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Ono M, Crompton T. A multidimensional toolkit for elucidating temporal trajectories in cell development in vivo. Development 2024; 151:dev204255. [PMID: 39611743 DOI: 10.1242/dev.204255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 11/17/2024] [Indexed: 11/30/2024]
Abstract
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.
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Affiliation(s)
- Masahiro Ono
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Tessa Crompton
- Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
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Webb LV, Barbarulo A, Huysentruyt J, Vanden Berghe T, Takahashi N, Ley S, Vandenabeele P, Seddon B. Survival of Single Positive Thymocytes Depends upon Developmental Control of RIPK1 Kinase Signaling by the IKK Complex Independent of NF-κB. Immunity 2019; 50:348-361.e4. [PMID: 30737145 PMCID: PMC6382466 DOI: 10.1016/j.immuni.2019.01.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 11/07/2018] [Accepted: 01/04/2019] [Indexed: 12/22/2022]
Abstract
NF-κB (nuclear factor κB) signaling is considered critical for single positive (SP) thymocyte development because loss of upstream activators of NF-κB, such as the IKK complex, arrests their development. We found that the compound ablation of RelA, cRel, and p50, required for canonical NF-κB transcription, had no impact upon thymocyte development. While IKK-deficient thymocytes were acutely sensitive to tumor necrosis factor (TNF)-induced cell death, Rel-deficient cells remained resistant, calling into question the importance of NF-κB as the IKK target required for thymocyte survival. Instead, we found that IKK controlled thymocyte survival by repressing cell-death-inducing activity of the serine/threonine kinase RIPK1. We observed that RIPK1 expression was induced during development of SP thymocytes and that IKK was required to prevent RIPK1-kinase-dependent death of SPs in vivo. Finally, we showed that IKK was required to protect Rel-deficient thymocytes from RIPK1-dependent cell death, underscoring the NF-κB-independent function of IKK during thymic development.
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Affiliation(s)
- Louise V Webb
- Present address: Francis Crick Institute, Mill Hill Laboratories, London NW7 1AA, UK
| | - Alessandro Barbarulo
- Division of Infection and Immunity, UCL Institute of Immunity and Transplantation, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK
| | - Jelle Huysentruyt
- VIB-UGent Center for Inflammation Research, VIB-UGent Research Building FSVM, Technologiepark 927, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Tom Vanden Berghe
- VIB-UGent Center for Inflammation Research, VIB-UGent Research Building FSVM, Technologiepark 927, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Nozomi Takahashi
- VIB-UGent Center for Inflammation Research, VIB-UGent Research Building FSVM, Technologiepark 927, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Steven Ley
- Division of Molecular Immunology, Imperial College, London, UK
| | - Peter Vandenabeele
- VIB-UGent Center for Inflammation Research, VIB-UGent Research Building FSVM, Technologiepark 927, Ghent 9052, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Benedict Seddon
- Division of Infection and Immunity, UCL Institute of Immunity and Transplantation, Royal Free Hospital, Rowland Hill Street, London NW3 2PF, UK.
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Identification of Candidate Genes Related to Inflammatory Bowel Disease Using Minimum Redundancy Maximum Relevance, Incremental Feature Selection, and the Shortest-Path Approach. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5741948. [PMID: 28293637 PMCID: PMC5331171 DOI: 10.1155/2017/5741948] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 01/11/2017] [Indexed: 02/08/2023]
Abstract
Identification of disease genes is a hot topic in biomedicine and genomics. However, it is a challenging problem because of the complexity of diseases. Inflammatory bowel disease (IBD) is an idiopathic disease caused by a dysregulated immune response to host intestinal microflora. It has been proven to be associated with the development of intestinal malignancies. Although the specific pathological characteristics and genetic background of IBD have been partially revealed, it is still an overdetermined disease and the blueprint of all genetic variants still needs to be improved. In this study, a novel computational method was built to identify genes related to IBD. Samples from two subtypes of IBD (ulcerative colitis and Crohn's disease) and normal samples were employed. By analyzing the gene expression profiles of these samples using minimum redundancy maximum relevance and incremental feature selection, 21 genes were obtained that could effectively distinguish samples from the two subtypes of IBD and the normal samples. Then, the shortest-path approach was used to search for an additional 20 genes in a large network constructed using protein-protein interactions based on the above-mentioned 21 genes. Analyses of the 41 genes obtained indicate that they are closely associated with this disease.
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Abstract
The ability of T cells to respond to a wide array of foreign antigens while avoiding reactivity to self is largely determined by cellular selection of developing T cells in the thymus. While a great deal is known about the cell types and molecules involved in T-cell selection in the thymus, our understanding of the spatial and temporal aspects of this process remain relatively poorly understood. Thymocytes are highly motile within the thymus and travel between specialized microenvironments at different phases of their development while interacting with distinct sets of self-peptides and peptide presenting cells. A knowledge of when, where, and how thymocytes encounter self-peptide MHC ligands at different stages of thymic development is key to understanding T-cell selection. In the past several years, our laboratory has investigated this topic using two-photon time-lapse microscopy to directly visualize thymocyte migration and signaling events, together with a living thymic slice preparation to provide a synchronized experimental model of T-cell selection in situ. Here, we discuss recent advances in our understanding of the temporal and spatial aspects of T-cell selection, highlighting our own work, and placing them in the context of work from other groups.
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Affiliation(s)
- Nadia Kurd
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Ellen A Robey
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
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Daley SR. MHCI and CD8 lineage commitment. Prolonged access to thymic epithelial MHCI seals CD8⁺ lineage commitment. Immunol Cell Biol 2015; 93:326-7. [PMID: 25753267 DOI: 10.1038/icb.2015.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Stephen R Daley
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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