Induction and transcriptional regulation of the co-inhibitory gene module in T cells

Abstract

Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated co-inhibitory receptor expression on CD4+ T cells promotes autoimmunity while sustained overexpression on CD8+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and cancer1,2. Here, we used RNA and protein expression profiling at single-cell resolution to identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, Tim-3, Lag-3, and TIGIT), but also a number of novel surface receptors. We functionally validated two novel co-inhibitory receptors, Activated protein C receptor (Procr) and Podoplanin (Pdpn). The module of co-inhibitory receptors is co-expressed in both CD4+ and CD8+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in multiple physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors Prdm1 and c-Maf as cooperative regulators of the co-inhibitory module, which we validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies novel regulators of T cell function with the potential to regulate autoimmunity and tumor immunity.

Impact of selective CD28 blockade on virus-specific immunity to a murine Epstein-Barr virus homolog

“…This expression pattern is consistent with a "cassette" of coordinately regulated coinhibitory receptors recently described in the literature. 29 Of note, CITRUS also identified a separate cluster that expressed high 2B4 but low PD-1, TIM-3, and (Figure 3C,D). There was also no significant difference between the abundance of cells expressing 2B4 (25 457) at this time point ( Figure 3D).…”

“…At 14 dpi, there was a significant decrease in the abundance of cells found within parent cluster 17 654 in both the CTLA-4Ig-and anti-CD28-dAb treated samples as compared to no treatment ( Figure 3A,B), but the abundance of cells in cluster 17 654 was not different between the two treatment groups. 29 Of note, CITRUS also identified a separate cluster that expressed high 2B4 but low PD-1, TIM-3, and exhaustion cassette of PD-1 + , TIM-3 + , and TIGIT + was still present (25 466), there was no difference in the abundance of cells within this node between experimental groups ( Figure 3C,D). This expression pattern is consistent with a "cassette" of coordinately regulated coinhibitory receptors recently described in the literature.…”

Going beyond a whack‐a‐mole game: A systems biology approach to immune tolerance

“…In a recent article, the authors and colleagues identified a new gene module that is induced by the regulatory cytokine, interleukin‐27 (IL‐27), and is found in multiple non‐responsive T‐cell states, such as exhaustion, dysfunction and tolerance . This study uncovered novel immune checkpoint molecules poised to become therapeutic targets.…”

“…Although many co‐inhibitory molecules that modulate T‐cell phenotype in autoimmune diseases have been investigated, it was unclear whether there is a common anchor underlying the expression of these molecules. Here, using single‐cell RNA‐seq and single‐cell mass cytometry, the author and colleagues showed the co‐expression of these co‐inhibitory molecules in the highly immunosuppressive tumor microenvironment . The core of the expression consisted of known co‐inhibitory molecules, such as PD‐1, TIM‐3, LAG‐3 and TIGIT, and co‐expressed with multiple new cell‐surface receptors.…”

“…Here, using single-cell RNA-seq and single-cell mass cytometry, the author and colleagues showed the co-expression of these co-inhibitory molecules in the highly immunosuppressive tumor microenvironment. 1 The core of the expression consisted of known co-inhibitory molecules, such as PD-1, TIM-3, LAG-3 and TIGIT, and coexpressed with multiple new cell-surface receptors. To identify the common regulator of these co-inhibitory molecules, the authors focused on the immunoregulatory cytokine, IL-27, as it has been shown to induce IL-10-secreting Tr1 cells that are immune suppressive and ameliorate experimental autoimmune encephalomyelitis, a murine experimental model of multiple sclerosis.…”