Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma

Targeting γc family cytokines with biologics: current status and future prospects

Over the recent decades the market potential of biologics has substantially expanded, and many of the top-selling drugs worldwide are now monoclonal antibodies or antibody-like molecules. The common gamma chain (γc) cytokines, Interleukin (IL-)2, IL-4, IL-7, IL-9, IL-15, and IL-21, play pivotal roles in regulating immune responses, from innate to adaptive immunity. Dysregulation of cell signaling by these cytokines is strongly associated with a range of immunological disorders, which includes cancer as well as autoimmune and inflammatory diseases. Given the essential role of γc cytokines in maintaining immune homeostasis, the development of therapeutic interventions targeting these molecules poses unique challenges. Here, we provide an overview of current biologics targeting either single or multiple γc cytokines or their respective receptor subunits across a spectrum of diseases, primarily focusing on antibodies, antibody-like constructs, and antibody-cytokine fusions. We summarize therapeutic biologics currently in clinical trials, highlighting how they may offer advantages over existing therapies and standard of care, and discuss recent advances in this field. Finally, we explore future directions and the potential of novel therapeutic intervention strategies targeting this cytokine family.

Th9-derived IL-9 in autoimmune diseases: An update

Autoimmune diseases (AIDs), such as rheumatoid arthritis, multiple sclerosis, and systemic lupus erythematosus, are caused by abnormal immune response that targets the body's own tissues. T-helper cell 9 (Th9) is a recently discovered subpopulation of T cells that primarily participates in inflammatory responses and immune regulation by secreting interleukin-9 (IL-9). IL-9 is a multifunctional cytokine that regulates the function of T and B cells, and also affects the activation and response of mast cells, macrophages, and other cells. Studies have shown that Th9 cells significantly affect the development of autoimmune diseases and are closely related to disease activity and pathological processes. Exploring drugs targeting Th9 cells or IL-9 and elucidating the regulatory mechanisms of Th9 and IL-9 in various AIDs will provide important insights for the development of novel therapeutic strategies.

Identification and validation of PARK7 as a novel mitochondria-related signature associated with immune microenvironment in asthma

BACKGROUND

Asthma is one of the most common respiratory diseases characterized by immune cell infiltration. However, the roles of mitochondria-related genes and their crosstalk with immune cell infiltration in asthma remain unclear. This study aimed to investigate the role and interaction of mitochondria-related genes and the immune cells in asthma through both bioinformatic analysis and experimental approaches.

METHODS

The microarray data GSE76262 was obtained from NCBI GEO datasets, and differentially expressed genes (DEGs) were acquired by GEO2R. DAVID database was used for Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Mitochondrial genes were downloaded from Human MitoCarta3.0, and then Mitochondria-related DEGs (MitoDEGs) were obtained. STRING database was used to construct the Protein-Protein Interaction network, and then the hub genes were identified. The receiver operating characteristic curves were used to assess the diagnostic effects of hub genes in asthma patients. The infiltration of immune cells was analyzed by using the ImmuCellAI database. The expression of hub MitoDEGs was validated in an HDM-induced animal model. The compound-23 was utilized to investigate the function of PARK7 both in vivo and in vitro.

RESULTS

Mitochondria were predicted to be involved in the pathology and physiology of asthma. The 47 MitoDEGs were identified, and three hub MitoDEGs (DNM1L, FIS1, and PARK7) were predicted to participate in asthma pathogenesis. Compared to DNM1L and FIS1, PARK7 had the most diagnostic effectiveness. The hub MitoDEGs were mainly positively associated with macrophages, monocytes, and CD8+T cells, while negatively associated with multiple CD4+T cells. Compared to the control group, the mRNA and protein expression levels of DNM1L, FIS1, and PARK7 were downregulated in the model group. Additionally, activating the function of PARK7 via compound-23 alleviated the mitochondrial damage, decreased the production of IL-25, IL-33, CCL17 and CCL20, subsequently improved the immune microenvironment and airway inflammation.

CONCLUSION

These results suggested that mitochondria-related genes were involved in the pathological processes of asthma, and verified the protective role of PARK7 in HDM-induced asthma models, which provided the potential insight into the clinical diagnosis and therapy of asthma.

FEM1B enhances TRAIL-induced apoptosis in T lymphocytes and monocytes

FEM1B is recognized for its significant pro-apoptotic function in colorectal cancer; however, its influence and mechanisms regarding apoptosis in immune cells remain inadequately elucidated. In this study, we demonstrated that FEM1B enhances TRAIL-induced apoptosis in Molt-4, Jurkat, THP-1, and U937 cell lines. Notably, the knockdown of FEM1B in transfected cells resulted in a reversal of the observed increase in cell apoptosis. Our findings indicate that FEM1B activates caspase-3 and caspase-8, but not caspase-9, in response to TRAIL stimulation, suggesting its involvement in the extrinsic caspase-dependent apoptotic pathway. Furthermore, we found that FEM1B interacted with TRAF2 and downregulates its expression in Molt-4 and Jurkat cells, thereby diminishing TRAF2's inhibitory effect on caspase-8. In THP-1 and U937 cells, FEM1B was found to upregulate TRAIL-R2, thereby promoting TRAIL-induced apoptosis. Knockout studies in murine models further corroborated that FEM1B facilitates TRAIL-induced apoptosis. These results demonstrate that FEM1B enhances TRAIL-induced apoptosis in T lymphocytes and monocytes through a caspase-dependent mechanism involving TRAF2 or TRAIL receptors.

Single-cell RNA sequencing reveals immunological link between house dust mite allergy and childhood asthma

Allergic asthma in children is typically associated with house dust mites (HDM) as the key allergen. Nevertheless, the diagnostic rate remains below 60% due to the absence of specific symptoms and diagnostic markers, which hinders the implementation of targeted personalized therapies. This study investigates immunological features of asthma with house dust mite (HDM) sensitisation in children, aiming to uncover diagnostic markers at single-cell resolution. The cohort comprised 8 children with physician-diagnosed asthma (age range: 4-11 years), stratified into groups based on HDM sensitization status. Single-cell RNA sequencing of peripheral blood mononuclear cells (PBMCs) was conducted, employing Seurat for cell identification and differential gene expression analysis. Enrichment analyses and LASSO regression identified signature genes related to cellular origin, with protein-protein interaction networks elucidating cellular communication differences between groups. A total of 11 distinct cell types were identified, with classical monocytes and monocytes being the predominant cell types that differentiated the two groups. Among these, 12 genes were up-regulated, and 40 down-regulated, mainly involving MHC-II complex and antigen presentation pathways, as validated by Gene Ontology and Gene Set Enrichment Analysis. The machine learning model accurately predicted cellular groupings, evidenced by an area under the curve of 0.83. Enhanced communication signals in HDM allergy cases involved monocytes, contrasting with reduced interactions in naive CD8 + cells. HLA-DR and HLA-DP were identified as the primary hallmark receptors, and the innate immunity differences with non-dust mite allergic asthma were characterized by 18 genes including top candidates MT-ND4 and RPS3A. Individuals with HDM-sensitized asthma exhibited altered expression of MHC-II complex genes in their PBMCs and distinct gene expression patterns in antigen-presenting cells, highlighting the critical role of HLA-DR and HLA-DP in the HDM allergen presentation.

Integrative, high-resolution analysis of single-cell gene expression across experimental conditions with PARAFAC2-RISE

Effective exploration and analysis tools are vital for the extraction of insights from single-cell data. However, current techniques for modeling single-cell studies performed across experimental conditions (e.g., samples) require restrictive assumptions or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that reduction and insight in single-cell exploration (RISE), an adaptation of the tensor decomposition method PARAFAC2, enables the dimensionality reduction and analysis of single-cell data across conditions. We demonstrate the benefits of RISE across distinct examples of single-cell RNA-sequencing experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus patient samples. RISE enables associations of gene variation patterns with patients or perturbations while connecting each coordinated change to single cells without requiring cell-type annotations. The theoretical grounding of RISE suggests a unified framework for many single-cell data modeling tasks while providing an intuitive dimensionality reduction approach for multi-sample single-cell studies across biological contexts. A record of this paper's transparent peer review process is included in the supplemental information.

E26 transformation-specific-1 controls asthma development by regulating the CD4+ Th2/Th17 immune response involved transcription factors in active genomic transcriptional regions

Asthma is a chronic respiratory disease characterized by airway inflammation and immune cell imbalance. The transcription factor E26 transformation-specific-1 regulates immune cell functions, but its role in asthma remains unclear. Here, we generated Ets1 heterozygous (Ets1+/-) mice by constitutively knocking out exons 7 and 8 of Ets1, confirmed significantly reduced Ets1 expression via western blot. Asthma models were then established in both wild-type and Ets1+/- mice, revealing more severe pulmonary inflammation in Ets1+/- mice. Then, we systematically explored the regulatory effects of Ets1 on immune cells function and inflammatory responses in asthma. Further analyses showed enhanced CD4+ helper T (Th) 2/Th17 cell responses and elevated interleukin-4 and interleukin-17A secretion in the asthma Ets1+/- mice. By combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we identified 17 transcription factors regulated by Ets1 and linked to the function of mitotic processes in asthma. These findings suggest that Ets1 mitigates asthma by modulating CD4+ Th2/Th17 immune responses and regulating transcription factors associated with cell cycle processes.

The immunology of asthma and chronic rhinosinusitis

Asthma and chronic rhinosinusitis (CRS) are common chronic inflammatory diseases of the respiratory tract that have increased in prevalence over the past five decades. The clinical relationship between asthma and CRS has been well recognized, suggesting a common pathogenesis between these diseases. Both diseases are driven by complex airway epithelial cell and immune cell interactions that occur in response to environmental triggers such as allergens, microorganisms and irritants. Advances, including a growing understanding of the biology of the cells involved in the disease, the application of multiomics technologies and the performance of large-scale clinical studies, have led to a better understanding of the pathophysiology and heterogeneity of asthma and CRS. This research has promoted the concept that these diseases consist of several endotypes, in which airway epithelial cells, innate lymphoid cells, T cells, B cells, granulocytes and their mediators are distinctly involved in the immunopathology. Identification of the disease heterogeneity and immunological markers has also greatly improved the protocols for biologic therapies and the clinical outcomes in certain subsets of patients. However, many clinical and research questions remain. In this Review, we discuss recent advances in characterizing the immunological mechanisms of asthma and CRS, with a focus on the main cell types and molecules involved in these diseases.

Single-cell RNA Sequencing Analysis of Sputum Cell Transcriptomes Reveals Pathways and Communication Networks That Contribute to the Pathogenesis of Asthma

Background

Asthma is driven by complex interactions amongst structural airway cells, cells of the immune system, and the environmental. While sputum cell characterization has been instrumental in studying asthma pathogenesis and refining treatment strategies, the nuances of cellular transcriptomes and intercellular communication in asthmatic sputum remain poorly understood.

Methods

We employed single-cell RNA sequencing to analyze cells isolated form the sputum from 16 asthma patients and 8 non-asthmatic controls. Cell identities were established using curated marker genes and SingleR annotation. We compared cell-specific gene expression and communication networks between asthmatic and control groups, correlating findings with distinct pathways that were dysregulated in asthma.

Findings

37,565 cellular transcriptomes were captured and analyzed. 15 distinct cell populations were identified, including various macrophages, monocytes, dendritic cells, and lymphocytes, along with rare cell types such as mast cells, innate lymphoid cells, bronchial epithelial cells, and eosinophils. Intercellular communication analysis indicated heightened signaling activity in asthma compared to controls, particularly in CD4+ T cells and dendritic cells which exhibited the most significant increases in RNA expression of outgoing signaling molecules. Notably, the ADAM12-SDC4 and CCL22-CCR4 ligand-receptor pathways demonstrated the strongest shifts between asthma and control subjects, particularly between dendritic cells and CD4 lymphocytes.

Interpretation

SC RNA seq profiling the asthma cellular transcriptome analysis of sputum highlights both innate and adaptive immune mechanisms that are significantly amplified in asthma. The elevated expression of ADAM12-SCD4 and CCL22-CC4 point to their critical role in asthma pathogenesis, suggesting potential avenues for targeted therapies and improved management of this chronic condition.

Research in context

Evidence Before This Study: Asthma is a chronic inflammatory disease of the airways driven by intricate interactions between airway structural and immune cells. Previous transcriptomic studies have focused on bulk RNA samples from the airway, leaving significant gaps in our understanding of the cellular dynamics that characterize the disease.Added Value of This Study: This study pioneers the use of single-cell RNA sequencing on sputum samples from patients with asthma, revealing a detailed landscape of cell phenotypes and dynamic communication patterns that distinguish asthmatic individuals from those without the disease. Notably, heightened intercellular communication was observed in asthma, particularly between CD4+ T cells and dendritic cells, confirming that there is a robust network of interactions between immune and structural cells. The notable increase of ADAM12-CCR4 communication from dendritic cells to other cell populations further emphasizes the dysregulation present in asthma.Implications of All Available Evidence: Our transcriptomic profiling illuminates distinct and amplified communication pathways involving CD4+ T cells and dendritic cells, aligning with established paradigms of both adaptive and innate immune responses in asthma pathogenesis. The identification of ADAM12 and CCR4 pathway dysregulation adds a critical layer to our understanding of the molecular mechanisms underpinning asthma, paving the way for potential therapeutic targets and personalized treatment strategies. Single cell profiling of the sputum has the capacity to characterize the breadth of cellular phenotypes, their functional status, and the communication in the airway at a level not previously attainable.

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.

Diverse microbial exposure exacerbates the development of allergic airway inflammation in adult mice

Background

Exposure to a diversity of microbes has been implicated in playing a major role in susceptibility to the development of allergic lung type diseases. The hygiene hypothesis suggests that those exposed to a broad diversity of microbes are more likely to be protected against developing allergic type diseases. However, changes in exposure to microbial diversity can occur in both younger individuals, as well as in adults, and the effects are not always understood.

Objective

We investigated the effect of exposure to broad microbial diversity on the airway T cell response in house dust mite (HDM) induced allergic airway disease (AAD, a model of allergic asthma).

Methods

We increased exposure to broad microbial diversity by co-housing specific pathogen free (SPF) adult or newborn mice with pet store mice (PSE or BiPSE, respectively). Mice were then exposed to HDM to induce AAD.

Results

We found that the effect of increased microbial exposure on the development of allergic airway inflammation differs by age. Increasing exposure to diverse microbes as adults exacerbates the development of allergic airway inflammation, whereas this was not observed when exposure occurred at birth.

Conclusion

We suggest that experimental evaluation of the hygiene hypothesis in inflammation, particularly those using mouse models, may need to consider age of the host and time of microbial exposure.

Capsule Summary

Mouse models of increased exposure to diverse microbial environment shown to differentially affect the development of allergic airway inflammation, depending on the age of microbial exposure.

Distinct features of a peripheral T helper subset that drives the B cell response in dengue virus infection

Dengue-virus-induced humoral immunity can increase the risk of severe disease, but the factors influencing this response are poorly understood. Here, we investigate the contribution of CD4+ T cells to B cell responses in human dengue infection. We identify a dominant peripheral PD-1+ T cell subset that accumulates in severe patients and could induce B cell differentiation via interleukin-21 (IL-21)-related pathway. Single-cell analyses reveal heterogeneity within PD-1+ cells, demonstrating the coexistence of subsets with "helper" (IL-21+) or "cytotoxic" characteristics. The IL-21+ subset displays a distinct clonotypic and transcriptomic signature compared to follicular helper T cells and persists as a memory in lymph nodes. Notably, we show that the IL-21+ subset seems to majorly drive the extrafollicular B cell responses in dengue. Our study establishes the peripheral IL-21+ subset as a potential determinant of the humoral response to dengue virus infection. These findings provide important insights into the T-cell-dependent regulation of humoral responses and can inform the design of effective dengue vaccines.

Glucocorticoid receptor inhibits Th2 immune responses by down-regulating Pparg and Gata3 in schistosomiasis

Introduction

The Th2 immune response plays a pivotal role in the pathogenesis of schistosomiasis, contributing to the formation of hepatic granulomas and fibrosis. While the glucocorticoid receptor (GR) is a ubiquitously expressed nuclear receptor that mediates anti-inflammatory effects, its impact on Th2 responses in schistosomiasis remains underexplored. Thus, this study aimed to investigate the potential impact of GR activation on the hepatic Th2 immune response in schistosomiasis using the synthetic glucocorticoid dexamethasone.

Method

In vivo, Schistosoma japonicum-infected mice were treated with dexamethasone, while in vitro studies were conducted on Th2 cells. Additionally, RNA sequencing and single-cell sequencing were integrated to identify key transcription factors influenced by GR activation during Th2 cell differentiation, with gene expression levels validated both in vivo and in vitro.

Results

In vivo, GR activation markedly reduced the size of Schistosoma egg granulomas and substantially repressed the transcription of key Th2-related cytokines, such as IL-4, IL-5, and IL-13. In vitro, GR activation inhibited the transcription of IL-4, IL-5, and IL-13, as well as the secretion of IL-4 in Th2 cells. An integrated analysis of RNA sequencing and single-cell sequencing revealed that GR activation downregulated the expression of two major transcription factors, Gata3 and Pparg, which were elevated in infected mouse livers and Th2 cells but decreased following dexamethasone treatment.

Conclusion

GR activation may suppress the Th2 immune response triggered by egg antigens by downregulating the expression of the key transcription factors Gata3 and Pparg. While these findings provide insights into a potential complementary therapeutic strategy, further research is necessary to assess the feasibility and safety of targeting GR activation for the treatment of schistosomiasis.

Integrative, high-resolution analysis of single cell gene expression across experimental conditions with PARAFAC2-RISE

Effective and scalable exploration and analysis tools are vital for the extraction of insights from large-scale single-cell data. However, current techniques for modeling single-cell studies performed across experimental conditions (e.g., samples, perturbations, or patients) require restrictive assumptions, lack flexibility, or do not adequately deconvolute condition-to-condition variation from cell-to-cell variation. Here, we report that Reduction and Insight in Single-cell Exploration (RISE), an adaptation of the tensor decomposition method PARAFAC2, enables the dimensionality reduction and analysis of single-cell data across conditions. We demonstrate the benefits of RISE across two distinct examples of single-cell RNA-sequencing experiments of peripheral immune cells: pharmacologic drug perturbations and systemic lupus erythematosus (SLE) patient samples. RISE enables straightforward associations of gene variation patterns with specific patients or perturbations, while connecting each coordinated change to single cells without requiring cell type annotations. The theoretical grounding of RISE suggests a unified framework for many single-cell data modeling tasks. Thus, RISE provides an intuitive universal dimensionality reduction approach for multi-sample single-cell studies across diverse biological contexts.

Exploring the immunological underpinnings of allergic conjunctivitis: the role of CD4 + T Cells and SLAM expression in ocular surface disease

BACKGROUND

Allergic conjunctivitis is a common ocular disease characterized by inflammation of the conjunctiva, often associated with environmental allergens. CD4 + T cells and signal lymphocyte activation molecule (SLAM) expression has been implicated in the pathogenesis of allergic conjunctivitis, but their roles and interactions remain unclear.

METHODS

This prospective cross-sectional observational study enrolled 100 participants, 50 with allergic conjunctivitis and 50 healthy controls, to investigate the relationship between peripheral blood CD4 + T cells, SLAM expression, and allergic conjunctivitis. Participants were evaluated using the Aston university allergy questionnaire (AUAQ), ocular surface disease index (OSDI), and dry eye questionnaire (DEQ-5). Peripheral blood mononuclear cells were isolated and analyzed for SLAM expression on CD4 + T cells using flow cytometry. Total serum IgE levels were measured using ELISA.

RESULTS

The allergic group demonstrated significantly higher AUAQ, OSDI, and DEQ-5 scores compared to the control group, indicating a more severe allergic and ocular surface disease burden. Flow cytometry analysis revealed a significant increase in SLAM expression on CD4 + T cells in the allergic group (22.6% ± 5.3%) compared to the control group (15.2% ± 4.7%) (p < 0.001). Total serum IgE levels were also significantly higher in the allergic group (255.3 ± 131.2 IU/mL) compared to the control group (36.7 ± 19.8 IU/mL) (p < 0.001). Spearman's rank correlation analysis indicated significant correlations between AUAQ and OSDI scores (R = 0.38, p < 0.001), and between TBUT and OSDI scores (R = 0.21, p = 0.008), suggesting that reduced tear film stability is associated with more severe ocular surface symptoms.

CONCLUSION

The study findings suggest a significant association between allergic symptoms, ocular surface disease, and immunological markers in individuals with allergic conjunctivitis. The increased SLAM expression on CD4 + T cells and elevated total serum IgE levels in the allergic group may play a pivotal role in the pathophysiology of allergic conjunctivitis. These insights could inform the development of targeted therapies that address both the allergic and ocular surface components of the disease, potentially improving management and outcomes for patients with allergic conjunctivitis.

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.

A reappraisal of IL-9 in inflammation and cancer

While much is known about the functional effects of type 2 cytokines interleukin (IL)-4, IL-5 and IL-13 in homeostasis and disease, we still poorly understand the functions of IL-9. Chronic inflammation seen in allergic diseases, autoimmunity and cancer is however frequently accompanied by overproduction of this elusive type 2 cytokine. Initially identified as a T cell and mast cell growth factor, and later as the hallmark cytokine defining TH9 cells, we now know that IL-9 is produced by multiple innate and adaptive immune cells. Recent evidence suggests that IL-9 controls discrete aspects of the allergic cascade, cellular responses of immune and stromal cells, cancer progression, tolerance and immune escape. Despite functioning as a pleiotropic cytokine in mucosal environments, like the lungs, the direct and indirect cellular targets of IL-9 are still not well characterized. Here, we discuss IL-9's cellular senders and receivers, focusing on asthma and cancer. Moreover, we review current research directions and the outlook of targeted therapy centered around the biology of IL-9.

IL-9 as a naturally orthogonal cytokine with optimal JAK/STAT signaling for engineered T cell therapy

Arming T cells with a synthetically orthogonal IL-9 receptor (o9R) permits facile engraftment and potent anti-tumor functions. We considered whether the paucity of natural IL-9R expression could be exploited for T cell immunotherapy given that, in mice, high doses of IL-9 were well-tolerated without discernible immune modulation. Compared to o9R, T cells engineered with IL-9R exhibit superior tissue infiltration, stemness, and anti-tumor activity. These qualities are consistent with a stronger JAK/STAT signal, which in addition to STAT1/3/5, unexpectedly includes STAT4 (canonically associated with IL-12 but not common γ-chain cytokines). IL-9R T cells are exquisitely sensitive to perturbations of proximal signaling, including structure-guided attenuation, amplification, and rebalancing of JAK/STAT signals. Biased IL-9R mutants uncover STAT1 as a rheostat between proliferative stem-like and terminally differentiated effector states. In summary, we identify native IL-9/IL-9R as a natural cytokine-receptor pair with near-orthogonal qualities and an optimal JAK/STAT signaling profile for engineered T cell therapy.

A population of c-kit+ IL-17A+ ILC2s in sputum from individuals with severe asthma supports ILC2 to ILC3 trans-differentiation

In prednisone-dependent severe asthma, uncontrolled sputum eosinophilia is associated with increased numbers of group 2 innate lymphoid cells (ILC2s). These cells represent a relatively steroid-insensitive source of interleukin-5 (IL-5) and IL-13 and are considered critical drivers of asthma pathology. The abundance of ILC subgroups in severe asthma with neutrophilic or mixed granulocytic (both eosinophilic and neutrophilic) airway inflammation, prone to recurrent infective exacerbations, remains unclear. Here, we found by flow cytometry that sputum ILC3s are increased in severe asthma with intense airway neutrophilia, whereas equivalently raised sputum ILC2s and ILC3s were found in severe asthma with mixed granulocytic inflammation. Unbiased clustering analyses identified an "intermediate-ILC2" population displaying markers of both ILC2s (prostaglandin D2 receptor 2; CRTH2, IL-5, and IL-13) and ILC3s (c-kit and IL-17A) that were most abundant in severe asthma with mixed granulocytic airway inflammation. Intermediate ILC2s correlated with airway neutrophilia and were associated with increased amounts of IL-1β and IL-18 in sputum supernatants. Coculture of sort-purified canonical ILC2s with IL-1β and IL-18 in vitro up-regulated c-kit and IL-17A as well as gene expression profiles related to both type 2 and type 17 inflammatory pathways. Together, we have identified an intermediate-ILC2 phenotype in the airways of individuals with severe mixed granulocytic asthma, representing a candidate therapeutic target for controlling neutrophilic airway inflammation.

Clinical and immunological outcomes after randomized trial of baked milk oral immunotherapy for milk allergy

BACKGROUNDCow's milk (CM) allergy is the most common food allergy in young children. Treatment with oral immunotherapy (OIT) has shown efficacy, but high rates of adverse reactions. The aim of this study was to determine whether baked milk OIT (BMOIT) could reduce adverse reactions while still inducing desensitization, and to identify immunological correlates of successful BMOIT.METHODSThis phase II, randomized trial evaluated the safety and efficacy of BMOIT in milk-allergic children 3-18 years old. After the initial placebo-controlled first year of treatment, placebo-treated participants crossed over to active BMOIT. Double-blind, placebo-controlled oral food challenges (OFCs) were conducted with BM after year 1 and to both BM and unheated milk (UM) after year 2. IgG and IgE antibodies were measured along with CM-specific (CM+) CD4+ memory T cell populations, profiled using flow cytometry and scRNA-Seq.RESULTSTwenty-one of 30 (70%) reached the primary endpoint of tolerating 4044 mg of BM protein at month 24, and 11 of 30 tolerated 2000 mg or more of UM protein. Dosing symptoms were common, but more than 98% were mild, with no severe reactions. Immunological changes associated with desensitization included increased CM IgG4, CM+ FOXP3+ cells, and Tregs and corresponding decreases in CM IgE, CM+ Th2A cells, and CD154+ cells. T cell and antibody measurements were combined to build a model that predicted UM OFC outcomes.CONCLUSIONBMOIT was well tolerated and induced desensitization to BM and UM. This desensitization corresponded to redistribution within antigen-specific antibody and T cell compartments that provided insight into the mechanistic changes that occur with OIT treatment.TRIAL REGISTRATIONClinicalTrials.gov NCT03462030.FUNDING: Myra Reinhardt Family Foundation (grant number 128388), NIH/NIAID (U19AI135731, T32AI125179, S10OD025052).

FOXO1 pathway activation by VISTA immune checkpoint restrains pulmonary ILC2 functions

Group 2 innate lymphoid cells (ILC2s) play a pivotal role in the development of airway hyperreactivity (AHR). However, the regulatory mechanisms governing ILC2 function remain inadequately explored. This study uncovers V-domain Ig suppressor of T cell activation (VISTA) as an inhibitory immune checkpoint crucial for modulating ILC2-driven lung inflammation. VISTA is upregulated in activated pulmonary ILC2s and plays a key role in regulating lung inflammation, as VISTA-deficient ILC2s demonstrate increased proliferation and function, resulting in elevated type 2 cytokine production and exacerbation of AHR. Mechanistically, VISTA stimulation activates Forkhead box O1 (FOXO1), leading to modulation of ILC2 proliferation and function. The suppressive effects of FOXO1 on ILC2 effector function were confirmed using FOXO1 inhibitors and activators. Moreover, VISTA-deficient ILC2s exhibit enhanced fatty acid oxidation and oxidative phosphorylation to meet their high energy demands. Therapeutically, VISTA agonist treatment reduces ILC2 function both ex vivo and in vivo, significantly alleviating ILC2-driven AHR. Our murine findings were validated in human ILC2s, whose function was reduced ex vivo by a VISTA agonist, and in a humanized mouse model of ILC2-driven AHR. Our studies unravel VISTA as an immune checkpoint for ILC2 regulation via the FOXO1 pathway, presenting potential therapeutic strategies for allergic asthma by modulating ILC2 responses.

Antioxidative and Anticancer Potential of Luteolin: A Comprehensive Approach Against Wide Range of Human Malignancies

Luteolin is widely distributed phytochemical, a flavonoid, in kingdom plantae. Luteolin with potential antioxidant activity prevent ROS-induced damages and reduce oxidative stress which is mainly responsible in pathogenesis of many diseases. Several chemo preventive activities and therapeutic benefits are associated with luteolin. Luteolin prevents cancer via modulation of numerous pathways, that is, by inactivating proteins; such as procaspase-9, CDC2 and cyclin B or upregulation of caspase-9 and caspase-3, cytochrome C, cyclin A, CDK2, and APAF-1, in turn inducing cell cycle arrest as well as apoptosis. It also enhances phosphorylation of p53 and expression level of p53-targeted downstream gene. By Increasing BAX protein expression; decreasing VEGF and Bcl-2 expression it can initiate cell cycle arrest and apoptosis. Luteolin can stimulate mitochondrial-modulated functions to cause cellular death. It can also reduce expression levels of p-Akt, p-EGFR, p-Erk1/2, and p-STAT3. Luteolin plays positive role against cardiovascular disorders by improving cardiac function, decreasing the release of inflammatory cytokines and cardiac enzymes, prevention of cardiac fibrosis and hypertrophy; enhances level of CTGF, TGFβ1, ANP, Nox2, Nox4 gene expressions. Meanwhile suppresses TGFβ1 expression and phosphorylation of JNK. Luteolin helps fight diabetes via inhibition of alpha-glucosidase and ChE activity. It can reduce activity levels of catalase, superoxide dismutase, and GS4. It can improve blood glucose, insulin, HOMA-IR, and HbA1c levels. This review is an attempt to elaborate molecular targets of luteolin and its role in modulating irregularities in cellular pathways to overcome severe outcomes during diseases including cancer, cardiovascular disorders, diabetes, obesity, inflammation, Alzheimer's disease, Parkinson's disease, hepatic disorders, renal disorders, brain injury, and asthma. As luteolin has enormous therapeutic benefits, it could be a potential candidate in future drug development strategies.

Causal role of immune cells in asthma: a Mendelian randomization study

BACKGROUND

Immune cells may have a significant role in the pathophysiology of asthma, according to increasing evidence, although it is yet unclear how immune cells cause asthma. Therefore, we aimed to use Mendelian randomization (MR) methods to investigate this causal relationship.

METHODS

This study explored the causal effects between immune cells and asthma using a two-sample MR technique. Using publicly available genetic data, the causal connection between asthma risk and 731 immune cell phenotypes was investigated. Sensitivity analysis guaranteed the results' stability. To further evaluate the existence of reverse causality, we employed reverse MR analysis.

RESULTS

According to the inverse-variance weighted (IVW) method, five immune cell phenotypes were found to be statistically significantly associated with asthma risk (p < 0.001). Among them, TCRgd %T cell (OR = 0.968, 95%CI = 0.951 - 0.986), TCRgd %lymphocyte (OR = 0.978, 95%CI = 0.965 - 0.991), HLA DR + NK AC (OR = 0.966, 95% CI = 0.947 - 0.986) and CD3 on CD4 Treg (OR = 0.956, 95%CI= 0.931 - 0.981), four phenotypes that resulted in a decreased risk of asthma. CD25 on transitional (OR = 1.033, 95%CI = 1.014 - 1.052) resulted in an increased risk of asthma. Reverse MR analysis revealed that asthma increases HLA DR + NK AC levels (p < 0.05).

CONCLUSION

The results of MR analysis showed a causal relationship between immune cell phenotype and asthma risk, which provides a direction for future asthma treatment.

Hypoxia-inducible factor 2α promotes pathogenic polarization of stem-like Th2 cells via modulation of phospholipid metabolism

T helper 2 (Th2) cells orchestrate immunity against parasite infection and promote tissue repair but promote pathology in asthma and tissue fibrosis. Here, we examined the mechanisms driving pathogenic differentiation of Th2 cells. Single-cell analyses of CD4+ T cells from asthma and chronic rhinosinusitis patients revealed high expression of the hypoxia-inducible factor (HIF)2α in Th2 cells. In mice, HIF2α deficiency impaired Th2 differentiation and alleviated asthmatic inflammation. Single-cell and lineage tracing approaches delineated a differentiation trajectory from TCF1+Ly108+ stem-like Th2 cells to the ST2+CD25+ pathogenic progeny, depending on a HIF2α-GATA3 circuit that modulated phospholipid metabolism and T cell receptor (TCR)-phosphatidylinositol 3-kinase (PI3K)-protein kinase B (AKT) activation via transcriptional regulation of the inositol polyphosphate multikinase (IPMK). Overexpression of IPMK in HIF2α-deficient cells promoted Phosphatidylinositol (3,4,5)-trisphosphate (PIP3) synthesis and pathogenic Th2 cell differentiation, whereas pharmacological inhibition of HIF2α impaired pathogenic differentiation of Th2 cells and mitigated airway inflammation. Our findings provide insight into the contextual cues that promote Th2-mediated pathology and suggest HIF2α as a therapeutic target in asthma.

Lung-resident lymphocytes and their roles in respiratory infections and chronic respiratory diseases

Recent scientific breakthroughs have blurred traditional boundaries between innate and adaptive immunity, revealing a sophisticated network of tissue-resident cells that deliver immediate, localized immune responses. These lymphocytes not only provide rapid frontline defense but also present a paradoxical role in the pathogenesis of respiratory diseases such as asthma, chronic obstructive pulmonary disease, pulmonary fibrosis, and the long-term tissue consequences of viral infections including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). This review traverses the intricate landscape of lung-resident lymphocytes, delving into their origins, diverse functions, and their dualistic impact on pulmonary health. We dissect their interactions with the microenvironment and the regulatory mechanisms guiding their activity, with an emphasis on their contribution to both immune protection and immunopathology. This review aims to elucidate the complex narrative of these cells, enhancing our understanding of the development of precise therapeutic strategies to combat acute and chronic pulmonary diseases. Through this exploration, the review aspires to shed light on the potential of harnessing lung-resident lymphocytes for the treatment of respiratory conditions.

MUC1-EGFR crosstalk with IL-6 by activating NF-κB and MAPK pathways to regulate the stemness and paclitaxel-resistance of lung adenocarcinoma

BACKGROUND

The chemotherapy resistance often leads to chemotherapy failure. This study aims to explore the molecular mechanism by which MUC1 regulates paclitaxel resistance in lung adenocarcinoma (LUAD), providing scientific basis for future target selection.

METHODS

The bioinformatics method was used to analyse the mRNA and protein expression characteristics of MUC1 in LUAD. RT-qPCR and ELISA were used to detect the mRNA and protein expression, flow cytometry was used to detect CD133+ cells, and cell viability was detected by CCK-8 assay. The mRNA-seq was performed to analyse the changes in expression profile, GO and KEGG analysis were used to explore the potential biological functions.

RESULTS

MUC1 is highly expressed in LUAD patients and is associated with a higher tumour infiltration. In paclitaxel resistance LUAD cells (A549/TAX cells), the expression of MUC1, EGFR/p-EGFR and IL-6 were higher than that of A549 cells, the proportion of CD133+ cells was significantly increased, and the expression of cancer stem cell (CSCs) transcription factors (NANOG, OCT4 and SOX2) were significantly up-regulated. After knocking down MUC1 in A549/Tax cells, the activity of A549/Tax cells was significantly decreased. Correspondingly, the expression of EGFR, IL-6, OCT4, NANOG, and SOX2 were significantly down-regulated. The mRNA-seq showed that knocking down MUC1 affected the gene expression, DEGs mainly enriched in NF-κB and MAPK signalling pathway.

CONCLUSION

MUC1 was highly expressed in A549/TAX cells, and MUC1-EGFR crosstalk with IL-6 may be due to the activation of NF-κB and MAPK pathways, which promote the enrichment of CSCs and lead to paclitaxel resistance.

Activated Tim-3/Galectin-9 participated in the development of multiple myeloma by negatively regulating CD4 T cells

The interaction between Tim-3 on T cells and its ligand Galectin-9 negatively regulates the cellular immune response. However, the regulation of Tim-3/Galectin-9 on CD4 T cell subsets in multiple myeloma (MM) remains unclear. The aim of this study was to investigate the relationship between the regulation of CD4 T cell subsets by the Tim-3/Galectin-9 pathway and clinical prognostic indicators in MM. Tim-3/Galectin-9 were detected by flow cytometry, PCR and ELISA in 60 MM patients and 40 healthy controls, and its correlation with clinical prognostic parameters was analyzed. The expressions of Tim-3 on CD4 T cells, Galectin-9 mRNA in PBMC and level of Galectin-9 protein in serum were significantly elevated in MM patients, especially those with poor prognostic indicators. In MM patients, Tim-3 was highly expressed on the surfaces of Th1, Th2, and Th17 cells, but lowly expressed on Treg. Moreover, level of cytokine IFN-γ in serum was negatively correlated with Tim-3+Th1 cell and Galectin-9mRNA, Galectin-9 protein level. In addition, cell culture experiments showed that the anti-tumor effect and the ability to secrete IFN-γ were restored by blocking the Tim-3/Galectin-9 pathway. In MM patients, Tim-3/Galectin-9 is elevated and associated with disease progression, by inhibiting the cytotoxic function of Th1, and also promoting Th2 and Th17 to be involved in immune escape of MM. Therefore, Tim-3/Galectin-9 may serve as a new immunotherapeutic target for MM patients.

Granzyme K+CD8+ T cells interact with fibroblasts to promote neutrophilic inflammation in nasal polyps

Sophisticated interactions between stromal and immune cells play crucial roles in various biological and pathological processes. In chronic rhinosinusitis with nasal polyps (CRSwNP), the upper airway inflammation in many patients is driven by TH2, ILC2, and eosinophils, thus being treated with glucocorticoids and anti-type 2 inflammation biologics. The resistance to these therapies is often associated with neutrophilic inflammation, which has also been widely identified in CRSwNP, but the underlying mechanisms remain unclear. Using single-cell analysis, spatial transcriptomics, and T-cell receptor sequencing, we identify an increased presence of granzyme K+(GZMK+) CD8+ T cells in NPs, which possess a phenotype distinct from the cytotoxic GZMB+ effector CD8+ T subset. GZMK+CD8+ T cells are found to express CXCR4 and interact with CXCL12-secreting fibroblasts, inducing the latter to produce neutrophil chemoattractants in a manner uniquely mediated by GZMK but not other granzymes. This GZMK+CD8+ T cell-fibroblast crosstalk is also observed in other inflammatory diseases. Furthermore, GZMK+CD8+ T cells exhibit a selective expansion of clones that recognize Epstein-Barr virus. Here, we show that GZMK marks a phenotypically distinct subset of effector CD8+ T cells that promote neutrophilic inflammation.

E-cigarette vapor extract alters human eosinophil gene expression in an effect mediated by propylene glycol, glycerin, and nicotine

E-cigarette use has become widespread, and its effects on airway inflammation and disease are not fully delineated. E-cigarette vapor extract (EVE) profoundly affects neutrophil function. We hypothesized that EVE also alters eosinophil function and thus could impact allergic airway disease. We employed RNA sequencing to measure the ex vivo effect of EVE components on human eosinophil transcription. Blood eosinophils from 9 nonvaping subjects without asthma were isolated by negative selection. Cells were incubated for 48 h with EVE consisting of glycerin, propylene glycol, and nicotine (EVE+), EVE without nicotine ("EVE-"), air-exposed media termed extract buffer (EB), or untreated media. Bulk RNA sequencing was performed. Transcriptomic analysis revealed that the EB, EVE-, and EVE+ conditions showed highly variable gene expression with respect to no treatment and each other. Differential gene expression analysis comparing a combination of EVE+, EVE-, and EB revealed 3,030 differentially expressed genes (DEGs) with an adjusted P value <0.05 and log2 fold change >0.5 or <0.5. There were 645 DEGs between EB and EVE-, 1,713 between EB and EVE+, and 404 between EVE- and EVE+. Gene set enrichment analysis demonstrated that DEGs between both EVE+ and EVE- and the EB control were positively enriched for heme metabolism and apoptosis and negatively enriched tumor necrosis factor α signaling, interferon γ signaling, and inflammatory response. Thus, EVE significantly alters eosinophil metabolic and inflammatory pathways, mediated by propylene glycol and glycerin, with both enhancing and unique effects of nicotine. This study motivates further research into the pathogenic effects of vaping on airway eosinophils and allergic airways disease.

Single-Cell Analysis: A Method for In-Depth Phenotyping of Cells Involved in Asthma

Asthma is a chronic inflammatory lung disease with high prevalence, making it one of the most common chronic conditions worldwide. Its pathophysiology is influenced by a range of genetic and environmental factors, resulting in a complex and heterogeneous disease profile. Asthma is primarily associated with a type 2 (T2) immune response, though non-T2 endotypes also contribute to disease pathology. Generally, asthma is characterized by the infiltration and activation of various cell types, including dendritic cells, eosinophils, innate lymphoid cells, lymphocytes, mast cells, and neutrophils, which participate in T1, T2, and T17 immune responses. Despite advances in understanding, many questions remain unresolved. Therefore, emerging omic techniques, such as single-cell RNA sequencing (scRNA-seq), offer novel insights into the underlying mechanisms of asthma and the roles of these immune cells. Recent scRNA-seq studies in asthma have identified multiple novel immune cell subtypes and clusters, suggesting their potential functions in disease pathology. The rapid advancement of scRNA-seq technology now enables in-depth investigation of individual cells within tissues, allowing for precise cell-type classification and detailed molecular profiling. Nonetheless, certain limitations persist, which require further refinement in future studies.

Private information leakage from single-cell count matrices

The increase in publicly available human single-cell datasets, encompassing millions of cells from many donors, has significantly enhanced our understanding of complex biological processes. However, the accessibility of these datasets raises significant privacy concerns. Due to the inherent noise in single-cell measurements and the scarcity of population-scale single-cell datasets, recent private information quantification studies have focused on bulk gene expression data sharing. To address this gap, we demonstrate that individuals in single-cell gene expression datasets are vulnerable to linking attacks, where attackers can infer their sensitive phenotypic information using publicly available tissue or cell-type-specific expression quantitative trait loci (eQTLs) information. We further develop a method for genotype prediction and genotype-phenotype linking that remains effective without relying on eQTL information. We show that variants from one study can be exploited to uncover private information about individuals in another study.

Unraveling heterogeneity and treatment of asthma through integrating multi-omics data

Asthma has become one of the most serious chronic respiratory diseases threatening people's lives worldwide. The pathogenesis of asthma is complex and driven by numerous cells and their interactions, which contribute to its genetic and phenotypic heterogeneity. The clinical characteristic is insufficient for the precision of patient classification and therapies; thus, a combination of the functional or pathophysiological mechanism and clinical phenotype proposes a new concept called "asthma endophenotype" representing various patient subtypes defined by distinct pathophysiological mechanisms. High-throughput omics approaches including genomics, epigenomics, transcriptomics, proteomics, metabolomics and microbiome enable us to investigate the pathogenetic heterogeneity of diverse endophenotypes and the underlying mechanisms from different angles. In this review, we provide a comprehensive overview of the roles of diverse cell types in the pathophysiology and heterogeneity of asthma and present a current perspective on their contribution into the bidirectional interaction between airway inflammation and airway remodeling. We next discussed how integrated analysis of multi-omics data via machine learning can systematically characterize the molecular and biological profiles of genetic heterogeneity of asthma phenotype. The current application of multi-omics approaches on patient stratification and therapies will be described. Integrating multi-omics and clinical data will provide more insights into the key pathogenic mechanism in asthma heterogeneity and reshape the strategies for asthma management and treatment.

IL-2 family cytokines IL-9 and IL-21 differentially regulate innate and adaptive type 2 immunity in asthma

BACKGROUND

Asthma is often accompanied by type 2 immunity rich in IL-4, IL-5, and IL-13 cytokines produced by TH2 lymphocytes or type 2 innate lymphoid cells (ILC2s). IL-2 family cytokines play a key role in the differentiation, homeostasis, and effector function of innate and adaptive lymphocytes.

OBJECTIVE

IL-9 and IL-21 boost activation and proliferation of TH2 and ILC2s, but the relative importance and potential synergism between these γ common chain cytokines are currently unknown.

METHODS

Using newly generated antibodies, we inhibited IL-9 and IL-21 alone or in combination in various murine models of asthma. In a translational approach using segmental allergen challenge, we recently described elevated IL-9 levels in human subjects with allergic asthma compared with nonasthmatic controls. Here, we also measured IL-21 in both groups.

RESULTS

IL-9 played a central role in controlling innate IL-33-induced lung inflammation by promoting proliferation and activation of ILC2s in an IL-21-independent manner. Conversely, chronic house dust mite-induced airway inflammation, mainly driven by adaptive immunity, was solely dependent on IL-21, which controlled TH2 activation, eosinophilia, total serum IgE, and formation of tertiary lymphoid structures. In a model of innate on adaptive immunity driven by papain allergen, a clear synergy was found between both pathways, as combined anti-IL-9 or anti-IL-21 blockade was superior in reducing key asthma features. In human bronchoalveolar lavage samples we measured elevated IL-21 protein within the allergic asthmatic group compared with the allergic control group. We also found increased IL21R transcripts and predicted IL-21 ligand activity in various disease-associated cell subsets.

CONCLUSIONS

IL-9 and IL-21 play important and nonredundant roles in allergic asthma by boosting ILC2s and TH2 cells, revealing a dual IL-9 and IL-21 targeting strategy as a new and testable approach.

Mechanism differences in the start time of sublingual immunotherapy in a mouse allergic airway inflammation model

Sublingual immunotherapy (SLIT) has received considerable attention as a method for allergen immunotherapy (AIT). However, the mechanism of SLIT, especially its timing, has not been thoroughly investigated. We evaluated therapeutic and prophylactic SLIT in an allergic airway inflammation model and evaluated their efficacies. Mice were intranasally exposed to Dermatophagoides farinae (Der f) extract and received SLIT before (prophylactic model) and after (therapeutic model) intranasal exposure of Der f. We investigated airway responsiveness, airway inflammation, allergen-specific antibodies, lung histology and single-cell RNA sequencing (scRNA-seq) and T-cell receptor sequencing were also investigated. SLIT in the therapeutic model was effective; however, the effects of SLIT in the prophylactic model were stronger and immune tolerance was maintained for three months. ScRNA-seq of lung CD4+CD25+ T cells revealed that the expansion of induced T regulatory (iTreg) cells was greater in the prophylactic model than that in the therapeutic model. Additionally, the TCR repertoire of iTregs from the prophylactic model was abundant, sharing many clones with the TCR repertoire of effector T cells. These data suggest that the prophylactic model of AIT is extremely effective and persistent, and may respond to allergen diversity, and provide evidence for the clinical recommendation of preventive AIT.

Single-cell analysis in rheumatic and allergic diseases: insights for clinical practice

Since the advent of single-cell RNA sequencing (scRNA-seq) methodology, single-cell analysis has become a powerful tool for exploration of cellular networks and dysregulated immune responses in disease pathogenesis. Advanced bioinformatics tools have enabled the combined analysis of scRNA-seq data and information on various cell properties, such as cell surface molecular profiles, chromatin accessibility and spatial information, leading to a deeper understanding of pathology. This Review provides an overview of the achievements in single-cell analysis applied to clinical samples of rheumatic and allergic diseases, including rheumatoid arthritis, systemic lupus erythematosus, systemic sclerosis, allergic airway diseases and atopic dermatitis, with an expanded scope beyond peripheral blood cells to include local diseased tissues. Despite the valuable insights that single-cell analysis has provided into disease pathogenesis, challenges remain in translating single-cell findings into clinical practice and developing personalized treatment strategies. Beyond understanding the atlas of cellular diversity, we discuss the application of data obtained in each study to clinical practice, with a focus on identifying biomarkers and therapeutic targets.

Deciphering cuproptosis-related signatures in pediatric allergic asthma using integrated scRNA-seq and bulk RNA-seq analysis

OBJECTIVE

Allergic asthma (AA) is common in children. Excess copper is observed in AA patients. It is currently unclear whether copper imbalance can cause cuproptosis in pediatric AA.

METHODS

The datasets about pediatric AA (GSE40732 and GSE40888) were obtained from Gene Expression Omnibus (GEO) database. The expression of cuproptosis-related genes (CRGs) and immune cell infiltration in pediatric AA samples were analyzed. Single-cell RNA sequencing (scRNA-seq) data (GSE193816) were used to evaluate the expression patterns of CRGs in AA. The identification of differentially expressed genes within clusters was conducted using weighted gene co-expression network analysis. Subsequently, disease progression and cuproptosis-related models were screened using random forest (RF), support vector machine (SVM), extreme gradient boosting (XGBoost), and general linear model (GLM) algorithms.

RESULTS

Four CRGs were notably increased in pediatric AA samples. CD4+ T cells, macrophages and mast cells exhibited a lower cuproptosis score in AA samples, indicating that these immune cells may be closely associated with cuproptosis in AA development. Co-expression network of CRGs in AA was constructed. AA samples were divided into two cuprotosis clusters. Following construction of four machine-learning models, SVM model exhibited the highest efficacy of prediction in the testing set (AUC = 0.952). SVM model containing five important variables can be used for prediction of AA.

CONCLUSION

This work provided a machine learning model containing five important variables, which may have good diagnostic efficiency for pediatric AA.

Activin A Promotes Differentiation of a Pathogenic Multicytokine IL-9-secreting CD4+ T Cell Population

The development of Th subsets results from cellular and cytokine cues that are present in the inflammatory environment. The developing T cell integrates multiple signals from the environment that sculpt the cytokine-producing capacity of the effector T cell. Importantly, T cells can discriminate similar cytokine signals to generate distinct outcomes, and that discrimination is critical in Th subset development. IL-9-secreting Th9 cells regulate multiple immune responses, including immunity to pathogens and tumors, allergic inflammation, and autoimmunity. In combination with IL-4, TGF-β or activin A promotes IL-9 production; yet, it is not clear if both TGF-β family members generate Th9 cells with identical phenotype and function. We observed that in contrast to TGF-β that efficiently represses Th2 cytokines in murine Th9 cultures, differentiation with activin A produced a multicytokine T cell phenotype with secretion of IL-4, IL-5, IL-13, and IL-10 in addition to IL-9. Moreover, multicytokine secreting cells are more effective at promoting allergic inflammation. These observations suggest that although TGF-β and IL-4 were identified as cytokines that stimulate optimal IL-9 production, they might not be the only cytokines that generate optimal function from IL-9-producing T cells in immunity and disease.

Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic risk to childhood-onset asthma

Asthma is a complex disease caused by genetic and environmental factors. Studies show that wheezing during rhinovirus infection correlates with childhood asthma development. Over 150 non-coding risk variants for asthma have been identified, many affecting gene regulation in T cells, but the effects of most risk variants remain unknown. We hypothesized that airway epithelial cells could also mediate genetic susceptibility to asthma given they are the first line of defense against respiratory viruses and allergens. We integrated genetic data with transcriptomics of airway epithelial cells subject to different stimuli. We demonstrate that rhinovirus infection significantly upregulates childhood-onset asthma-associated genes, particularly in non-ciliated cells. This enrichment is also observed with influenza infection but not with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or cytokine activation. Overall, our results suggest that rhinovirus infection is an environmental factor that interacts with genetic risk factors through non-ciliated airway epithelial cells to drive childhood-onset asthma.

Heterogeneous IL-9 Production by Circulating Skin-Tropic and Extracutaneous Memory T Cells in Atopic Dermatitis Patients

Interleukin (IL)-9 is present in atopic dermatitis (AD) lesions and is considered to be mainly produced by skin-homing T cells expressing the cutaneous lymphocyte-associated antigen (CLA). However, its induction by AD-associated triggers remains unexplored. Circulating skin-tropic CLA+ and extracutaneous/systemic CLA- memory T cells cocultured with autologous lesional epidermal cells from AD patients were activated with house dust mite (HDM) and staphylococcal enterotoxin B (SEB). Levels of AD-related mediators in response to both stimuli were measured in supernatants, and the cytokine response was associated with different clinical characteristics. Both HDM and SEB triggered heterogeneous IL-9 production by CLA+ and CLA- T cells in a clinically homogenous group of AD patients, which enabled patient stratification into IL-9 producers and non-producers, with the former group exhibiting heightened HDM-specific and total IgE levels. Upon allergen exposure, IL-9 production depended on the contribution of epidermal cells and class II-mediated presentation; it was the greatest cytokine produced and correlated with HDM-specific IgE levels, whereas SEB mildly induced its release. This study demonstrates that both skin-tropic and extracutaneous memory T cells produce IL-9 and suggests that the degree of allergen sensitization reflects the varied IL-9 responses in vitro, which may allow for patient stratification in a clinically homogenous population.

Asthma Pathogenesis: Phenotypes, Therapies, and Gaps: Summary of the Aspen Lung Conference 2023

Although substantial progress has been made in our understanding of asthma pathogenesis and phenotypes over the nearly 60-year history of the Aspen Lung Conferences on asthma, many ongoing challenges exist in our understanding of the clinical and molecular heterogeneity of the disease and an individual patient's response to therapy. This report summarizes the proceedings of the 2023 Aspen Lung Conference, which was organized to review the clinical and molecular heterogeneity of asthma and to better understand the impact of genetic, environmental, cellular, and molecular influences on disease susceptibility, heterogeneity, and severity. The goals of the conference were to review new information about asthma phenotypes, cellular processes, and cellular signatures underlying disease heterogeneity and treatment response. The report concludes with ongoing gaps in our understanding of asthma pathobiology and provides some recommendations for future research to better understand the clinical and basic mechanisms underlying disease heterogeneity in asthma and to advance the development of new treatments for this growing public health problem.

TL1A priming induces a multi-cytokine Th9 cell phenotype that promotes robust allergic inflammation in murine models of asthma

Multi-cytokine-producing Th9 cells secrete IL-9 and type 2 cytokines and mediate mouse and human allergic inflammation. However, the cytokines that promote a multi-cytokine secreting phenotype have not been defined. Tumor necrosis factor superfamily member TL1A signals through its receptor DR3 to increase IL-9. Here we demonstrate that TL1A increases expression of IL-9 and IL-13 co-expressing cells in murine Th9 cell cultures, inducing a multi-cytokine phenotype. Mechanistically, this is linked to histone modifications allowing for increased accessibility at the Il9 and Il13 loci. We further show that TL1A alters the transcription factor network underlying expression of IL-9 and IL-13 in Th9 cells and increases binding of transcription factors to Il9 and Il13 loci. TL1A-priming enhances the pathogenicity of Th9 cells in murine models of allergic airway disease through the increased expression of IL-9 and IL-13. Lastly, in both chronic and memory-recall models of allergic airway disease, blockade of TL1A signaling decreases the multi-cytokine Th9 cell population and attenuates the allergic phenotype. Taken together, these data demonstrate that TL1A promotes the development of multi-cytokine Th9 cells that drive allergic airway diseases and that targeting pathogenic T helper cell-promoting cytokines could be an effective approach for modifying disease.

Severe Allergy as a Chronic Inflammatory Condition From a Systems Biology Perspective

Persistent and unresolved inflammation is a common underlying factor observed in several and seemingly unrelated human diseases, including cardiovascular and neurodegenerative diseases. Particularly, in atopic conditions, acute inflammatory responses such as those triggered by insect venom, food or drug allergies possess also a life-threatening potential. However, respiratory allergies predominantly exhibit late immune responses associated with chronic inflammation, that can eventually progress into a severe phenotype displaying similar features as those observed in other chronic inflammatory diseases, as is the case of uncontrolled severe asthma. This review aims to explore the different facets and systems involved in chronic allergic inflammation, including processes such as tissue remodelling and immune cell dysregulation, as well as genetic, metabolic and microbiota alterations, which are common to other inflammatory conditions. Our goal here was to deepen on the understanding of an entangled disease as is chronic allergic inflammation and expose potential avenues for the development of better diagnostic and intervention strategies.

Immunological factors, important players in the development of asthma

Asthma is a heterogeneous disease, and its development is the result of a combination of factors, including genetic factors, environmental factors, immune dysfunction and other factors. Its specific mechanism has not yet been fully investigated. With the improvement of disease models, research on the pathogenesis of asthma has made great progress. Immunological disorders play an important role in asthma. Previously, we thought that asthma was mainly caused by an imbalance between Th1 and Th2 immune responses, but this theory cannot fully explain the pathogenesis of asthma. Recent studies have shown that T-cell subsets such as Th1 cells, Th2 cells, Th17 cells, Tregs and their cytokines contribute to asthma through different mechanisms. For the purpose of the present study, asthma was classified into distinct phenotypes based on airway inflammatory cells, such as eosinophilic asthma, characterized by predominant eosinophil aggregates, and neutrophilic asthma, characterized by predominant neutrophil aggregates. This paper will examine the immune mechanisms underlying different types of asthma, and will utilize data from animal models and clinical studies targeting specific immune pathways to inform more precise treatments for this condition.

Single-cell transcriptomic and T cell antigen receptor analysis of human cytomegalovirus (hCMV)-specific memory T cells reveals effectors and pre-effectors of CD8+- and CD4+-cytotoxic T cells

Latent human cytomegalovirus (hCMV) infection can pose a serious threat of reactivation and disease occurrence in immune-compromised individuals. Although T cells are at the core of the protective immune response to hCMV infection, a detailed characterization of different T cell subsets involved in hCMV immunity is lacking. Here, in an unbiased manner, we characterized over 8000 hCMV-reactive peripheral memory T cells isolated from seropositive human donors, at a single-cell resolution by analysing their single-cell transcriptomes paired with the T cell antigen receptor (TCR) repertoires. The hCMV-reactive T cells were highly heterogeneous and consisted of different developmental and functional memory T cell subsets such as, long-term memory precursors and effectors, T helper-17, T regulatory cells (TREGs) and cytotoxic T lymphocytes (CTLs) of both CD4 and CD8 origin. The hCMV-specific TREGs, in addition to being enriched for molecules known for their suppressive functions, showed enrichment for the interferon response signature gene sets. The hCMV-specific CTLs were of two types, the pre-effector- and effector-like. The co-clustering of hCMV-specific CD4-CTLs and CD8-CTLs in both pre-effector as well as effector clusters suggest shared transcriptomic signatures between them. The huge TCR clonal expansion of cytotoxic clusters suggests a dominant role in the protective immune response to CMV. The study uncovers the heterogeneity in the hCMV-specific memory T cells revealing many functional subsets with potential implications in better understanding of hCMV-specific T cell immunity. The data presented can serve as a knowledge base for designing vaccines and therapeutics.

TL1A is an epithelial alarmin that cooperates with IL-33 for initiation of allergic airway inflammation

Epithelium-derived cytokines or alarmins, such as interleukin-33 (IL-33) and thymic stromal lymphopoietin (TSLP), are major players in type 2 immunity and asthma. Here, we demonstrate that TNF-like ligand 1A (TL1A) is an epithelial alarmin, constitutively expressed in alveolar epithelium at steady state in both mice and humans, which cooperates with IL-33 for early induction of IL-9high ILC2s during the initiation of allergic airway inflammation. Upon synergistic activation by IL-33 and TL1A, lung ILC2s acquire a transient IL-9highGATA3low "ILC9" phenotype and produce prodigious amounts of IL-9. A combination of large-scale proteomic analyses, lung intravital microscopy, and adoptive transfer of ILC9 cells revealed that high IL-9 expression distinguishes a multicytokine-producing state-of-activated ILC2s with an increased capacity to initiate IL-5-dependent allergic airway inflammation. Similar to IL-33 and TSLP, TL1A is expressed in airway basal cells in healthy and asthmatic human lungs. Together, these results indicate that TL1A is an epithelium-derived cytokine and an important cofactor of IL-33 in the airways.

Expression and clinical significance of interleukin-10, transforming growth factor-β1, and CD4+CD25 cytokines in paediatric allergic rhinitis with allergic asthma

Introduction

It was intended to research the level changes and clinical significance of interleukin (IL)-10, transforming growth factor β1 (TGF-β1), and CD4+CD25 cytokines in paediatric allergic rhinitis (AR) accompanied with allergic asthma (AA).

Material and methods

Eighty children of AA with AR receiving immunotherapy indications were included as the experimental group (EG), while another 40 healthy children in the same period were selected as the control group (CG). IL-10, TGF-β1, and CD4+CD25 levels in cells of the two groups before and after treatment were compared and analysed.

Results

The serum TGF-β1 level was determined as 1,045.7 ±44.7 pg/ml in the EG at admission, remarkably higher than that in the CG (p < 0.05). The IL-10 level was 21.4 ±2.8 pg/ml; CD4+CD25 cells accounted for 9.2 ±2.4%, CD4+CD25high cells accounted for 0.6 ±0.3%. These were all greatly lower than those in the CG (p < 0.05). At discharge, the serum TGF-β1 level in the EG was 903.7 ±29.4 pg/ml, which was still memorably higher than that in the CG (p < 0.05). The IL-10 level changed to 32.8 ±3.7 pg/ml; the percentage of CD4+CD25 was 11.3 ±1.8, respectively, among CD4+T cells. These were also notably lower than those in the CG at discharge (p < 0.05).

Conclusions

IL-10, TGF-β1, and CD4+CD25 level changes in cells might be of reference value as therapeutic indicators for clinical treatment or evaluation of paediatric AR with AA.

IL-33 induced gene expression in activated Th2 effector cells is dependent on IL-1RL1 haplotype and asthma status

Asthma is a heterogeneous respiratory disease caused by the interaction between environmental and genetic factors [1]. The IL-33 and IL-1RL1 genes are strongly associated with childhood-onset and type-2 high asthma, and the asthma risk alleles amplify interleukin (IL)-33 pathway activity [2]. Environmental factors, such as allergens and viral infections, trigger bronchial epithelial cells to release IL-33, which can activate signalling by binding to the IL-1RL1/IL-1RAcP receptor complex [3], and contribute to hyper-responsiveness, remodelling and chronic type 2 inflammation of the airways [4].

IL-33 response in Th2 cells is specific to asthma and represents a high risk haplotype, highlighting its role in airway wall cells. Yet, its detection is challenging in bulk asthma transcriptomes due to the scarcity of effector Th2 cells. https://bit.ly/3WhuMbo

Dimethyl fumarate alleviates allergic asthma by strengthening the Nrf2 signaling pathway in regulatory T cells

Allergic asthma is a widely prevalent inflammatory condition affecting people across the globe. T cells and their secretory cytokines are central to the pathogenesis of allergic asthma. Here, we have evaluated the anti-inflammatory impact of dimethyl fumarate (DMF) in allergic asthma with more focus on determining its effect on T cell responses in allergic asthma. By utilizing the ovalbumin (OVA)-induced allergic asthma model, we observed that DMF administration reduced the allergic asthma symptoms and IgE levels in the OVA-induced mice model. Histopathological analysis showed that DMF treatment in an OVA-induced animal model eased the inflammation in the nasal and bronchial tissues, with a particular decrease in the infiltration of immune cells. Additionally, RT-qPCR analysis exhibited that treatment of DMF in an OVA-induced model reduced the expression of inflammatory cytokine (IL4, IL13, and IL17) while augmenting anti-inflammatory IL10 and Foxp3 (forkhead box protein 3). Mechanistically, we found that DMF increased the expression of Foxp3 by exacerbating the expression of nuclear factor E2-related factor 2 (Nrf2), and the in-vitro activation of Foxp3+ Tregs leads to an escalated expression of Nrf2. Notably, CD4-specific Nrf2 deletion intensified the allergic asthma symptoms and reduced the in-vitro iTreg differentiation. Meanwhile, DMF failed to exert protective effects on OVA-induced allergic asthma in CD4-specific Nrf2 knock-out mice. Overall, our study illustrates that DMF enhances Nrf2 signaling in T cells to assist the differentiation of Tregs, which could improve the anti-inflammatory immune response in allergic asthma.

Semaphorin 3 a restores the ability of type 1 regulatory T cells to suppress food allergy

Food allergy (FA) is a common immune disorder that involves dysfunctional immune regulation. More remedies for restoring immune regulation are necessary. Semaphorin 3 A (Sema3a) is a secreted protein of the semaphorin family, which plays a role in immune responses at all stages. The objective of this study is to gain an understanding of how Sema3a can restore the immune regulatory abilities of type 1 regulatory T cells (Tr1 cells). In this study, blood samples were taken from patients with FA. Tr1 cells were purified from blood samples using flow cytometry cell sorting, using LAG3 and CD49b as surface markers. RNA sequencing was employed to examine the characteristics of Tr1 cells. We observed an exaggerated increase in ER stress in peripheral Tr1 cells of FA patients. Enforced expression of spliced X-box protein-1 (XBP1s, one of the key molecules in ER stress) resulted in suppression of interleukin (IL)-10 expression in CD4+ T cells. Eukaryotic initiation factor 2a (eIF2a) mediated the effects of XBP1 on suppressing IL-10 expression in Tr1 cells. The use of Sema3a resulted in a decrease in ER stress, and an increase in IL-10 expression in Tr1 cells of FA patients. Sema3a administration reduced experimental FA by increasing the number of Tr1 cells. In conclusion, IL-10 expression in Tr1 cells is disturbed by ER stress. Sema3a treatment restores the expression of IL-10 and the immunosuppressive capability of Tr1 cells.

ERS International Congress 2023: highlights from the Basic and Translational Sciences Assembly

Early career members of Assembly 3 (Basic and Translational Sciences) of the European Respiratory Society (ERS) summarise the key messages discussed during six selected sessions that took place at the ERS International Congress 2023 in Milan, Italy. Aligned with the theme of the congress, the first session covered is "Micro- and macro-environments and respiratory health", which is followed by a summary of the "Scientific year in review" session. Next, recent advances in experimental methodologies and new technologies are discussed from the "Tissue modelling and remodelling" session and a summary provided of the translational science session, "What did you always want to know about omics analyses for clinical practice?", which was organised as part of the ERS Translational Science initiative's aims. The "Lost in translation: new insights into cell-to-cell crosstalk in lung disease" session highlighted how next-generation sequencing can be integrated with laboratory methods, and a final summary of studies is presented from the "From the transcriptome landscape to innovative preclinical models in lung diseases" session, which links the transcriptome landscape with innovative preclinical models. The wide range of topics covered in the selected sessions and the high quality of the research discussed demonstrate the strength of the basic and translational science being presented at the international respiratory conference organised by the ERS.