Antigen-specific regulatory T-cell responses against aeroantigens and their role in allergy

Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq

Introduction

The functional programs of CD4+ T helper (Th) cell clones play a central role in shaping immune responses to different challenges. While advances in single-cell RNA sequencing (scRNA-Seq) have significantly improved our understanding of the diversity of Th cells, the relationship between scRNA-Seq clusters and the traditionally characterized Th subsets remains ambiguous.

Methods

In this study, we introduce TCR-Track, a method leveraging immune repertoire data to map phenotypically sorted Th subsets onto scRNA-Seq profiles.

Results and discussion

This approach accurately positions the Th1, Th1-17, Th17, Th22, Th2a, Th2, T follicular helper (Tfh), and regulatory T-cell (Treg) subsets, outperforming mapping based on CITE-Seq. Remarkably, the mapping is tightly focused on specific scRNA-Seq clusters, despite 4-year interval between subset sorting and the effector CD4+ scRNA-Seq experiment. These findings highlight the intrinsic program stability of Th clones circulating in peripheral blood. Repertoire overlap analysis at the scRNA-Seq level confirms that the circulating Th1, Th2, Th2a, Th17, Th22, and Treg subsets are clonally independent. However, a significant clonal overlap between the Th1 and cytotoxic CD4+ T-cell clusters suggests that cytotoxic CD4+ T cells differentiate from Th1 clones. In addition, this study resolves a longstanding ambiguity: we demonstrate that, while CCR10+ Th cells align with a specific Th22 scRNA-Seq cluster, CCR10-CCR6+CXCR3-CCR4+ cells, typically classified as Th17, represent a mixture of bona fide Th17 cells and clonally unrelated CCR10low Th22 cells. The clear distinction between the Th17 and Th22 subsets should influence the development of vaccine- and T-cell-based therapies. Furthermore, we show that severe acute SARS-CoV-2 infection induces systemic type 1 interferon (IFN) activation of naive Th cells. An increased proportion of effector IFN-induced Th cells is associated with a moderate course of the disease but remains low in critical COVID-19 cases. Using integrated scRNA-Seq, TCR-Track, and CITE-Seq data from 122 donors, we provide a comprehensive Th scRNA-Seq reference that should facilitate further investigation of Th subsets in fundamental and clinical studies.

The role of allergen-specific regulatory T cells in the control of allergic disease

Allergies result from an antigen-specific loss of tolerance against innocuous foreign substances. Allergen immunotherapy (AIT) aims to reverse the pathogenic response and to re-establish physiological tolerance. However, the tolerogenic mechanisms that prevent allergy in healthy and act during AIT are still obscure. Foxp3 expressing 'regulatory' CD4 T cells (Tregs) are essential mediators of tolerance against allergens. It remains controversial which antigen specificity of Tregs is required to prevent allergy and the role of allergen-specific Tregs during AIT. Recent work provided precise insight into physiological T cell responses against environmental and food compounds. This identified Treg responses mainly against peptides and proteins not involved in immune pathology, revealing an unexpected role of Treg antigen specificity for tolerance. This review will focus on antigen-specific Treg responses against food and airborne allergens, and the impact of the technological approach utilized for antigen-specific Treg characterization is discussed, with critical points to be addressed in future research.

Reducing the solubility of the major birch pollen allergen Bet v 1 by particle-loading mitigates Th2 responses

BACKGROUND

Solubility is a common feature of allergens. However, the causative relationship between this protein-intrinsic feature and sensitization capacity of allergens is not fully understood. This study aimed to proof the concept of solubility as a protein intrinsic feature of allergens.

METHODS

The soluble birch pollen allergen Bet v 1 was covalently coupled to 1 μm silica particles. IgE-binding and -cross-linking capacity was assessed by inhibition ELISA and mediator release assay, respectively. Alterations in adjuvanticity by particle-loading were investigated by activation of dendritic cells, mast cells and the Toll-like receptor 4 pathway as well as by Th2 polarization in an IL-4 reporter mouse model. In BALB/c mice, particle-loaded and soluble Bet v 1 were compared in a model of allergic sensitization. Antigen uptake and presentation was analysed by restimulating human Bet v 1-specific T cell lines.

RESULTS

Covalent coupling of Bet v 1 to silica particles resulted in an insoluble antigen with retained IgE-binding and -cross-linking capacity and no increase in adjuvanticity. In vivo, particle-loaded Bet v 1 induced significantly lower Bet v 1-specific (s)IgE, whereas sIgG1 and sIgG2a levels remained unaffected. The ratio of Th2 to Th1 cells was significantly lower in mice sensitized with particle-loaded Bet v 1. Particle-loading of Bet v 1 resulted in a 24-fold higher T cell activation capacity in Bet v 1-specific T cell lines, indicating more efficient uptake and presentation than of soluble Bet v 1.

CONCLUSIONS

Our results show that solubility is a decisive factor contributing to the sensitization capacity of allergens. The reduction in sensitization capacity of insoluble, particle-loaded antigens results from enhanced antigen uptake and presentation compared to soluble allergens.

Neoadjuvant PARPi or chemotherapy in ovarian cancer informs targeting effector Treg cells for homologous-recombination-deficient tumors

Homologous recombination deficiency (HRD) is prevalent in cancer, sensitizing tumor cells to poly (ADP-ribose) polymerase (PARP) inhibition. However, the impact of HRD and related therapies on the tumor microenvironment (TME) remains elusive. Our study generates single-cell gene expression and T cell receptor profiles, along with validatory multimodal datasets from >100 high-grade serous ovarian cancer (HGSOC) samples, primarily from a phase II clinical trial (NCT04507841). Neoadjuvant monotherapy with the PARP inhibitor (PARPi) niraparib achieves impressive 62.5% and 73.6% response rates per RECIST v.1.1 and GCIG CA125, respectively. We identify effector regulatory T cells (eTregs) as key responders to HRD and neoadjuvant therapies, co-occurring with other tumor-reactive T cells, particularly terminally exhausted CD8+ T cells (Tex). TME-wide interferon signaling correlates with cancer cells upregulating MHC class II and co-inhibitory ligands, potentially driving Treg and Tex fates. Depleting eTregs in HRD mouse models, with or without PARP inhibition, significantly suppresses tumor growth without observable toxicities, underscoring the potential of eTreg-focused therapeutics for HGSOC and other HRD-related tumors.

T-cell subsets in allergy and tolerance induction

Antigen-specific T lymphocytes are the central regulators of tolerance versus immune pathology against otherwise innocuous antigens and key targets of antigen-specific immune therapy. Recent advances in the understanding of T cells in tolerance and allergy resulted from improved technologies to directly characterize allergen-specific T cells by multiparameter flow cytometry or single-cell sequencing. This unravelled phenotypically and functionally distinct populations, such as Type 2a T helper cells (Th2a), follicular Th cells (Tfh), regulatory T cells (Treg), Type 1 regulatory T cells (Tr1), and follicular T regulatory cells. Here we will discuss the role of the different Th-cell subsets in the healthy state, during sensitization and development of allergy, and in tolerance induction by allergen immunotherapy (AIT). To date, the mechanisms of AIT as the only causal treatment of allergy are not completely understood. The analyses of allergen-specific T cells directly ex vivo during AIT support the concept of specific-Th2(a) cell deletion rather than an expansion of allergen-specific Tr1 or Treg cells as underlying mechanism.

Analysis of Circulating Food Antigen-Specific T-Cells in Celiac Disease and Inflammatory Bowel Disease

To demonstrate and analyze the specific T-cell response following barrier disruption and antigen translocation, circulating food antigen-specific effector T-cells isolated from peripheral blood were analyzed in patients suffering from celiac disease (CeD) as well as inflammatory bowel disease (IBD). We applied the antigen-reactive T-cell enrichment (ARTE) technique allowing for phenotypical and functional flow cytometric analyses of rare nutritional antigen-specific T-cells, including the celiac disease-causing gliadin (gluten). For CeD, patient groups, including treatment-refractory cases, differ significantly from healthy controls. Even symptom-free patients on a gluten-free diet were distinguishable from healthy controls, without being previously challenged with gluten. Moreover, frequency and phenotype of nutritional antigen-specific T-cells of IBD patients directly correlated to the presence of small intestinal inflammation. Specifically, the frequency of antigen specific T-cells as well as pro-inflammatory cytokines was increased in patients with active CeD or Crohn's disease, respectively. These results suggest active small intestinal inflammation as key for the development of a peripheral food antigen-specific T-cell response in Crohn's disease and celiac disease.

Antigen specificity and cross-reactivity drive functionally diverse anti-Aspergillus fumigatus T cell responses in cystic fibrosis

BACKGROUNDThe fungus Aspergillus fumigatus causes a variety of clinical phenotypes in patients with cystic fibrosis (pwCF). Th cells orchestrate immune responses against fungi, but the types of A. fumigatus-specific Th cells in pwCF and their contribution to protective immunity or inflammation remain poorly characterized.METHODSWe used antigen-reactive T cell enrichment (ARTE) to investigate fungus-reactive Th cells in peripheral blood of pwCF and healthy controls.RESULTSWe show that clonally expanded, high-avidity A. fumigatus-specific effector Th cells, which were absent in healthy donors, developed in pwCF. Individual patients were characterized by distinct Th1-, Th2-, or Th17-dominated responses that remained stable over several years. These different Th subsets target different A. fumigatus proteins, indicating that differential antigen uptake and presentation directs Th cell subset development. Patients with allergic bronchopulmonary aspergillosis (ABPA) are characterized by high frequencies of Th2 cells that cross-recognize various filamentous fungi.CONCLUSIONOur data highlight the development of heterogenous Th responses targeting different protein fractions of a single fungal pathogen and identify the development of multispecies cross-reactive Th2 cells as a potential risk factor for ABPA.FUNDINGGerman Research Foundation (DFG), under Germany's Excellence Strategy (EXC 2167-390884018 "Precision Medicine in Chronic Inflammation" and EXC 2051-390713860 "Balance of the Microverse"); Oskar Helene Heim Stiftung; Christiane Herzog Stiftung; Mukoviszidose Institut gGmb; German Cystic Fibrosis Association Mukoviszidose e.V; German Federal Ministry of Education and Science (BMBF) InfectControl 2020 Projects AnDiPath (BMBF 03ZZ0838A+B).

Nasal delivery of an immunotherapeutic vaccine in thermosensitive hydrogel against allergic asthma

Asthma poses a significant threat to public health, with an estimated burden of over 334 million people worldwide. Available treatments are often inadequate. We developed a thermo-sensitive hydrogel vaccine containing allergen and FK506 that induced immune tolerance via intranasal administration to treat experimental allergic asthma. The hydrogel delivery system was formulated based on Poloxamer 407 (P407), Carbopol 974P NF, and Polyoxyl 15 hydroxystearate (Kolliphor HS15, HS15). It flowed freely at room temperature and rapidly formed a hydrogel in the nasal cavity once the temperature rose over 33 °C. Ovalbumin and FK506 were slowly released from the hydrogel form and their mucosal residence time was significantly prolonged compared to the liquid formulation. In both an OVA-induced asthma model and an HDM-induced asthma model, the vaccines formulated in hydrogel gave lower levels of eosinophilic inflammation, and airway remodeling. The reduction of lung function was ameliorated, and Foxp3-expressing CD4 + Treg cells were significantly higher. The frequency of Foxp3 + Tregs in lung-draining lymph nodes (dLNs) was correlated with the amelioration. Depletion of Foxp3 + Treg cells abolished the beneficial effects of the allergen/FK506 hydrogel vaccinations. Thus, the allergen/FK506 hydrogel formulation has the potential to be a delivery system for therapeutic allergy vaccines to induce immune tolerance.

Microbial Dysbiosis Tunes the Immune Response Towards Allergic Disease Outcomes

The hygiene hypothesis has been popularized as an explanation for the rapid increase in allergic disease observed over the past 50 years. Subsequent epidemiological studies have described the protective effects that in utero and early life exposures to an environment high in microbial diversity have in conferring protective benefits against the development of allergic diseases. The rapid advancement in next generation sequencing technology has allowed for analysis of the diverse nature of microbial communities present in the barrier organs and a determination of their role in the induction of allergic disease. Here, we discuss the recent literature describing how colonization of barrier organs during early life by the microbiota influences the development of the adaptive immune system. In parallel, mechanistic studies have delivered insight into the pathogenesis of disease, by demonstrating the comparative effects of protective T regulatory (Treg) cells, with inflammatory T helper 2 (Th2) cells in the development of immune tolerance or induction of an allergic response. More recently, a significant advancement in our understanding into how interactions between the adaptive immune system and microbially derived factors play a central role in the development of allergic disease has emerged. Providing a deeper understanding of the symbiotic relationship between our microbiome and immune system, which explains key observations made by the hygiene hypothesis. By studying how perturbations that drive dysbiosis of the microbiome can cause allergic disease, we stand to benefit by delineating the protective versus pathogenic aspects of human interactions with our microbial companions, allowing us to better harness the use of microbial agents in the design of novel prophylactic and therapeutic strategies.

Epithelial cell-derived CD83 restores immune tolerance in the airway mucosa by inducing regulatory T-cell differentiation

The mechanism of generation of regulatory T cells (Treg) remains incompletely understood. Recent studies show that CD83 has immune regulatory functions. This study aims to investigate the role of epithelial cell-derived CD83 in the restoration of immune tolerance in the airway mucosa by inducing the Treg differentiation. In this study, CD83 and ovalbumin (OVA)-carrying exosomes were generated from airway epithelial cells. An airway allergy mouse model was developed to test the role of CD83/OVA-carrying exosomes in the suppression of airway allergy by inducing Treg generation. We observed that mouse airway epithelial cells expressed CD83 that could be up-regulated by CD40 ligand. The CD83 deficiency in epithelial cells retarded the Treg generation in the airway mucosa. CD83 up-regulated transforming growth factor-β-inducible early gene 1 expression in CD4+ T cells to promote Foxp3 expression. Exposure of primed CD4+ T cells to CD83/OVA-carrying exosomes promoted antigen-specific Treg generation. Administration of CD83/OVA-carrying exosomes inhibited experimental airway allergic response. In summary, airway epithelial cells express CD83 that is required in the Treg differentiation in the airway mucosa. Administration of CD83/OVA-carrying exosomes can inhibit airway allergy that has the translation potential in the treatment of airway allergic disorders.

Ssu72 Dual-Specific Protein Phosphatase: From Gene to Diseases

More than 70% of eukaryotic proteins are regulated by phosphorylation. However, the mechanism of dephosphorylation that counteracts phosphorylation is less studied. Phosphatases are classified into 104 distinct groups based on substrate-specific features and the sequence homologies in their catalytic domains. Among them, dual-specificity phosphatases (DUSPs) that dephosphorylate both phosphoserine/threonine and phosphotyrosine are important for cellular homeostasis. Ssu72 is a newly studied phosphatase with dual specificity that can dephosphorylate both phosphoserine/threonine and phosphotyrosine. It is important for cell-growth signaling, metabolism, and immune activation. Ssu72 was initially identified as a phosphatase for the Ser5 and Ser7 residues of the C-terminal domain of RNA polymerase II. It prefers the cis configuration of the serine-proline motif within its substrate and regulates Pin1, different from other phosphatases. It has recently been reported that Ssu72 can regulate sister chromatid cohesion and the separation of duplicated chromosomes during the cell cycle. Furthermore, Ssu72 appears to be involved in the regulation of T cell receptor signaling, telomere regulation, and even hepatocyte homeostasis in response to a variety of stress and damage signals. In this review, we aim to summarize various functions of the Ssu72 phosphatase, their implications in diseases, and potential therapeutic indications.

Innovative Systems to Deliver Allergen Powder for Epicutaneous Immunotherapy

Allergy is a disorder owing to hyperimmune responses to a particular kind of substance like food and the disease remains a serious healthcare burden worldwide. This unpleasant and sometimes fatal allergic disease has been tackled vigorously by allergen-specific immunotherapy over a century, but the progress made so far is far from satisfactory for some allergies. Herein, we introduce innovative, allergen powder-based epicutaneous immunotherapies (EPIT), which could potentially serve to generate a new stream of technological possibilities that embrace the features of super safety and efficacious immunotherapy by manipulating the plasticity of the skin immune system via sufficient delivery of not only allergens but also tolerogenic adjuvants. We attempt to lay a framework to help understand immune physiology of the skin, epicutaneous delivery of powdered allergy, and potentials for tolerogenic adjuvants. Preclinical and clinical data are reviewed showing that deposition of allergen powder into an array of micropores in the epidermis can confer significant advantages over intradermal or subcutaneous injection of aqueous allergens or other epicutaneous delivery systems to induce immunological responses toward tolerance at little risk of anaphylaxis. Finally, the safety, cost-effectiveness, and acceptability of these novel EPITs are discussed, which offers the perspective of future immunotherapies with all desirable features.

Functionally specialized human CD4+ T-cell subsets express physicochemically distinct TCRs

The organizational integrity of the adaptive immune system is determined by functionally discrete subsets of CD4⁺ T cells, but it has remained unclear to what extent lineage choice is influenced by clonotypically expressed T-cell receptors (TCRs). To address this issue, we used a high-throughput approach to profile the αβ TCR repertoires of human naive and effector/memory CD4⁺ T-cell subsets, irrespective of antigen specificity. Highly conserved physicochemical and recombinatorial features were encoded on a subset-specific basis in the effector/memory compartment. Clonal tracking further identified forbidden and permitted transition pathways, mapping effector/memory subsets related by interconversion or ontogeny. Public sequences were largely confined to particular effector/memory subsets, including regulatory T cells (Tregs), which also displayed hardwired repertoire features in the naive compartment. Accordingly, these cumulative repertoire portraits establish a link between clonotype fate decisions in the complex world of CD4⁺ T cells and the intrinsic properties of somatically rearranged TCRs.

Nucleic Acid-Based Approaches for Tumor Therapy

Within the last decade, the introduction of checkpoint inhibitors proposed to boost the patients' anti-tumor immune response has proven the efficacy of immunotherapeutic approaches for tumor therapy. Furthermore, especially in the context of the development of biocompatible, cell type targeting nano-carriers, nucleic acid-based drugs aimed to initiate and to enhance anti-tumor responses have come of age. This review intends to provide a comprehensive overview of the current state of the therapeutic use of nucleic acids for cancer treatment on various levels, comprising (i) mRNA and DNA-based vaccines to be expressed by antigen presenting cells evoking sustained anti-tumor T cell responses, (ii) molecular adjuvants, (iii) strategies to inhibit/reprogram tumor-induced regulatory immune cells e.g., by RNA interference (RNAi), (iv) genetically tailored T cells and natural killer cells to directly recognize tumor antigens, and (v) killing of tumor cells, and reprograming of constituents of the tumor microenvironment by gene transfer and RNAi. Aside from further improvements of individual nucleic acid-based drugs, the major perspective for successful cancer therapy will be combination treatments employing conventional regimens as well as immunotherapeutics like checkpoint inhibitors and nucleic acid-based drugs, each acting on several levels to adequately counter-act tumor immune evasion.

Anti-fungal T cell responses in the lung and modulation by the gut-lung axis

The lung is a central organ for immune-environmental interactions ranging from tolerance against harmless substances to protection against pathogens, which are particularly sensitive to regulation by the intestinal microbiota. Airborne fungi, can cause variety of diseases, including allergies and inflammatory disorders, as well as life-threatening invasive infections. Remarkable differences exist between ubiquitous fungal species with regard to protective immune mechanisms. Recent data have surprisingly identified Aspergillus-specific regulatory T cells as an essential tolerance checkpoint and provided mechanistic insight for the loss of tolerance in the course of immune pathologies. Furthermore, pathogenic Th17 cells in Aspergillus-associated inflammatory disease seem to be induced by cross-reactivity to the intestinal commensal Candida albicans. Here we review and discuss what is known about fungus-specific T cell responses in the lung how they are modulated by the gut-lung axis and in particular discussing the modulation of adaptive immune responses by cross-reactivity to the microbiota.

[Allergo-oncology: what allergologists and oncologists can learn from each other : Regulatory T cells in allergy and cancer]

BACKGROUND

The immune system has substantial involvement in the pathophysiology of allergies and cancer. The complexity of the immune system is well balanced in health, in so-called immune homeostasis. In many diseases, as in allergies and cancer, this balance is disturbed. The tolerance to foreign but harmless substances, such as tree or grass pollen, is no longer sufficiently given in allergic patients. In cancer patients, the immune system is tolerant to harmful tumor cells. Thus, allergies and cancer show an opposing pattern in terms of immune tolerance. The group of regulatory T cells occupies a central position here.

OBJECTIVE

This article deals with the function of regulatory T cells in detail. This group of immune cells and its interaction with other involved immune cells and messenger signals in the pathophysiology and treatment of allergies and cancer are presented.

METHODS

A review article was compiled based on the pertinent literature.

RESULTS

The regulatory T cells of cancer patients are a mechanism of the so-called tumor escape phenomenon to hide from the immune system. The tumor uses danger signals, e.g., the HMGB1 protein, to mediate tolerance to the immune system through these cells and thus avoid elimination. In allergic patients, these cells are underrepresented and can be induced by a specific immunotherapy, in order to achieve tolerance to the allergens and thus a causal treatment.

CONCLUSION

Regulatory T cells play an important role in the pathogenesis of cancer and allergies, and thus represent a therapeutic target.

Functions and regulation of T cell-derived interleukin-10

Interleukin (IL)-10 is an essential anti-inflammatory cytokine and functions as a negative regulator of immune responses to microbial antigens. IL-10 is particularly important in maintaining the intestinal microbe-immune homeostasis. Loss of IL-10 promotes the development of inflammatory bowel disease (IBD) as a consequence of an excessive immune response to the gut microbiota. IL-10 also functions more generally to prevent excessive inflammation during the course of infection. Although IL-10 can be produced by virtually all cells of the innate and adaptive immune system, T cells constitute a non-redundant source for IL-10 in many cases. The various roles of T cell-derived IL-10 will be discussed in this review. Given that IL-10 is at the center of maintaining the delicate balance between effective immunity and tissue protection, it is not surprising that IL-10 expression is highly dynamic and tightly regulated. We summarize the environmental signals and molecular pathways that regulate IL-10 expression. While numerous studies have provided us with a deep understanding of IL-10 biology, the majority of findings have been made in murine models, prompting us to highlight gaps in our knowledge about T cell-derived IL-10 in the human system.

The effect of regulatory T cells on tolerance to airborne allergens and allergen immunotherapy

Forkhead box P3-positive regulatory T (Treg) cells are essential mediators of tolerance against self-antigens and harmless exogenous antigens. Treg cell deficiencies result in multiple autoimmune and allergic syndromes in neonates. How Treg cells affect conventional allergies against aeroantigens, which are restricted to a few specific proteins released from inhaled particles, remains controversial. The hallmarks of antigen-specific loss of tolerance are allergen-specific T_H2 cells and IgE. However, difficulties in identifying the rare allergen-specific Treg cells have obscured the cellular basis of tolerance to aeroallergens, which is also a major obstacle for the rational design of novel and more efficient allergen-specific immunotherapies. Recent technological progress allowing characterization of allergen-specific effectors and Treg cells with minimal in vitro manipulation revealed their detailed contribution to tolerance. The data identified inhaled particles as immunodominant Treg cell targets in healthy and allergic subjects. Conversely, the supposed immunodominant major allergens being rapidly released from inhaled particles apparently do not actively induce tolerance but are ignored by the immune system. Here, the partially contradictory data on various allergen-specific T-cell types in healthy subjects, allergic patients, and patients undergoing allergen-specific immunotherapy are discussed and integrated into one model, postulating Treg cell-dependent and Treg cell-independent checkpoints of tolerance and allergy development.