Clone tracking through repeated malaria reveals high-fidelity CD4+ memory responses

Few studies have assessed the clonality and functional fidelity of human CD4+ T cells responding to repeated infections in vivo. We utilized broad, longitudinal single-cell RNA and TCR tracking to study the functional stability and memory potential of thousands of CD4+ T cell clonotypes through repeated Plasmodium falciparum (Pf) infections over the course of hundreds of days. Strikingly, nearly all memory CD4+ T cell clonotypes displayed a strong preference for one of seven different subsets—Tcm, Th1, cytotoxic Th1, Th2, Th17, Treg, and Tr1. This phenomenon, which we call “clonal fidelity,” was influenced by clonal expansion, demonstrating an in vivo relationship between T cell polarization and proliferation. Using clone tracking, we characterized subset-specific trajectories of CD4+ T cell activation and identified clonotypes with specific reactivity to Plasmodium falciparum (Pf) blood-stage antigens. Tr1 cells, a peripherally-induced regulatory subset distinct from FOXP3+ Tregs, accounted for nearly 90% of Pf-specific CD4+ T cells. Tracking T cell clones longitudinally in humans, we observed malaria-induced clonal expansion of Tr1 effectors, long-term persistence of Tr1 memory cells, and high-fidelity recall responses following reinfection. Ultimately, this work establishes clonal fidelity as a natural phenomenon and demonstrates the stable, long-term memory potential of the previously enigmatic Tr1 cell.

Methods
These processed data files are seurat objects that were generated from raw data available from NCBI (BioProject PRJNA1129481).

The code used to generate these files is available on GitHub (jason-nideffer/clone-tracking-in-malaria).

These files can be used (in conjunction with code available on GitHub) to reproduce the figures in the manuscript titled: "Clone tracking through repeated malaria reveals high-fidelity CD4+ memory responses."