Tissue-specific heterogeneity of Human T follicular helper cells marked by unique transcriptomes and regulatory architecture

Abstract T follicular helper (T FH) cells represent a distinct lineage of CD4 T cells that engage with cognate B cells, facilitating the production of high affinity vaccine- and pathogen-specific antibodies. In humans, T FHcells can be detected in several tissues throughout the body, each representing a unique cellular environment complete with distinct signaling molecules. Despite T FHcell importance to human health, it remains unclear if and how anatomical location results in diversity among T FHcells. Here, we detail tissue-specific heterogeneity of human T FHcells reflected in both transcriptome and chromatin architecture. T FHcells sourced from circulating peripheral blood (cT FH), lung lymph nodes (lnT FH), tonsils (tT FH), and an in vitro differentiation model (exT FH), were subjected to RNA-sequencing and ATAC-sequencing. When comparing expression of conical T FHgenes, including BCL6 and PDCD1, a spectrum in magnitude emerged: cT FH< exT FH< lnT FH< tT FH. Increased chromatin accessibility at proximal cis-regulatory elements occurred within the loci of T FHgenes in a similar tissue-dependent fashion and correlated with transcript levels. Additionally, unique gene signatures were detected in each T FHpopulation, including the presence of distinct transcription factor networks, implying tissue specific T FHfunctionality. Integrating PageRank and scRNA-seq of tT FHcells revealed BCL-6, ASCL2, TOX, TOX2, and AIOLOS as potential regulators of the T FHgene program. Collectively, these findings detail tissue specific diversity amongst human T FHcells, while highlighting key developmental networks which could influence the design of future immunological therapies targeting T FHcells. Supported by grants from NIH: (RO1 AI113021, F32 AI161857)