T follicular helper (TFH) cells are specialized effector CD4+ T cells that help B cells develop germinal centers and memory. However, the transcription factors that regulate TFH differentiation remain incompletely understood. Here we report that selective loss of either Lef1 (LEF-1) or Tcf7 (TCF-1) resulted in TFH defects, while deletion of Lef1 and Tcf7 severely impaired TFH differentiation and germinal centers. Forced expression of LEF-1 enhanced TFH differentiation. LEF-1 and TCF-1 coordinated TFH differentiation by two general mechanisms. First, they established the responsiveness of naïve CD4+ T cells to TFH signals. Second, they promoted early TFH differentiation via the multipronged approach of sustaining expression of IL-6Rα and gp130, enhancing ICOS expression, and promoting expression of Bcl6.

The CD4+ and CD8+ T cell dichotomy is essential for effective cellular immunity. How the individual T cell identity is established remains poorly understood. Here we show that the high mobility group (HMG) transcription factors Tcf1 and Lef1 are essential for repressing CD4+ lineage-associated genes including Cd4, Foxp3 and Rorc in CD8+ T cells. Tcf1- and Lef1-deficient CD8+ T cells exhibit histone hyperacetylation, which is ascribed to an unexpected intrinsic histone deacetylase (HDAC) activity in Tcf1 and Lef1. Mutating five conserved amino acids in the Tcf1 HDAC domain diminishes the HDAC activity and the ability to suppress CD4+ lineage genes in CD8+ T cells. These findings reveal that sequence-specific transcription factors can utilize intrinsic HDAC activity to guard cell identity by repressing lineage-inappropriate genes.

Activated CD8+ T cells differentiate into cytotoxic effector (TEFF) cells that eliminate target cells. How TEFF cell identity is established and maintained remains less understood. Here we show Runx3 deficiency limits clonal expansion and impairs upregulation of cytotoxic molecules in TEFF cells. Runx3-deficient CD8+ TEFF cells aberrantly upregulate genes characteristic of follicular helper T (TFH) cell lineage, including Bcl6, Tcf7 and Cxcr5. Mechanistically, the Runx3-CBFβ complex deploys H3K27me3 to Bcl6 and Tcf7 genes to suppress the TFH program. Ablating Tcf7 in Runx3-deficient CD8+ TEFF cells prevents the upregulation of TFH genes and ameliorates their defective induction of cytotoxic genes. As such, Runx3-mediated Tcf7 repression coordinately enforces acquisition of cytotoxic functions and protects the cytotoxic lineage integrity by preventing TFH-lineage deviation.

T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Using strand-specific RNA-seq, we observed that intron retention is prevalent in polyadenylated transcripts in resting CD4+ T cells and is significantly reduced upon T cell activation. Several lines of evidence suggest that intron-retained transcripts are less stable than fully spliced transcripts. Strikingly, the decrease in intron retention (IR) levels correlate with the increase in steady-state mRNA levels. Further, the majority of the genes upregulated in activated T cells are accompanied by a significant reduction in IR. Of these 1583 genes, 185 genes are predominantly regulated at the IR level, and highly enriched in the proteasome pathway, which is essential for proper T cell proliferation and cytokine release. These observations were corroborated in both human and mouse CD4+ T cells. Our study revealed a novel post-transcriptional regulatory mechanism that may potentially contribute to coordinated and/or quick cellular responses to extracellular stimuli such as an acute infection.

Tcf1 and Lef1 have versatile functions in regulating T cell development and differentiation, but intrinsic requirements for these factors in regulatory T (T reg) cells remain to be unequivocally defined. Specific ablation of Tcf1 and Lef1 in T reg cells resulted in spontaneous multi-organ autoimmunity that became more evident with age. Tcf1/Lef1-deficient T regs showed reduced protection against experimentally induced colitis, indicative of diminished immuno-suppressive capacity. Transcriptomic analysis revealed that Tcf1 and Lef1 were responsible for positive regulation of a subset of T reg–overrepresented signature genes such as Ikzf4 and Izumo1r. Unexpectedly, Tcf1 and Lef1 were necessary for restraining expression of cytotoxic CD8+ effector T cell–associated genes in T reg cells, including Prdm1 and Ifng. Tcf1 ChIP-seq revealed substantial overlap between Tcf1 and Foxp3 binding peaks in the T reg cell genome, with Tcf1-Foxp3 cooccupancy observed at key T reg signature and cytotoxic effector genes. Our data collectively indicate that Tcf1 and Lef1 are critical for sustaining T reg suppressive functions and preventing loss of self-tolerance.