Transcriptomic Profiling of Human Effector and Regulatory T Cell Subsets Identifies Predictive Population Signatures

After activation, CD4⁺ Th cells differentiate into functionally specialized populations that coordinate distinct immune responses and protect against different types of pathogens. In humans, these effector and memory Th cell subsets can be readily identified in peripheral blood based on their differential expression of chemokine receptors that govern their homeostatic and inflammatory trafficking. Foxp3⁺ regulatory T (Treg) cells can also be divided into subsets that phenotypically mirror each of these effector populations and share expression of key transcription factors and effector cytokines. In this study, we performed comprehensive transcriptional profiling of 11 phenotypically distinct Th and Treg cell subsets sorted from peripheral blood of healthy individuals. Despite their shared phenotypes, we found that mirror Th and Treg subsets were transcriptionally dissimilar and that Treg cell populations showed limited transcriptional diversity compared with Th cells. We identified core transcriptional signatures shared across all Th and Treg cell populations and unique signatures that define each of the Th or Treg populations. Finally, we applied these signatures to bulk Th and Treg RNA-sequencing data and found enrichment of specific Th and Treg cell populations in different human tissues. These results further define the molecular basis for the functional specialization and differentiation of Th and Treg cell populations and provide a new resource for examining Th and Treg specialization in RNA-sequencing data.

Cutting Edge: Tissue Antigen Expression Levels Fine-Tune T Cell Differentiation Decisions In Vivo

Immune homeostasis in peripheral tissues is, to a large degree, maintained by the differentiation and action of regulatory T cells (Treg) specific for tissue Ags. Using a novel mouse model, we have studied the differentiation of naive CD4⁺ T cells into Foxp3⁺ Treg in response to a cutaneous Ag (OVA). We found that expression of OVA resulted in fatal autoimmunity and in prevention of peripheral Treg generation. Inhibiting mTOR activity with rapamycin rescued the generation of Foxp3⁺ T cells. When we varied the level of Ag expression to modulate TCR signaling, we found that low Ag concentrations promoted the generation of Foxp3⁺ T cells, whereas high levels expanded effector T cells and caused severe autoimmunity. Our findings indicate that the expression level of tissue Ag is a key determinant of the balance between tissue-reactive effector and peripheral Foxp3⁺ T cells, which determines the choice between tolerance and autoimmunity.

H. pylori modulates DC functions via T4SS/TNFα/p38-dependent SOCS3 expression

Background

Helicobacter pylori (H. pylori) is a gram-negative bacterium that chronically infects approximately 50% of the world’s human population. While in most cases the infection remains asymptomatic, 10% of infected individuals develop gastric pathologies and 1–3% progress to gastric cancer. Although H. pylori induces severe inflammatory responses, the host’s immune system fails to clear the pathogen and H. pylori can persist in the human stomach for decades. As suppressor of cytokine signaling (SOCS) proteins are important feedback regulators limiting inflammatory responses, we hypothesized that H. pylori could modulate the host’s immune responses by inducing SOCS expression.

Methods

The phenotype of human monocyte-derived DCs (moDCs) infected with H. pylori was analyzed by flow cytometry and multiplex technology. SOCS expression levels were monitored by qPCR and signaling studies were conducted by means of Western blot. For functional studies, RNA interference-based silencing of SOCS1–3 and co-cultures with CD4⁺ T cells were performed.

Results

We show that H. pylori positive gastritis patients express significantly higher SOCS3, but not SOCS1 and SOCS2, levels compared to H. pylori negative patients. Moreover, infection of human moDCs with H. pylori rapidly induces SOCS3 expression, which requires the type IV secretion system (T4SS), release of TNFα, and signaling via the MAP kinase p38, but appears to be independent of TLR2, TLR4, MEK1/2 and STAT proteins. Silencing of SOCS3 expression in moDCs prior to H. pylori infection resulted in increased release of both pro- and anti-inflammatory cytokines, upregulation of PD-L1, and decreased T-cell proliferation.

Conclusions

This study shows that H. pylori induces SOCS3 via an autocrine loop involving the T4SS and TNFα and p38 signaling. Moreover, we demonstrate that high levels of SOCS3 in DCs dampen PD-L1 expression on DCs, which in turn drives T-cell proliferation.

Human CD4+CD103+ cutaneous resident memory T cells are found in the circulation of healthy individuals

Tissue-resident memory T cells (T_RM) persist locally in nonlymphoid tissues where they provide frontline defense against recurring insults. T_RM at barrier surfaces express the markers CD103 and/or CD69, which function to retain them in epithelial tissues. In humans, neither the long-term migratory behavior of T_RM nor their ability to reenter the circulation and potentially migrate to distant tissue sites has been investigated. Using tissue explant cultures, we found that CD4⁺CD69⁺CD103⁺ T_RM in human skin can down-regulate CD69 and exit the tissue. In addition, we identified a skin-tropic CD4⁺CD69^-CD103⁺ population in human lymph and blood that is transcriptionally, functionally, and clonally related to the CD4⁺CD69⁺CD103⁺ T_RM population in the skin. Using a skin xenograft model, we confirmed that a fraction of the human cutaneous CD4⁺CD103⁺ T_RM population can reenter circulation and migrate to secondary human skin sites where they reassume a T_RM phenotype. Thus, our data challenge current concepts regarding the strict tissue compartmentalization of CD4⁺ T cell memory in humans.

Identification of functionally unique CD4 T cells that are the circulating counterparts of epidermal resident memory T cells

As a barrier organ, the skin contains specialized T cell populations that combat infection and also help maintain tissue homeostasis and promote wound repair. Circulating skin-tropic T cells can also be identified in the blood based on their expression of the cutaneous lymphocyte antigen (CLA), but the developmental and functional relationships between these circulating CLA+ T cells and tissue-resident T cells in the skin are not fully understood. Using 33-parameter Cytometry by time-of-flight (CyTOF) analysis we identified a novel population of skin-tropic CD4+ T cells in human blood that expresses the CD103 integrin and phenotypically and functionally resembles epidermal resident memory T cells (TRM) in the skin. RNA sequencing identified a set of signature genes shared by circulating CD103+CLAhi T cells in the blood and epidermal TRM cells in the skin, and suggested that CD103+CLAhiT cells contribute to normal skin function and response to tissue damage. Finally, using humanized NSG mice carrying full-thickness human skin grafts we demonstrated that, despite their identification as TRM, CD103+CLAhi T cells in the skin are capable of exiting the tissue and re-entering circulation. Thus, CD103+CLAhi T cells in the blood represent a circulating T cell population of cutaneous TRM, and this provides novel opportunities for the study and therapeutic manipulation of TRM cells in the contexts of cutaneous infection, inflammation, and tissue-repair.