Single-cell atlas of hepatic T cells reveals expansion of liver-resident naive-like CD4+ T cells in primary sclerosing cholangitis

BACKGROUND & AIMS

Little is known about the composition of intrahepatic immune cells and their contribution to the pathogenesis of primary sclerosing cholangitis (PSC). Herein, we aimed to create an atlas of intrahepatic T cells and thereby perform an in-depth characterization of T cells in inflamed human liver.

METHODS

Different single-cell RNA sequencing methods were combined with in silico analyses on intrahepatic and peripheral T cells from patients with PSC (n = 11) and healthy donors (HDs, n = 4). Multi-parameter flow cytometry and functional in vitro experiments were conducted on samples from patients with PSC (n = 24), controls with other liver diseases and HDs.

RESULTS

We identified a population of intrahepatic naive-like CD4⁺ T cells, which was present in all liver diseases tested, but particularly expanded in PSC. This population had a transcriptome and T cell receptor repertoire similar to circulating naive T cells but expressed a set of genes associated with tissue residency. Their periductal location supported the concept of tissue-resident naive-like T cells in livers of patients with PSC. Trajectory inference suggested that these cells had the developmental propensity to acquire a T helper 17 (T_H17) polarization state. Functional and chromatin accessibility experiments revealed that circulating naive T cells in patients with PSC were predisposed to polarize towards T_H17 cells.

CONCLUSION

We report the first atlas of intrahepatic T cells in PSC, which led to the identification of a previously unrecognized population of tissue-resident naive-like T cells in the inflamed human liver and to the finding that naive CD4⁺ T cells in PSC harbour the propensity to develop into T_H17 cells.

LAY SUMMARY

The composition of intrahepatic immune cells in primary sclerosing cholangitis (PSC) and their contribution to disease pathogenesis is widely unknown. We analysed intrahepatic T cells and identified a previously uncharacterized population of liver-resident CD4⁺ T cells which are expanded in the livers of patients with PSC compared to healthy liver tissue and other liver diseases. These cells are likely to contribute to the pathogenesis of PSC and could be targeted in novel therapeutic approaches.

MAIT cell development in mice and humans

MAIT cells arise in the thymus following rearrangement of a T cell receptor (TCR) reactive against microbial vitamin B2-derived metabolites presented by the MHC-Ib molecule, MR1. Mechanisms that are conserved in mammals ensure the frequent production of MR1-restricted TCRs and the intra-thymic differentiation of MR1-restricted thymocytes into effector cells. Upon thymic egress and migration into non-lymphoid tissues, additional signals modulate MAIT cell functions according to each local tissue environment. Here, we review the recent progress made towards a better understanding of the establishment of this major immune cell subset.

Functions of human liver CD69+CD103-CD8+ T cells depend on HIF-2α activity in healthy and pathologic livers

BACKGROUND & AIMS

Human liver CD69⁺CD8⁺ T cells are ~95% CD103^- and ~5% CD103⁺. Although CD69⁺CD103⁺CD8⁺ T cells show tissue residency and robustly respond to antigens, CD69⁺CD103^-CD8⁺ T cells are not yet well understood.

METHODS

Liver perfusate and paired peripheral blood were collected from healthy living donors and recipients with cirrhosis during liver transplantation. Liver tissues were obtained from patients with acute hepatitis A. Phenotypic and functional analyses were performed by flow cytometry. Gene expression profiles were determined by microarray and quantitative reverse transcription PCR. PT-2385 was used to inhibit hypoxia-inducible factor (HIF)-2α.

RESULTS

Human liver CD69⁺CD103^-CD8⁺ T cells exhibited HIF-2α upregulation with a phenotype of tissue residency and terminal differentiation. CD103^- cells comprised non-hepatotropic virus-specific T cells as well as hepatotropic virus-specific T cells, but CD103⁺ cells exhibited only hepatotropic virus specificity. Although CD103^- cells were weaker effectors on a per cell basis than CD103⁺ cells, following T cell receptor or interleukin-15 stimulation, they remained the major CD69⁺CD8⁺ effector population in the liver, surviving with less cell death. An HIF-2α inhibitor suppressed the effector functions and survival of CD69⁺CD103^-CD8⁺ T cells. In addition, HIF-2α expression in liver CD69⁺CD103^-CD8⁺ T cells was significantly increased in patients with acute hepatitis A or cirrhosis.

CONCLUSIONS

Liver CD69⁺CD103^-CD8⁺ T cells are tissue resident and terminally differentiated, and their effector functions depend on HIF-2α. Furthermore, activation of liver CD69⁺CD103^-CD8⁺ T cells with HIF-2α upregulation is observed during liver pathology.

LAY SUMMARY

The immunologic characteristics and the role of CD69⁺CD103^-CD8⁺ T cells, which are a major population of human liver CD8⁺ T cells, remain unknown. Our study shows that these T cells have a terminally differentiated tissue-resident phenotype, and their effector functions depend on a transcription factor, HIF-2α. Furthermore, these T cells were activated and expressed higher levels of HIF-2α in liver pathologies, suggesting that they play an important role in immune responses in liver tissues and the pathogenesis of human liver disease.

Mucosal-Associated Invariant T Cells in Tumors of Epithelial Origin

Mucosal-associated invariant T (MAIT) cells are innate T lymphocytes that circulate in blood and also reside in mucosal tissues. Blood MAIT cells are typically highly Th1-polarized, while those in mucosal tissues include both Th1- and Th17-polarized subsets. MAIT cells mount cytokine and cytolytic responses as a result of T cell receptor (TCR)-mediated recognition of microbially derived metabolites of riboflavin (vitamin B₂) presented by the MR1 antigen-presenting molecule. Additionally, MAIT cells can be activated by inflammatory cytokines produced by antigen-presenting cells (APCs) that have been exposed to pathogen-associated molecular patterns (PAMPs). Since the antigenic metabolites of riboflavin recognized by MAIT cells are produced by many microorganisms, including pathogens as well as non-pathogenic colonists, the inflammatory state of the tissue may be a key feature that determines the nature of MAIT cell responses. Under normal conditions where inflammatory cytokines are not produced, MAIT cell responses to microbial metabolites may simply serve to help maintain a healthy balance between epithelial cells and microbial colonists. In contrast, in situations where inflammatory cytokines are produced (e.g., pathogenic infection or damage to epithelial tissue), MAIT cell responses may be more potently pro-inflammatory. Since chronic inflammation and microbial drivers are associated with tumorigenesis and also trigger MAIT cell responses, the nexus of MAIT cells, local microbiomes, and epithelial cells may play an important role in epithelial carcinogenesis. This chapter reviews current information about MAIT cells and epithelial tumors, where the balance of evidence suggests that enrichment of Th17-polarized MAIT cells at tumor sites associates with poor patient prognosis. Studying the role of MAIT cells and their interactions with resident microbes offers a novel view of the biology of epithelial tumor progression and may ultimately lead to new approaches to target MAIT cells clinically.

A novel spleen-resident immature NK cell subset and its maturation in a T-bet-dependent manner

NK cells are thought to develop primarily in the bone marrow during adult life. However, increasing evidence shows that NK cell developmental intermediates can be found in different peripheral tissues with unique characteristics. Here, we identified a unique NK cell subset with the CD49a^-CD49b^- phenotype in the spleen. These cells displayed an immature phenotype and weak abilities in cytotoxicity and cytokine production. Adoptive transfer experiments revealed that they could develop into mature conventional NK (cNK) cells. Transcriptome analysis further confirmed their immature features. Parabiosis experiments revealed that these cells maintained tissue-resident properties in the spleen. Moreover, T-bet deficiency intrinsically impaired the ability of these cells to develop into mature cNK cells. Thus, our study identified a spleen-resident immature NK cell subset that could undergo extramedullary maturation in a T-bet dependent manner.

Superior B. pertussis Specific CD4+ T-Cell Immunity Imprinted by Natural Infection

Pertussis remains endemic in vaccinated populations due to waning of vaccine-induced immunity and insufficient interruption of transmission. Correlates of long-term protection against whooping cough remain elusive but increasing evidence from experimental models indicates that the priming of particular lineages of B. pertussis (Bp) specific CD4+ T cells is essential to control bacterial load. Critical hallmarks of these protective CD4+ T cell lineages in animals are suggested to be their differentiation profile as Th1 and Th17 cells and their tissue residency. These features seem optimally primed by previous infection but insufficiently or only partially by current vaccines. In this review, evidence is sought indicating whether infection also drives such superior Bp specific CD4+ T cell lineages in humans. We highlight key features of effector immunity downstream of Th1 and Th17 cell cytokines that explain clearing of primary Bp infections in naïve hosts, and effective prevention of infection in convalescent hosts during secondary challenge. Outstanding questions are put forward that need answers before correlates of human Bp infection-primed CD4+ T cell immunity can be used as benchmark for the development of improved pertussis vaccines.

Tissue-resident MAIT cell populations in human oral mucosa exhibit an activated profile and produce IL-17

Mucosa‐associated invariant T (MAIT) cells are unconventional T lymphocytes defined by their innate‐like characteristics and broad antimicrobial responsiveness. Whether MAIT cells are part of the tissue‐resident defense in the oral mucosal barrier is unknown. Here, we found MAIT cells present in the buccal mucosa, with a tendency to cluster near the basement membrane, and located in both epithelium and the underlying connective tissue. Overall MAIT cell levels were similar in the mucosa compared to peripheral blood, in contrast to conventional T cells that showed an altered representation of CD4⁺ and CD8⁺ subsets. The major mucosal MAIT cell subset displayed a tissue‐resident and activated profile with high expression of CD69, CD103, HLA‐DR, and PD‐1, as well as a skewed subset distribution with higher representation of CD4^–/CD8^– double‐negative cells and CD8αα⁺ cells. Interestingly, tissue‐resident MAIT cells had a specialized polyfunctional response profile with higher IL‐17 levels, as assessed by polyclonal stimulus and compared to tissue nonresident and circulating populations. Furthermore, resident buccal MAIT cells were low in perforin. Together, these data indicate that MAIT cells form a part of the oral mucosal T cell compartment, where they exhibit a tissue‐resident‐activated profile biased toward IL‐17 production.

Human T cell immune surveillance: Phenotypic, functional and migratory heterogeneity for tailored immune responses

The human immune system constantly provides a balance between pathogen clearance as well as tolerance for autoantigens and the commensal microbiota. This is achieved by immune responses, which are highly specialized and diversified in terms of their phenotype, function, regulation and location. Despite the complexity that is inherent to human immunity, our current knowledge is primarily shaped by very reductionist insights gained from peripheral blood T cells. Since only 2% of human T cells recirculate in the blood, the vast majority remains undetected by common sampling strategies and therefore unexplored. This review highlights and discusses recent developments in human T cell immune surveillance with a particular focus on functional and migratory T cell heterogeneity and provides a critical framework for new conceptual ideas, which could serve as a starting point in the quest for novel targeted therapies for chronic tissue restricted inflammatory diseases.