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After activation, CD4+ T helper (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 to 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-seq 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-seq data.

Tissue-resident memory T cells (TRM) persist locally in nonlymphoid tissues where they provide frontline defense against recurring insults. TRM 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 TRM 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+ TRM 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+ TRM population in the skin. Using a skin xenograft model, we confirmed that a fraction of the human cutaneous CD4+CD103+ TRM population can reenter circulation and migrate to secondary human skin sites where they reassume a TRM phenotype. Thus, our data challenge current concepts regarding the strict tissue compartmentalization of CD4+ T cell memory in humans.

Chemically defined serum-free media are increasingly used as a tool to help standardize experiments by eliminating the potential variability contributed by pooled serum. These media are formulated for the culture and expansion of specific cell types, maintaining cell viability without the need for exogenous animal proteins. Formulated serum-free media could thus help improve viability and reduce variability during sample preparation for flow cytometry, yet a thorough analysis of how such media impact fluorochrome–Ab conjugates has not been performed. In this study, we expose fluorescent Ab-labeled cells or Ab capture beads to white light in the presence of various hematopoietic cell culture media and provide evidence that formulated serum-free media permit rapid light-initiated fluorescent dye degradation in a cell-independent manner. We observed fluorescence signal loss of several dyes, which included fluorescence spillover into adjacent detectors. Finally, photostability of Ab–fluorochrome conjugates in formulated serum-free media is partially restored in the presence of either serum or vitamin C, implicating reactive oxygen species in the observed signal loss. Thus, our data indicate that formulated serum-free media designed to standardize cell culture are not currently optimized for use with fluorochrome–Ab conjugates, and thus, extreme caution should be exercised when using these media in cytometric experiments.

Summary Multiple sclerosis is an inflammatory T cell-mediated autoimmune disease. In a Phase II clinical trial, high-dose immunosuppressive therapy combined with autologous CD34+ haematopoietic stem cell transplant resulted in 69·2% of subjects remaining disease-free without evidence of relapse, loss of neurological function or new magnetic resonance imaging (MRI) lesions to year 5 post-treatment. A combination of CyTOF mass cytometry and multi-parameter flow cytometry was used to explore the reconstitution kinetics of immune cell subsets in the periphery post-haematopoietic cell transplant (HSCT) and the impact of treatment on the phenotype of circulating T cells in this study population. Repopulation of immune cell subsets progressed similarly for all patients studied 2 years post-therapy, regardless of clinical outcome. At month 2, monocytes and natural killer (NK) cells were proportionally more abundant, while CD4 T cells and B cells were reduced, relative to baseline. In contrast to the changes observed at earlier time-points in the T cell compartment, B cells were proportionally more abundant and expansion in the proportion of naive B cells was observed 1 and 2 years post-therapy. Within the T cell compartment, the proportion of effector memory and late effector subsets of CD4 and CD8 T cells was increased, together with transient increases in proportions of CD45RA-regulatory T cells (Tregs) and T helper type 1 (Th1 cells) and a decrease in Th17·1 cells. While none of the treatment effects studied correlated with clinical outcome, patients who remained healthy throughout the 5-year study had significantly higher absolute numbers of memory CD4 and CD8 T cells in the periphery prior to stem cell transplantation.

Tissue-resident memory T cells (TRM) persist locally in non-lymphoid tissues, providing front-line defense against recurring insults. However, strict tissue compartmentalization of memory may pose certain disadvantages for a large barrier organ like the skin, and the long-term migratory behavior of human TRM and their contribution to the memory pool have not been fully elucidated. TRM at barrier surfaces are defined in part by expression of the markers CD103 and/or CD69 which function to retain TRM in epithelial tissues. Here, we found that CD4+CD69+CD103+ TRM in human skin can downregulate CD69, exit the tissue and be identified as a phenotypically unique population in the circulation of healthy individuals. These circulating TRM produce the cytokines IL-22 and IL-13, and express genes consistent with a role in host-defense and tissue-repair responses. RNA- and TCR-sequencing demonstrated that CD103+ TRM in the blood are transcriptionally and clonally related to CD69+CD103+ TRM in the skin. Furthermore, using a skin xenograft model, we confirmed that human cutaneous CD103+ TRM can exit the skin, enter the circulation, and recirculate to secondary human skin sites where they re-assume a TRM phenotype. Thus, although as a population CD4+ TRM in the skin are largely sessile, recirculation of cutaneous CD4+CD103+ TRM does occur in the steady state in humans, and these recirculating (rc)TRM cells can promote the spread of this functionally specialized T cell population throughout the skin.

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.