Characterization of germinal center and circulating T follicular helper cells using both intracellular and surface CITE-seq

Abstract

Abstract T follicular helper (TFH) cells are a CD4+ T cell subset that play a critical role in the formation of germinal centers (GC). TFH cells are essential to produce protective antibody responses through regulation of clonal selection & differentiation into activated antibody-secreting & memory B cells. TFH cell differentiation is a multistep process that begins with presentation of antigen by dendritic cells to naïve CD4+ T cells, where CD4+ T cells commit to the TFH lineage by expressing the lineage defining transcription factor B cell lymphoma 6 (Bcl-6). TFH cells are phenotypically characterized by high expression of C-X-C chemokine receptor 5 (CXCR5) & programmed cell death-1 (PD-1) on the cell surface. CXCR5+ memory CD4+ T cells present in peripheral blood represent a circulating TFH (cTFH) cell subset. In contrast to TFH cells, cTFH cells may express low levels of Bcl-6 with numerous reports of subsets that differ both phenotypically & functionally. Here we characterise the heterogeneous subsets of TFH & cTFH cells using a combination of intracellular CITE-seq, surface CITE-seq and whole transcriptome single-cell RNA sequencing (scRNA-seq) analysis. Germinal center and circulating TFH cells were enriched by sorting memory CD4+, CXCR5+, PD-1+, and memory CD4+ CXCR5+ cells, respectively. We examined the expression of Bcl-6 & other transcription factors, using protein and RNA expression data, across pre-TFH, TFH & cTFH cells. Together, these data demonstrate how a combination of intracellular CITE-seq, surface CITE-seq & scRNA-seq may be used to deepen our understanding of the differentiation states & subsets of cells present at low abundance, by enabling detection of intracellular and surface protein along with high-quality mRNA.