title: Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.
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 dissectionin 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-stagePlasmodiuminfection 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.
authors.affiliation: 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.
authors.forename: Tapio
authors.initials: T
authors.lastname: Lönnberg
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Valentine
authors.initials: V
authors.lastname: Svensson
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Kylie R
authors.initials: KR
authors.lastname: James
authors.affiliation: Department of Microbiology and Immunology, The Peter Doherty Institute, University of Melbourne, Parkville, Victoria, Australia.
authors.forename: Daniel
authors.initials: D
authors.lastname: Fernandez-Ruiz
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Ismail
authors.initials: I
authors.lastname: Sebina
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Ruddy
authors.initials: R
authors.lastname: Montandon
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Megan S F
authors.initials: MS
authors.lastname: Soon
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Lily G
authors.initials: LG
authors.lastname: Fogg
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Arya Sheela
authors.initials: AS
authors.lastname: Nair
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Urijah
authors.initials: U
authors.lastname: Liligeto
authors.affiliation: 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.
authors.forename: Michael J T
authors.initials: MJ
authors.lastname: Stubbington
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Lam-Ha
authors.initials: LH
authors.lastname: Ly
authors.affiliation: 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.
authors.forename: Frederik Otzen
authors.initials: FO
authors.lastname: Bagger
authors.affiliation: Department of Computer Science, University of Sheffield, Sheffield, UK.
authors.forename: Max
authors.initials: M
authors.lastname: Zwiessele
authors.affiliation: Department of Computer Science, University of Sheffield, Sheffield, UK.
authors.forename: Neil D
authors.initials: ND
authors.lastname: Lawrence
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Fernando
authors.initials: F
authors.lastname: Souza-Fonseca-Guimaraes
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Patrick T
authors.initials: PT
authors.lastname: Bunn
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Christian R
authors.initials: CR
authors.lastname: Engwerda
authors.affiliation: 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.
authors.forename: William R
authors.initials: WR
authors.lastname: Heath
authors.affiliation: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Oliver
authors.initials: O
authors.lastname: Billker
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK.
authors.forename: Oliver
authors.initials: O
authors.lastname: Stegle
authors.affiliation: QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland, Australia.
authors.forename: Ashraful
authors.initials: A
authors.lastname: Haque
authors.affiliation: 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.
authors.forename: Sarah A
authors.initials: SA
authors.lastname: Teichmann