditions: unstimulated fresh ex vivo, IL-2 only stimulated and TCR+CD28+IL-2 stimulated, conferring increasingly stronger activation signals. We wished to capture the magnitude and progression of 3D chromatin shifts and correlate these to expression changes under the two stimulations. While some genome organization changes occurred concomitant with changes in gene expression, there were at least as many changes that occurred without corresponding changes in expression. Counter to the hypothesis that Topologically Associated domains (TADs) are largely invariant structures providing a scaffold for dynamic looping contacts between enhancers and pr omotors, we found that there were at least as many dynamic TAD changes. Stimulation with IL-2 alone triggered many changes in genome organization and many of these changes were strengthened by additional TCR and CD28 co-receptor stimulation. This suggests a stepwise process whereby mCD4+ T cells undergo sequential buildup of 3D architecture induced by distinct or combined stimuli likely to "prime" or "de-prime" them for expression responses to subsequent TCR-antigen ligation or additional cytokine stimulation.

    Keywords: 3D-genome organization, memory CD4+ T-cells, sequential immune activation, Gene Expression Regulation, Hi-C, IL-2, enhancer-promoter interactions, primed/de-primed genes

    Received: 21 Oct 2024; Accepted: 07 Jan 2025.

    Copyright: © 2025 Ward, De Las Heras, Schirmer and Fassati. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Alex Ward, University College London, London, United Kingdom

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.