Divergent cytokine and transcriptional signatures control functional T follicular helper cell heterogeneity (scRNAseq/CITEseq)

CD4+ T follicular helper (Tfh) cells support tailored B cell responses against multiple classes of pathogens. To reveal how diverse Tfh phenotypes are established, we profiled Tfh cells in response to viral, helminth and bacterial infection. We identified a core Tfh signature that is distinct from CD4+ T follicular regulatory and effector cells and identified pathogen-specific transcriptional modules that shape Tfh function. Cytokine-transcriptional Tfh programming demonstrated that type I interferon and TGFbeta signaling direct individual Tfh phenotypes to instruct B cell output. Cytokine-directed Tfh transcriptional phenotypes are shared within human germinal centers (GCs), but distinct Tfh phenotypes dominate between donors and following immune challenge or in antibody-mediated disease. Finally, we identified novel cell surface markers that align with distinct Tfh phenotypes. Thus, we provide a comprehensive resource of Tfh diversity in humans and mice, to enable immune monitoring during infection and disease and to inform the development of context-specific vaccines. Paired single cell RNA sequencing (scRNAseq) and surface protein sequencing (CITEseq) analysis of Tfh cells from human adult tonsils samples.