Plasmodium infection induces phenotypic, clonal, and spatial diversity among differentiating CD4+ T cells
Cameron G. Williams,
Marcela L. Moreira,
Takahiro Asatsuma,
Hyun Jae Lee,
Shihan Li,
Irving Barrera,
Evan Murray,
Megan S.F. Soon,
Jessica A. Engel,
David S. Khoury,
Shirley Le,
Brooke J. Wanrooy,
Dominick Schienstock,
Yannick O. Alexandre,
Oliver P. Skinner,
Rainon Joseph,
Lynette Beattie,
Scott N. Mueller,
Fei Chen,
Ashraful Haque
Affiliations
Cameron G. Williams
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Marcela L. Moreira
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Takahiro Asatsuma
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Hyun Jae Lee
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Shihan Li
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Irving Barrera
Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
Evan Murray
Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
Megan S.F. Soon
QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
Jessica A. Engel
QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD 4006, Australia
David S. Khoury
Kirby Institute, University of New South Wales, Kensington, NSW 2052, Australia
Shirley Le
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Brooke J. Wanrooy
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Dominick Schienstock
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Yannick O. Alexandre
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Oliver P. Skinner
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Rainon Joseph
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Lynette Beattie
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Scott N. Mueller
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia
Fei Chen
Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
Ashraful Haque
Department of Microbiology and Immunology, University of Melbourne, located at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC 3000, Australia; Corresponding author
Summary: Naive CD4+ T cells must differentiate in order to orchestrate immunity to Plasmodium, yet understanding of their emerging phenotypes, clonality, spatial distributions, and cellular interactions remains incomplete. Here, we observe that splenic polyclonal CD4+ T cells differentiate toward T helper 1 (Th1) and T follicular helper (Tfh)-like states and exhibit rarer phenotypes not elicited among T cell receptor (TCR) transgenic counterparts. TCR clones present at higher frequencies exhibit Th1 skewing, suggesting that variation in major histocompatibility complex class II (MHC-II) interaction influences proliferation and Th1 differentiation. To characterize CD4+ T cell interactions, we map splenic microarchitecture, cellular locations, and molecular interactions using spatial transcriptomics at near single-cell resolution. Tfh-like cells co-locate with stromal cells in B cell follicles, while Th1 cells in red pulp co-locate with activated monocytes expressing multiple chemokines and MHC-II. Spatial mapping of individual transcriptomes suggests that proximity to chemokine-expressing monocytes correlates with stronger effector phenotypes in Th1 cells. Finally, CRISPR-Cas9 gene disruption reveals a role for CCR5 in promoting clonal expansion and Th1 differentiation. A database of cellular locations and interactions is presented: https://haquelab.mdhs.unimelb.edu.au/spatial_gui/.
