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Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Nair AS, Liligeto U, Stubbington MJT, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria. Sci Immunol 2017; 2. [PMID: 28345074 DOI: 10.1126/sciimmunol.aal2192] [Citation(s) in RCA: 183] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Differentiation of naïve CD4+ T cells into functionally distinct T helper subsets is crucial for the orchestration of immune responses. Due to extensive heterogeneity and multiple overlapping transcriptional programs in differentiating T cell populations, this process has remained a challenge for systematic dissection in vivo. By using single-cell transcriptomics and computational analysis using a temporal mixtures of Gaussian processes model, termed GPfates, we reconstructed the developmental trajectories of Th1 and Tfh cells during blood-stage Plasmodium infection in mice. By tracking clonality using endogenous TCR sequences, we first demonstrated that Th1/Tfh bifurcation had occurred at both population and single-clone levels. Next, we identified genes whose expression was associated with Th1 or Tfh fates, and demonstrated a T-cell intrinsic role for Galectin-1 in supporting a Th1 differentiation. We also revealed the close molecular relationship between Th1 and IL-10-producing Tr1 cells in this infection. Th1 and Tfh fates emerged from a highly proliferative precursor that upregulated aerobic glycolysis and accelerated cell cycling as cytokine expression began. Dynamic gene expression of chemokine receptors around bifurcation predicted roles for cell-cell in driving Th1/Tfh fates. In particular, we found that precursor Th cells were coached towards a Th1 but not a Tfh fate by inflammatory monocytes. Thus, by integrating genomic and computational approaches, our study has provided two unique resources, a database www.PlasmoTH.org, which facilitates discovery of novel factors controlling Th1/Tfh fate commitment, and more generally, GPfates, a modelling framework for characterizing cell differentiation towards multiple fates.
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Affiliation(s)
- Tapio Lönnberg
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Valentine Svensson
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kylie R James
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Daniel Fernandez-Ruiz
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ismail Sebina
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Ruddy Montandon
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Megan S F Soon
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Lily G Fogg
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Arya Sheela Nair
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Urijah Liligeto
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Michael J T Stubbington
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lam-Ha Ly
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Frederik Otzen Bagger
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge, UK
| | - Max Zwiessele
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | - Neil D Lawrence
- Department of Computer Science, University of Sheffield, Sheffield, UK
| | | | - Patrick T Bunn
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Christian R Engwerda
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - William R Heath
- Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia; The Australian Research Council Centre of Excellence in Advanced Molecular Imaging, The University of Melbourne, Parkville, Victoria, Australia
| | - Oliver Billker
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ashraful Haque
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia
| | - Sarah A Teichmann
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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