European Journal of Immunology

Introduction: Tumor-reactive T cell receptors (TCRs) are promising candidates for the manufacturing of safe and effective adoptive TCR-T cell therapies, but their efficient identification remains a major challenge. We previously established an antigen-agnostic TCR-repertoire analysis workflow that prioritizes candidate TCRs based on intratumoral clonal expansion and high tumor-to-non-tumor (T/N) frequency ratios. Here, we investigated whether T/N-selected clonotypes show independent transcriptional and spatial features consistent with tumor association. Methods: Bulk and single-cell TCR repertoire sequencing of paired tumor and adjacent non-tumor tissues was used to identify clonotypes with high T/N ratios across 15 cancer cases, comprising six non-small cell lung cancers, five pancreatic cancers, two breast cancers, and two colorectal cancers. Candidate clonotypes were further characterized by paired single-cell TCR and gene expression profiling and, in two PDAC cases, by Xenium spatial transcriptomics to assess their cellular phenotype, spatial localization, and proximity to malignant cells. Results: High T/N ratios consistently marked T cell clonotypes with features of tumor reactivity across the studied solid tumor entities. The analysis included Cluster-A, a lead T cell cluster comprising highly similar TCRs shared among 14 HLA-A*02:01-positive patients in the present cohort. Cluster-A clonotypes were consistently enriched in tumor relative to matched non-tumor tissue, and previous functional studies demonstrated tumor recognition by Cluster-A members. In a focused analysis of a pancreatic cancer case, Cluster-A CD8 T cells were selectively detected in tumor tissue, preferentially localized near malignant epithelial cells, and displayed an antigen-experienced effector-memory phenotype with prominent expression of granzymes A and K (GZMA/GZMK). Importantly, in another PDAC case that lacked Cluster-A clonotypes, these features extended to independent clonotypes, revealing a continuous tumor-association axis in which increasing T/N ratios were associated with progressively closer localization to malignant cells and increased GZMA/GZMK expression. Thus, repertoire enrichment, spatial tumor proximity, and effector-associated transcriptional states converged across independent tumor-enriched clonotypes. Outlook: These findings support the T/N ratio as a robust primary criterion for identifying candidate tumor-reactive TCRs. Integration of single-cell and spatial transcriptomics provides supporting biological evidence of tumor association and a framework for prioritizing therapeutic TCR candidates when functional validation is limited.

Antiviral monoclonal antibodies (mAbs) rely on Fc-mediated effector functions, which depend on interactions with Fc receptors (FcRs) expressed on immune cells such as monocytes and dendritic cells (DCs). While combinations of antiviral mAbs with type I interferons (IFN-I) or IFN inducers are being explored to enhance therapeutic efficacy, the impact of these immunomodulators on FcR expression remains poorly understood. In this study, we investigated the effects of IFN-2, IFN-{beta}, and the IFN-inducer TAK-981 (a SUMOylation inhibitor) on FcR modulation and functional activation in human monocyte subsets and monocyte-derived DCs (moDCs). Using flow cytometry and imaging techniques, we mapped the expression of activating Fc{gamma}Rs (CD64, CD32A, CD16A) and neonatal FcR (FcRn) under steady-state and stimulated conditions. We found that IFN-I selectively downregulates CD16A expression in classical monocytes while preserving other FcRs, whereas TAK-981 reduces FcRn expression in classical monocytes without affecting CD16A. Additionally, IFN-{beta} and TAK-981 but not IFN-2, selectively enhanced Fc{gamma}RI expression in moDC. IFN-{beta} also induced a stronger maturation and functional activation program in monocytes and moDCs compared with IFN-2, whereas TAK-981 largely reproduced the IFN-{beta}-driven phenotype and secretory profile. Furthermore, we demonstrated that IFN-I signaling alters the spatial distribution of FcRs, with IFN-{beta} and TAK-981 promoting distinct redistribution patterns of Fc{gamma}Rs in monocytes and moDCs. These findings reveal a novel layer of FcR regulation, highlighting that IFN-I and IFN inducers differentially modulate FcR expression, localization, and functional activation in a cell-type- and stimulus-specific manner. Overall, this work provides a framework for understanding how IFN-I-based immunotherapies may influence Fc-mediated immune functions while preserving FcRn-dependent antibody persistence.

Background Vitiligo is an acquired depigmenting disorder characterised by melanocyte loss. While immune responses against melanocytes are implicated in its pathogenesis, melanocyte detachment, melanocyte senescence and aberrant epidermal differentiation are increasingly characterised as additional pathological features. Granzyme B (GzmB), classically recognised as an intracellular effector of perforin-dependent cytotoxicity, is increased in vitiligo lesions; however, its extracellular contribution to vitiligo pathology remains unclear. Objectives To determine whether extracellular GzmB contributes to depigmentation and epidermal pathological features relevant to vitiligo, and to define its cellular source and underlying mechanisms. Methods Human vitiligo skin samples, murine depigmentation models and cultured human epidermal cells were analysed. The functional effects of extracellular GzmB were examined by subcutaneous administration of recombinant GzmB in mice. A rhododendrol (RD)-induced leukoderma model was used to evaluate the disease relevance of GzmB and the therapeutic effect of topical GzmB inhibition with VTI-1002. Results GzmB-positive cells were markedly increased in active vitiligo lesions and were predominantly associated with tryptase-positive cells, with limited co-distribution with CD8 or perforin. Vitiligo lesions also showed melanocyte detachment, increased p16INK4A-positive melanocytes and aberrant keratinocyte differentiation. These pathological features were recapitulated in vivo by extracellular GzmB administration, accompanied by focal depigmentation. In cultured melanocytes, GzmB exerted no cytotoxic effects but reduced attachment strength and induced a senescence-associated phenotype characterised by decreased extracellular matrix- and adhesion-related gene expression, increased p16INK4A level, elevated senescence-associated {beta}-galactosidase activity and activation of transforming growth factor-{beta}/SMAD signalling. In keratinocytes, extracellular GzmB promoted aberrant differentiation associated with activation of p53 signalling. Topical inhibition of GzmB in RD-induced leukoderma attenuated depigmentation progression, melanocyte detachment, melanocyte senescence and abnormal epidermal differentiation. Conclusions Extracellular GzmB promotes depigmentation associated with inducing melanocyte detachment, melanocyte senescence and aberrant keratinocyte differentiation. These findings identify extracellular GzmB as a previously underrecognised pathogenic mediator and potential therapeutic target in vitiligo-associated depigmentation.

The non-canonical NF-kappa B pathway, in which NFKB2 plays a central role, is critical for lymphoid organ development and immune homeostasis. Pathogenic NFKB2 variants have been strongly associated with a broad spectrum of human pathologies, notably immunodysregulation syndromes, characterized by recurrent infections, autoantibody production and endocrine abnormalities. The mechanisms underlying the resulting immune defects remain incompletely understood. In the present study, we characterized the immune phenotype of a novel rat model harboring a Nfkb2 non-sense mutation located in the c-terminal region of the gene (c.2602T>A; p.Tyr867*, Nfkb2p.Tyr867*). This variant has been identified in patients with a familial form of common variable immunodeficiency (CVID) presenting with autoimmunity manifestations. Using this model, we demonstrate that mutated NFKB2 resulted in profound alterations of the thymic microenvironment, including reduced K5+ medullary thymic epithelial cells and decreased AIRE expression, accompanied by altered thymocyte development and impaired thymic regulatory T populations. Peripheral lymphoid organization was also profoundly affected, with absence of lymph nodes, defects in the splenic marginal zone, and alterations of CD4+ and CD8+ T-cell homeostasis, including impaired Treg populations and reduced ICOS expression on CD4+ T cells. The B-cell compartment was markedly altered, with impaired B-cell maturation, characterized by accumulation of IgM+IgD- transitional cells and a marked reduction of IgD+ mature B cells. These abnormalities were associated with impaired humoral immunity and complete absence of circulating immunoglobulins. Collectively, our findings define a systemic combined immunodeficiency phenotype in the Nfkb2-mutated rat, highlighting its utility for studying the role of non-canonical NF-kB signaling in immune system organization and adaptative immunity.

The transcriptional and cell repertoire changes of lymph node (LN) T cells following influenza vaccination have been under-investigated across different ethnicities. Draining (dLN) and non-draining (ndLN) axillary LN cells from 17 participants with genotypically varied African or Asian ancestry (ISRCTN13657999) were collected by fine needle aspiration (FNA) before, 5 days and 42 days after adjuvanted influenza vaccination and analysed by single-cell RNA-sequencing (scRNA-seq). The early dLN transcriptional profile and cellular dynamics were distinct from the ndLN; BACH2 expressing T cells were highly induced, exhibiting stem-like and unique quiescence signatures. Proliferating T follicular helper cells (Tfh) were enriched in dLN and Th1-like Tfh predominated with highly induced transcriptional changes. The BACH2+ T cell state and Th1-like Tfh cells, transcriptionally distinct from germinal centre (GC) T cells, were co-localised with LAMP3+ dendritic cells in the T cell zone of publicly available LN datasets, a region that was also distinct from GC Tfh niches. Together, these findings indicate that the induction of a robust, proliferative, and transcriptionally diverse Tfh response, alongside a discrete subset of BACH2+ T cells, represents a marked feature of the early T cell zone immune response to adjuvanted influenza vaccine in the dLN.

The skull bone marrow axis has recently emerged as an important source of immune cells during neuroinflammation, including in the experimental autoimmune encephalomyelitis (EAE) , the mouse model of multiple sclerosis. The cribriform plate bone marrow (cpBM), is a portion of the ethmoid bone of the skull of mice, and is positioned next to nasal regions. At the cribriform plate olfactory nerves pass through the skull and recent evidence supports that it represents an important immune niche with links to CSF outflow and connections to cpBM. Previous data supports cellular composition of the ethmoid bone marrow in mice is altered in neuroinflammation suggesting it senses inflammatory cues, but the exact nature of these changes is still unclear. Here using scRNAseq and flow cytometry of the ethmoid bone marrow region we test how the region responds to EAE. In addition we also compare the cpBM region with systemic bone marrow in the femur to understand region specific differences. We report that neuroinflammation creates a regulatory response at these sites and implicates the cpBM in controlling these effects. A better understanding of the cribriform niche may offer new treatments for neuroinflammatory disease

CD11c+CD21- B cells are overrepresented in rheumatoid arthritis (RA). Here we delineate their functional state at site of inflammation and its molecular basis. Phenotypic profiling of paired blood and synovial fluid from patients with anti-citrullinated protein antibody (ACPA) seropositive RA (N=12), seronegative RA (N=10) and spondyloarthritis (N=8), demonstrated a striking enrichment of CD11c+CD21- B cells in synovial fluid in all three diseases (average of CD19+ cells: 67%, 49% and 51%). In ACPA-positive RA we identified increased proportions of CD11c+IgG+CD27low cells and several stages of pre-plasmablasts. The CD11c+CD21- cells had a phenotype indicating BCR activation, proliferation, and antigen presentation. This B-cell profile was mirrored by a LAG3+CTLA4+TIGIT+ peripheral helper T-cell program in ACPA-positive RA, contrasting a CCR6+ Th17-skewing in seronegative RA. Single-cell spatial proteomics revealed a unique CD11chighCD21 low B-cell surface architecture including a BCR co-receptor-tetraspanin signature with CD72-CD81 co-localization, which was elevated in RA. CD11c+ cells also displayed CD44-CD52/CD59 and MHCII-CD40/CD84 immune-modules absent in other B-cell subsets. In summary, CD11c+CD21- B cells are highly diverse, and while an activated antigen-experienced synovial profile was shared between disease groups, ACPA+ RA showed evidence of increased extrafollicular plasmablast differentiation. Surface receptor organization implicated a favoured BCR responsiveness, complement resistance and antigen presentation.

Introduction: Neoepitopes form the basis of tumor-specific immune responses. Tissue biopsy, the primary source for neoepitope detection, is limited and invasive. Therefore, we aimed to identify neoepitopes by mutanome-guided immunopeptidomics from plasma of cancer patients. Methods: Mass spectrometry (MS) data analysis of HLA ligands from plasma (n = 4) was guided by patient-specific mutanomes of cell-free DNA (cfDNA) from plasma or tumor genomic DNA (tgDNA) from tissue. Matched tumor tissue and healthy donor plasma served as controls. Neoepitopes were validated with synthetic peptides, and immunogenicity was assessed using IFN-gamma ELISpot and intracellular cytokine staining. Results: Wild-type immunopeptidomes from tissue and plasma overlapped by 58%, with 91% of plasma HLA ligands rediscovered in tissue. 13 out of 15 tumor-associated HLA ligands detected in plasma were rediscovered in the matching tissue. However, no neoepitopes in plasma were identified by immunopeptidomics guided by cfDNA mutanomes, likely reflecting the limited overlap between cfDNA and tgDNA mutanomes (15%). Using the tgDNA mutanome as a complementary reference, two neoepitopes were detected in one patient's plasma, albeit at the MS detection limit. Both neoepitopes were also discovered in tissue, along with three tissue-exclusive neoepitopes. Two tissue-exclusive neoepitopes induced antigen-specific T cell responses in healthy donor PBMCs. Conclusion: In summary, plasma immunopeptidomics enables profiling of HLA ligands from wild-type proteins, including TAAs. In principle, neoepitope detection from plasma at the peptide level is feasible, but tissue remains the gold standard for variant calling and neoepitope identification. Improved detection methods may enable minimally invasive approaches in the future.

Despite its relative anti-inflammatory nature, IgG4 is involved in a variety of pathological conditions such as autoimmune disease and cancer. To investigate whether the IgG4 repertoire presents any abnormalities in diseases where IgG4 autoantibodies predominate, we charted longitudinal IgG4 repertoires in health, in an IgG4-mediated autoimmune disease (AID; muscle-specific kinase myasthenia gravis (MuSK MG)), and in IgG1/IgG3 mediated AIDs (acetylcholine receptor (AChR) MG and Lambert-Eaton myasthenic syndrome (LEMS). In total, we assessed 218 samples of 69 donors using mass spectrometry-based antibody repertoire analysis, covering a timespan of up to eight years. Despite being superficially inconspicuous in clonal diversity and abundances, we detected a slightly elevated number of IgG4 clones in MuSK MG patients compared to healthy donors. Notably, this observation did not coincide with drastic repertoire changes during treatment, suggesting that a large portion of the IgG4 repertoire is not significantly affected by common MuSK MG treatment regimens. Comparing the IgG4 antibody repertoires of all donors, we found that they were exceptionally unique for each individual. Against what would be expected in the case of a constantly adapting antibody repertoire, a large portion of the IgG4 clones remained stable without any further maturation. This observation even extended to patients receiving B cell depleting or IgG modulating treatments. Our findings suggest that a dominating fraction of the IgG4 pool may be produced by long-lived plasma cells, which are unaffected by disease or medical interventions.

Tuberculosis (TB) disease consistently causes the highest number of annual deaths from infectious disease and is responsible for over 100 million disability-adjusted-life-years annually. Despite the dramatic impact on human health, TB treatments are intensive and moderately effective, while Bacille Calmette-Guerin (BCG), the primary TB vaccine strategy and the oldest vaccine in circulation, needs updating. One gap in knowledge is that the vaccine primed lung immune environment has not been systematically profiled following TB challenge, making it challenging to interpret how various vaccine strategies provide protection. Here we profiled the male and female mouse lung immune environment using Mass Cytometry by Time of Flight (CyTOF) and bacterial burden (colony forming units, CFU), to systematically identify immune cells contributing to Mycobacterium tuberculosis (Mtb) infection or vaccine-induced protection. We investigated the mouse immune system after various infection outcomes including primary Mtb infection, Mtb reinfection, Mtb challenge after BCG vaccination and Mtb challenge after vaccination with a live attenuated Mtb vaccine. Across all conditions we identified Thy1.2 expression on NK cells as a new candidate for a sex-specific correlate of protection. Our results further replicate and support known immune responses for vaccine-induced protection, such as T-cell activation and infiltration. These findings highlight the pan-immune response to vaccine-induced protection, showcase the importance of sex in rodent models of TB, and identify novel host immune candidates to protect the lung against TB disease.

CD8 T cell exhaustion during chronic infection and cancer is marked by impaired effector function and limited responsiveness to stimulation. While memory CD8 T cells can be activated TCR-independently by IL-12 and IL-18, it remains unclear whether exhausted cells, despite diminished TCR responsiveness, retain this cytokine-driven effector capacity. Here, we show that IL-12 and IL-18 stimulation induce robust IFN{gamma} production in exhausted CD8 T cells from chronic LCMV Cl13 infection, exceeding responses to antigen-specific stimulation. This activation does not result in upregulation of Tox, suggesting engagement of transcriptional circuits distinct from those promoting exhaustion. Single-cell transcriptomics revealed an innate acting T cell (TIA)-specific gene signature enriched within exhausted populations in chronic infection and tumor-infiltrating lymphocytes, particularly at the interface of intermediate and terminal exhaustion. Using heterologous Legionella pneumophila infection, we confirmed in vivo bystander responsiveness of exhausted CD8 T cells, reducing bacterial burden, highlighting their functional capacity. Our findings demonstrate that exhausted CD8 T cells retain inducible effector capacity through IL-12 and IL-18 stimulation, providing new insights into possible routes to activate exhausted T cells.

Dendritic cells (DCs) are central orchestrators of antiviral immunity but can be exploited by HIV-1 to facilitate systemic dissemination. HIV-1 recognition by CD169 triggers massive endocytosis (MEND)-related internalization of viral particles into sac-like compartments in monocyte-derived dendritic cells (MDDCs), thereby promoting trans-infection of CD4+ T cells. However, MDDCS represent only one DC subpopulation, and whether other physiologically relevant DC subsets exhibit similar behavior remains unclear. Moreover, endogenous CD169 expression and viral capture have not been fully characterized in cDC1, DC2, or pDCs, while remain unknown in DC3. We therefore investigated the contribution of these DC subsets to CD169-mediated HIV-1 capture and subsequent viral dissemination. We used flow cytometry to assess CD169 expression and viral capture across DC subsets differentiated from CD34 hematopoietic stem and progenitor cells (HSPC) obtained from bone marrow (BM) and cord blood (CB), two sources that differ in cellular maturity. Confocal microscopy was used to evaluate sac-like compartment formation following immune activation with IFN- or LPS and treatment with MEND inhibitors. Trans-infection capacity was quantified by measuring luciferase activity in TZM-bl reporter cells. We identified cDC1, DC2, DC3, moDC (similar to MDDCs), and pDC subsets following the differentiation of CD34 HSPC from both CB and BM. Among these populations, DC2, DC3, and moDC displayed high CD169 expression, which was significantly upregulated by IFN- or LPS stimulation. BM-derived DCs exhibited higher basal CD169 expression than CB-derived DCs, whereas stimulation induced greater CD169 upregulation in CB-derived DCs. DC2, DC3, and moDC efficiently captured HIV-1 particles in cultures derived from both sources, and viral uptake was further enhanced by immune activation. Viral internalization into sac-like compartments depended on CD169 binding and MEND-related mechanisms, ultimately facilitating HIV-1 transfer to target cells. DC2 and DC3 are key dendritic cell subsets that support CD169 dependent HIV-1 capture and are associated with MEND-driven internalization into sac-like compartments and subsequent viral transfer to target cells, as was previously described for moDCs. We further observed distinct basal and inducible CD169 expression profiles in BM- and CB-derived DCs, consistent with source-dependent maturation states. These results identify DC2 and DC3 as key cellular contributors to HIV-1 dissemination.

While different antigen-presenting cell (APC) populations can drive divergent T-cell fates even when presenting identical antigens (Ags), our ability to trace these specific in vivo interaction histories remains constrained by a lack of compatible molecular tools. Here, we describe an enhanced Labeling Immune Partnerships by SorTagging Intercellular Contacts (LIPSTIC) platform utilizing the immunologically inert human CD58/CD2 receptor-ligand pair (SrtA-hCD58/G5-hCD2). This system provides a modular alternative to previous LIPSTIC animal models and enables the detection and recovery of T cells following Ag-dependent interactions with distinct APC populations in vitro and in vivo. We applied this approach to interrogate the role of type 3 innate lymphoid cells (ILC3s), an unconventional ROR{gamma}t Ag-presenting population whose role in shaping Ag-specific T cells in vivo remain poorly defined. Modified LIPSTIC successfully recorded cognate interactions between ILC3s and naive CD4 T cells in the spleen and enabled direct comparison with CD4+ T cells activated by conventional dendritic cells (cDCs). Although interactions with ILC3s resulted in lower frequency of in vivo-labeled T cells than cDC2s, CD4+ T cells showed comparable cell division and expression of activation markers irrespectively of an APC type. Together, these findings establish SrtA-hCD58/G5-hCD2 as a versatile LIPSTIC receptor-ligand pair for tracking cell-cell interactions in vivo and provide a robust tool for studying how APC identity influences Ag-specific T-cell responses.

Background: Giant cell arteritis (GCA), traditionally considered T cell-driven, exhibits vascular B/plasma-cell infiltrates and altered circulating B-cell homeostasis, suggesting a pathogenic role for B cells. Relapse is common in newly diagnosed GCA (nGCA), yet predictive biomarkers remain elusive. Objective: To characterize circulating B-cell subpopulations in nGCA and assess their association with 12-month relapse. Methods: Baseline multiparametric flow cytometry was performed on peripheral blood samples from consecutive patients with nGCA and sex/age-matched healthy controls (HC). Patients received standard treatment per 2018 EULAR recommendations and were followed longitudinally. Results: 102 patients with nGCA and 102 matched HC were included. One-year outcome data were available for 55 patients, of whom 34 relapsed and 21 remained relapse-free. Baseline B-cell homeostasis differed by disease course. Non-relapsers showed reduced total CD19+ B-cell counts and contraction of most B-cell subsets, while CD27-IgD-double-negative (DN) B-cell counts remained comparable to HC. Conversely, relapsers maintained total B-cell numbers above HC despite reduced memory compartments, driven by expanded naive and DN B cells, alongside preserved plasmablast and transitional B-cell counts. At 6 months, total B-cell counts increased only in non-relapsers. DN B cells showed the greatest divergence between groups and independently predicted relapse. DN B-cell counts also correlated with circulating T peripheral helper cell numbers, supporting extrafollicular immune pathway activation. Conclusion: nGCA is characterized by outcome-dependent disturbances in B-cell homeostasis. Expansion of the DN B-cell compartment identifies a relapse-prone immunophenotype and represents a clinically relevant biomarker for early risk stratification.

Epidermodysplasia verruciformis (EV) is characterized by susceptibility to cutaneous {beta}-human papillomaviruses, persistent viral lesions and an increased risk of cutaneous squamous cell carcinoma (cSCC). We investigated whether expression of Toll-like receptors 3, 4, 5 and 9 (TLR3, TLR4, TLR5 and TLR9) differs across histological states within EV. Immunoreactivity was quantified by digital H-score using QuPath in 97 specimens from 28 patients, comprising 13 lesion-free skin samples, 15 flat warts and 69 cSCCs. Prespecified comparisons evaluated flat wart versus lesion-free skin, cSCC versus non-neoplastic tissue and invasive versus in situ cSCC, with invasive tumour differentiation assessed secondarily. Patient-clustered generalized estimating equations and false-discovery-rate (FDR) correction were used for inference. After correction for multiple testing, TLR9 H-scores were higher in flat warts than in lesion-free skin ({beta}=60.58; q=0.0332). Compared with non-neoplastic tissue, cSCC showed lower TLR3 ({beta}=-81.40; q=0.00745), higher TLR4 ({beta}=55.59; q=0.04793) and lower TLR9 expression ({beta}=-34.80; q=0.03412). TLR5 showed a nominal increase in cSCC that did not meet the FDR threshold. None of the four receptors differed significantly between invasive and in situ cSCC, and no differentiation trend remained significant after FDR correction. These findings show receptor-specific differences in TLR expression across histological states of EV, particularly involving TLR3, TLR4 and TLR9, although the diagnostic and prognostic significance of these tissue patterns remains to be established.

The generation of appropriate responses to the intestinal microbiota is an essential aspect of immune homeostasis. Studies of microbes that elicit stereotyped, antigen-specific CD4 T cell responses support the view that immune recognition of the microbiota is specific, relatively limited, and largely skewed toward Tregs, but recent profiling efforts have suggested that recognition of the microbiota may be broader and less regulatory. Such studies have mostly tracked responses to single antigens or used mice that acquire their microbiota after weaning, which has made it difficult to generalize the rules that govern microbiota-mediated T cell responses. Here we comprehensively profile, for the first time, the T cell response to the microbiota at homeostasis, and develop a panel of tools to track multiple, endogenous microbiota-reactive CD4 T cell populations in vivo. Our profiling reveals a broad microbiota-reactive T cell response that is Treg-biased but that also contains non-Treg responses to specific microbes. We find that certain microbiota-reactive T cells require priming during early-life to efficiently establish their Treg identity, while others do not. Our findings illustrate an unappreciated antigen-specific complexity in programming of microbiota-reactive T cells and underscore the importance of studying responses to the microbiota under homeostatic conditions.

Oral premalignant lesions (OPLs) are common; however, histopathological grading incompletely identifies lesions destined for cancer. To define tissue ecosystems that precede malignant transformation, we integrated single-cell-resolution Xenium spatial transcriptomics of 20 HPV-negative biospecimens from 16 patients, with independent single-cell RNA sequencing and immunofluorescence data from 38 patients with OPLs after quality control. Progressive OPLs exhibit a coordinated epithelial-immune program comprising MX1/NOTCH3-high KRT14+/KRT15+ basal epithelial states, S100A9-high inflammatory macrophages, TIGIT-high, exhaustion-associated T cells, and altered dendritic cell states. Spatial analyses showed that T cells and dendritic cells were displaced from the basal epithelial interface, and that epithelial neighborhoods were depleted of dendritic cells but enriched for TIGIT-high T cells, revealing immune reorganization not captured by cellular abundance alone. Independent single-cell and protein-level analyses reproduced basal epithelial interferon/stress programs, S100A9-associated myeloid inflammation, TIGIT-high, exhaustion-associated T-cell programs, and dendritic cell redistribution. Ligand-receptor inference suggested convergent myeloid and lymphoid signals linked to epithelial stress, checkpoint regulation, and extracellular matrix remodeling. Functionally, recombinant S100A9 accelerated wound closure in oral epithelial and cancer cells, whereas S100A9 and S100A8/S100A9 enhanced oral cancer cell proliferation. These responses were attenuated by pharmacologic inhibition of TLR4 or RAGE. Together, these data define a spatially organized, myeloid-skewed, checkpoint-enriched ecosystem present before invasion and suggest S100A9-TLR4/RAGE signaling and epithelial-immune geometry as candidate mechanisms and biomarkers for oral cancer interception.

Whether human tumor-specific CD4 T cells can drive antitumor immunity in cancers lacking tumor-cell MHC class II expression has not been established. In MHC class II-negative melanoma and breast cancer, CD4 T cells with a transcriptional signature of tumor specificity correlated with myeloid and CD8 T cell activation. Using a patient-derived NY-ESO-specific, HLA-DP04-restricted TCR, we tested whether human CD4 T cells could control tumors through indirect antigen presentation. In vitro, CD4 T cells inhibited HLA-DP-negative melanoma growth through recognition of tumor-derived antigen on antigen presenting cells (APC). In humanized mice, CD4 T cell transfer induced regression of HLA-DP-negative tumors, and control required HLA-matched human APCs. CD4 T cell transfer induced endogenous CD8 T cell proliferation and myeloid activation that mirrored immune programs correlated with the presence of these cells in patients. These findings establish that human tumor-specific CD4 T cells coordinate antitumor immunity through APC without direct tumor recognition, supporting their therapeutic relevance in MHC class II-negative cancers.

Objective: Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) frequently present as overlap syndromes, characterized by shared sexual dimorphism and elevated intestinal Veillonella dispar (V. dispar) abundance, yet exhibiting distinct hallmark pathological manifestations. This study aimed to elucidate the shared pathogenesis, phenotypic differentiation mechanisms and sex-specific predisposition of AIH and PBC induced by V. dispar. Methods: Clean-grade and germ-free (GF) mice were employed to establish AIH and PBC models. Model induction involved oral gavage of V. dispar and intraperitoneal injection of either liver-specific antigen S100 (for AIH) or a pyruvate dehydrogenase complex E2 subunit (PDC-E2) mimetic peptide (for PBC). Single-cell RNA sequencing, metabolomics, transmission electron microscopy, western blotting, and flow cytometry were utilized to elucidate the underlying mechanisms. Results: V. dispar successfully induced autoimmune liver disease-like features in mice, characterized by significant intrahepatic B cell infiltration. Mechanistically, V. dispar caused systemic arginine reduction, leading to intrinsic apoptosis of gonadal stromal cells and a subsequent reduction in testosterone. This decreased testosterone weakened its inhibitory effect on B cell activating factor (BAFF) secretion, thereby amplifying B cell-mediated immune responses. Furthermore, in the presence of S100 or PDC-E2 mimetic peptide, V. dispar also facilitated Th17 cell activation, which guided the phenotypic differentiation into AIH or PBC, respectively. Consistent with these findings, our clinical observations revealed that patients with AIH and PBC tended to harbor enriched V. dispar, along with lower serum arginine and testosterone. In addition, elevated serum levels of BAFF and IL-17 were also observed in these patients. Conclusion: V. dispar induces reduced testosterone levels and upregulation of BAFF, leading to intrahepatic B cell expansion, which serves as the common pathogenic basis for AIH and PBC. The presence of S100 and PDC-E2 subsequently drives further maturation of these expanded B cells and promotes Th17 cell activation, thereby determining the phenotypic divergence between AIH and PBC.

Autoreactive B cells must escape immune tolerance mechanisms to drive autoimmune disease, potentially through alternative paths to memory and antibody-secreting cell formation. "Atypical" B cells represent one such alternative pathway and are expanded in several human autoimmune diseases. Atypical B cells display phenotypic heterogeneity, but how this connects with differences in transcriptional programming, isotype switching and somatic hypermutation is incompletely understood in type 1 diabetes (T1D). Screening efforts to detect T1D prior to clinical diabetes onset affords an opportunity to study B cells early in immunopathogenesis, in which they primarily function as antigen-presenting cells. Prior evidence points to atypical B cell populations as reservoirs for islet autoreactivity in human T1D. We therefore developed sorting strategies to enrich for atypical and other autoreactive-prone B cell populations from the peripheral blood of early-stage T1D individuals and performed single-cell RNA/BCR-sequencing. We identified four transcriptionally defined atypical B cell clusters, each showing differential upregulation of atypical B cell defining genes. Additional gene expression changes were noted in broadly transcriptionally similar, but phenotypically distinct atypical B cell populations, with differences noted in the average extent of isotype switching and somatic hypermutation. Some atypical B cell populations showed extensive clonal sharing with classical memory or plasmablast subsets, consistent with relationships amongst these subsets. B cells reactive against a key islet autoantigen, insulin, were enriched in select atypical B cell populations. These findings highlight specific atypical B cell populations and features with potential value as biomarkers of disease progression or response to immunotherapy in T1D, and potentially other autoimmune diseases.