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bioRxiv2026

Structural and Immunological Alterations at the Human Cribriform Plate in Streptococcus pyogenes Meningitis: A Case Study

Streptococcus pyogenes or group A Streptococcus (GAS) meningitis is a rare but deadly infection with a high mortality. Its mechanisms of invasion are unknown, but it has been proposed to enter either through the cribriform plate olfactory nerve bundles or the blood brain barrier. Knowledge of how GAS impacts the cribriform plate olfactory nerves can help us better understand GAS pathogenesis and invasion, as well as how it impacts the olfactory nerve bundles. Here we present the case of a 39-year-old otherwise healthy man who presented to the local emergency department with altered mental status and expired the following day. Neuropathologic examination revealed bacterial leptomeningitis; blood and cerebrospinal fluid cultures both grew Streptococcus pyogenes. Examination of the cribriform plate was notable for perineural accumulation of GAS around certain olfactory nerve bundles. The accumulation around nerves seems to be random and not correlated to size. Nerves that are impacted by GAS as well as nerves that are not impacted display similar levels of gliosis markers GFAP and podoplanin. Neuropeptide Y, a neuropeptide that implicated in neuro-proliferation and hunger was found to colocalize with CD68 positive immune cells within the nasal epithelium, leading to speculations of its involvement in the inflammatory profile during this case of GAS meningitis. Cribriform plate skull channels had undergone width expansion within the patient, pointing towards local bone marrows involvement during infections. These findings are essential to better understanding the human cribriform plates role in CNS immune response and drainage.

neuroscience↗

bioRxiv2026

Immunological responses to hydrogel-aided induced pluripotent stem cell-derived dopaminergic progenitor transplants in immunodeficient versus cyclosporine immunosuppressed rats.

The success of stem cell-derived brain repair for Parkinsons is limited by the variable survival and poor maturation of dopaminergic progenitors after transplantation into the Parkinsonian brain. One approach that has been developed to improve this is engraftment of the cells within a neurotrophin-enriched collagen hydrogel. Although this has been shown to improve progenitor survival and maturation in athymic nude rats, the same beneficial effects of the hydrogel were not seen in cyclosporine immunosuppressed rats. To determine the reasons for these differences, the aim of this study was to assess the local and systemic immune responses to progenitor transplantation in these two recipient groups. To do so, human induced pluripotent stem cell-derived dopaminergic progenitors were transplanted into 6-hydroxydopamine-lesioned striatum of athymic or cyclosporine immunosuppressed rats. The cells were transplanted either alone, with the neurotrophins GDNF and BDNF, in an unloaded collagen hydrogel, or in a neurotrophin-loaded collagen hydrogel. Post-mortem assessment included both graft site and blood analysis of immune cell populations. As expected, nude rats showed a pronounced innate immune cell response at the graft site but no T-cell recruitment or activation locally or systemically. In contrast, while the immunosuppressed rats also showed the expected innate immune cells response to the transplant, there was also infiltration of CD4+ and CD8+ T cells at the site of transplantation as well as circulating activated T-cells. Thus, this study suggests that the benefits of the hydrogel that were seen in the athymic nude rats did not manifest in the cyclosporine immunosuppressed rats due to incomplete immunosupression. This study shows the importance of careful optimisation of the immunosuppressive regime chosen before xenotransplantation experiments.

neuroscience↗

bioRxiv2026

Human cardiomyocytes with trisomy 21 exhibit heightened susceptibility and immunological response to SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, is associated with significant cardiovascular complications, including myocardial injury and long-term cardiac dysfunction. Individuals with Down syndrome (trisomy 21) exhibit increased susceptibility to severe COVID-19 outcomes, yet the cardiomyocyte-intrinsic mechanisms underlying this vulnerability remain poorly understood. To investigate genotype-specific responses to SARS-CoV-2 infection, we generated induced pluripotent stem cell-derived cardiomyocytes from individuals with trisomy 21 and their euploid, sex-matched biological relatives. Cardiomyocytes were inoculated with SARS-CoV-2, and viral susceptibility was assessed by immunofluorescence. Bulk RNA sequencing was performed under baseline and infected conditions to define transcriptional programs associated with viral response. Trisomy 21 iPSC-CMs exhibited increased susceptibility to SARS-CoV-2 infection, with greater viral protein expression and a higher proportion of infected cardiomyocytes compared to controls. Baseline transcriptomic analysis revealed no significant differences in canonical viral entry factors including ACE2 and TMPRSS2, suggesting that differential susceptibility is not driven by entry receptor availability. Following infection, both trisomy 21 and euploid control groups activated conserved antiviral pathways; however, trisomy 21 cardiomyocytes displayed a markedly amplified transcriptional response, with substantially greater numbers of differentially expressed genes. Upregulated pathways included interferon signaling, NF-{kappa}B activation, cytokine and chemokine signaling, and innate immune responses, while downregulated pathways were enriched for cardiomyocyte structural integrity, calcium handling, and metabolic processes. Notably, inflammatory and cytokine-related transcripts were significantly more elevated in trisomy 21 cells, consistent with an exaggerated immune response. These findings provide mechanistic insight into the increased cardiovascular risk observed in individuals with Down syndrome and highlight dysregulated immune signaling as a potential therapeutic target in this high-risk population.

Cell Biology↗

bioRxiv2026

Tuning T-cell immunological synapse by modular DNA-Nanobody engagers for precision immunotherapy

Bispecific T-cell engagers (TCEs) are a promising class of cancer immunotherapies, but their clinical use is limited by toxicity and insufficient specificity. Tuning the T cell- tumor interface through engager architecture may address these drawbacks. To this end, we engineered hybrid constructs composed of two nanobodies targeting CD3 and the model tumor antigen HER2, respectively, connected by rigid DNA linkers of variable length. Using cytotoxicity assays and hybrid biophysical platforms, we demonstrate a linker-length dependence of cell spreading on antigen, target killing and cytokine release, revealing a functional decoupling between killing and cytokine secretion, and implicating the glycocalyx as a key player. Through the addition of EGFR targeting, we also generate trispecific constructs implementing an "OR-gate" logic to address tumor heterogeneity and reduce resistance due to antigen loss. Overall, these versatile constructs show great therapeutic promise, and at the same time serve as platforms to test hypotheses on biophysical mechanisms.

synthetic biology↗

bioRxiv2025

Tensor-Based Integration of Time-Series Measurements Reveals Relationships Between Underlying Disease, Early Injury, and CD4+ Polarization in Liver Transplantation

For patients with end-stage liver failure, liver transplantation (LT) remains the standard-of-care, though five-year allograft survival rates remain below 80%. Liver ischemia reperfusion injuries (LIRI) arise during transplant and contribute to allograft dysfunction. While many drivers of LIRI have been well-characterized, the relationships between LIRI and later immunological signatures remain poorly understood, possibly because of limited integrated studies examining immunological signatures across the LT process. Furthermore, the role of underlying disease in LT remains poorly understood as it is unknown if later immunological signatures are universal or etiology dependent. To better examine etiology- and LIRI-driven immunological mechanisms across the LT lifetime, we collected cytokine and liver function test (LFT) measurements from LT donors and recipients at multiple pre- and post-operative timepoints. By developing a tensor-based factorization method to integrate these longitudinal measurements, we reduced the datasets to four immunological signatures that manifested across cytokines, LFTs, and time. Correlative analyses revealed associations between these integrated immunological signatures with etiology and LIRI. Later integration of allograft survival into this factorization method reduced these four signatures to two that were predictive of five-year allograft survival. Examination of these signatures prognostic of allograft survival found that CD4+ hyperpolarization towards Th1 or Th2 subtypes impaired growth factor expression and led to increased allograft loss risk. Clinical correlates revealed that donor and recipient age alongside etiology and donor liver health modulate this balance of CD4+ polarization in LT. Collectively, these results link immunological mechanisms to etiology and LIRI offering immediately actionable clinical insights alongside etiology- and donor-specific therapeutic targets for improving LT outcomes.

immunology↗

bioRxiv2025

EpImAge: An Epigenetic-Immune Clock for Disease-Associated Biological Aging

BackgroundWe present EpImAge, an explainable deep learning tool that integrates epigenetic and immunological markers to create a highly accurate, disease-sensitive biological age predictor. This novel approach bridges two key hallmarks of aging - epigenetic alterations and immunosenescence. MethodsFirst, epigenetic and immunologic data from the same participants was used for AI models predicting levels of 24 cytokines from blood DNA methylation. Second, open-source epigenetic data (25 thousand samples) was used for generating synthetic immunological biomarkers and training an age estimation model. ResultsUsing state-of-the-art deep neural networks optimized for tabular data analysis, EpImAge achieves competitive performance metrics against 33 epigenetic clock models, including an overall mean absolute error of 7 years and a Pearson correlation of 0.85 in healthy controls, while demonstrating robust sensitivity across multiple disease categories. Explainable AI revealed the contribution of each immunological feature to the age prediction. ConclusionsThe sensitivity to multiple diseases due to combining immunologic and epigenetic profiles is promising for both research and clinical applications. EpImAge is released as an easy-to-use web tool that generates the age estimates and levels of immunological parameters for methylation data, with the detailed report on the contribution of input variables to the model output for each sample.

systems biology↗

bioRxiv2026

Functional Immuno-metagenomics Seizes the Alteration of Microbiota-Immune Interactions at the Early Onset of Multiple Sclerosis

Aberrant health states are characterized by an alteration in microbial composition. Gut microbiota shapes the immune response and potential abnormal host-microbiota interactions warrant inclusion into the framework for identifying a distorted microbiota. Here, we decipher the host surveillance system based on IgA-microbe interactions and leverage it to develop the species Immunomodulatory score (IMscore) to assess immunological imprint based on species IgA opsonisation, abundance and prevalence. We demonstrate its advantage in depicting core immunologically active gut microbiota composed of known and yet-to-be-characterized species across three independent cohorts. We then aggregated IMscores into a global Immunologically active Gut microbiota index (IMGindex) to quantify symbiotic or aberrant microbe-immune interactions at whole community level. We demonstrate IMGindex robustness in depicting altered microbe-immune crosstalk at the early onset of Multiple Sclerosis. Our proof-of-concept study demonstrates the importance of monitoring antibody vigilance over enteric microbes for personalised assessment of gut microbiota health. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=180 SRC="FIGDIR/small/699307v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1beec85org.highwire.dtl.DTLVardef@19a2b54org.highwire.dtl.DTLVardef@929cb8org.highwire.dtl.DTLVardef@16f29aa_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights and eTOC blurbHighlights 1) IMscore measures immunological imprint of known and uncharacterized species 2) IMscore highlights a core immunologically active gut microbiota 3) IMscore is translated into a community level IMGindex to measure microbiome health 4) IMGindex identifies aberrant microbe-immune responses at the early onset of MS eTOC blurb Nthuku et al. developed an approach to measure a distorted gut microbiota based on the antibody surveillance system over enteric microbes. An immunological imprint for each known and yet-to-be-characterised microbe was assessed and, then, transformed into a global community index for personal monitoring of gut dysbiosis.

microbiology↗

bioRxiv2020

Crystal structure of the giant panda MHC class I complex: first insights into the viral peptide presentation profile in the bear family

The viral cytotoxic T lymphocyte (CTL) epitope peptides presented by classical MHC-I molecules require the assembly of a peptide-MHC-I-{beta}2m (aka pMHC-I) trimolecular complex for TCR recognition, which is the critical activation link for triggering antiviral T cell immunity. Ursidae includes 5 genera and 8 species; however, research on T cell immunology in this family, especially structural immunology, is lacking. In this study, the structure of the key trimolecular complex pMHC-1 (aka pAime-128), which binds a peptide from canine distemper virus, was solved for the first time using giant panda as a representative species of Ursidae. The structural characteristics of the giant panda pMHC-I complex, including the unique pockets in the peptide-binding groove (PBG), were analyzed in detail. Comparing the panda pMHC-I to others in the bear family and extending the comparison to other mammals revealed distinct features. The interaction between MHC-I and {beta}2m, the features of pAime-128 involved in TCR docking and CD8 binding, the anchor sites in the PBG, and the CTL epitopes of potential viruses that infect pandas were concretely clarified. Unique features of pMHC-I viral antigen presentation in the panda were revealed by solving the three-dimensional structure of pAime-128. The distinct characteristics of pAime-128 indicate an unusual event that emerged during the evolution of the MHC system in the bear family. These results provide a new platform for research on panda CTL immunity and the design of vaccines for application in the bear family. IMPORTANCEUrsidae includes 5 genera and 8 species; however, the study of its immunology, especially structural immunology, is extremely rare to date. In this paper, we first crystallized the key complex pMHC-I, taking the giant panda as its representative species. Structural characteristics of the giant panda pMHC-I complexes, contains the unique pockets of PBG were analyzed in detail. Comparison of the panda pMHC-I in the bear family and other mammals, almost definite features was displayed. Meanwhile, the interaction between HC and LV, the unique features of pMHC-I in the CD8 binding and TCR docking, validation of anchor site in the PBG, and epitopes of potential viruses infected with the pandas, were concretely clarified. These unique characteristics of pMHC-I clearly indicate an unusual situation during the evolution of MHC molecules in the endangered pandas. These results also provide a novel platform for further study of panda T cell immunology and vaccines.

immunology↗

bioRxiv2022

Carbon ion irradiation plus CTLA4 blockade elicits therapeutic immune responses in a murine tumor model

Radiotherapy can act as an in situ vaccine thereby activating tumor-specific immune responses that prevent tumor outgrowth in treated patients. While carbon ion radiotherapy has shown superior biophysical properties over conventional photon irradiation, the immunological effects induced have remained largely uncovered. The combination of radiotherapy with immune checkpoint inhibition (radioimmunotherapy) aims at further enhancement of anti-tumor immunity; however, studies on the immune cell composition in irradiated and distant tumors following radioimmunotherapy with carbon ions are scarce. We have established a bilateral tumor model by time shifted transplantation of murine, Her2+ EO771 tumor cells onto the flanks of immune competent mice followed by selective irradiation of the primal tumor, while sparing the consecutive tumor. We demonstrate that CTLA4-but not PD-L1-based radioimmunotherapy induces complete tumor rejection in our model. Intriguingly, local tumor control caused in situ immunization resulting even in eradication of non-irradiated, distant tumors. Moreover, cured mice were protected against EO771 rechallenge indicative of long lasting, tumor-protective immunological memory. Deconvolution of the treatment induced immunological effects by single cell RNA-sequencing (scRNA-seq) and concomitant flow cytometric analyses revealed in irradiated tumors predominating myeloid cells that developed into distinct tumor-associated macrophage clusters with upregulated expression of TNF and IL1 responsive genes, as well as activation of NK cells. Non-irradiated tumors showed higher frequencies of naive T cells in irradiated mice, which were activated when combined with CTLA4 blockade. In conclusion, radioimmunotherapy with carbon ions plus CTLA4 inhibition reshapes the tumor-infiltrating immune cell composition and can induce complete rejection even of non-irradiated tumors. Our data present a rationale to combine radiotherapy approach with CTLA4 blockade to achieve durable anti-tumor immunity. Evaluation of future radioimmunotherapy approaches should thus not only focus on the immunological impacts at the site of irradiation but should also consider systemic immunological effects that might affect outgrowth of non-irradiated tumors.

immunology↗

bioRxiv2021

The Immune Signatures Data Resource: A compendium of systems vaccinology datasets

Vaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines, including those targeting seasonal influenza, yellow fever, and hepatitis B. These data are made available to the broader scientific community through the ImmuneSpace data portal and analysis engine leveraging the NIH/NIAID ImmPort repository1,2. However, a barrier to progress in this area is that comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines and includes transcriptional profiles and antibody response measurements. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses. [Table 1]

systems biology↗

bioRxiv2022

ePlatypus: an ecosystem for computational analysis of immunogenomics data

The maturation of systems immunology methodologies requires novel and transparent computational frameworks capable of integrating diverse data modalities in a reproducible manner. Here, we present the ePlatypus computational immunology ecosystem for immunogenomics data analysis, with a focus on adaptive immune repertoires and single-cell sequencing. ePlatypus is a web-based platform and provides programming tutorials and an integrative database that elucidates selection patterns of adaptive immunity. Furthermore, the ecosystem links novel and established bioinformatics pipelines relevant for single-cell immune repertoires and other aspects of computational immunology such as predicting ligand-receptor interactions, structural modeling, simulations, machine learning, graph theory, pseudotime, spatial transcriptomics and phylogenetics. The ePlatypus ecosystem helps extract deeper insight in computational immunology and immunogenomics and promote open science. Accessibilityhttps://alexyermanos.github.io/Platypus/index.html

immunology↗

bioRxiv2023

Antibody-mediated depletion of select T cell subsets in blood and tissue of nonhuman primates

Understanding the immunological control of pathogens requires a detailed evaluation of the mechanistic contributions of individual cell types within the immune system. While knockout mouse models that lack certain cell types have been used to help define the role of those cells, the biological and physiological characteristics of mice do not necessarily recapitulate that of a human. To overcome some of these differences, studies often look towards nonhuman primates (NHPs) due to their close phylogenetic relationship to humans. To evaluate the immunological role of select cell types, the NHP model provides distinct advantages since NHP more closely mirror the disease manifestations and immunological characteristics of humans. However, many of the experimental manipulations routinely used in mice (e.g., gene knock-out) cannot be used with the NHP model. As an alternative, the in vivo infusion of monoclonal antibodies that target surface proteins on specific cells to either functionally inhibit or deplete cells can be a useful tool. Such depleting antibodies have been used in NHP studies to address immunological mechanisms of action. In these studies, the extent of depletion has generally been reported for blood, but not thoroughly assessed in tissues. Here, we evaluated four depleting regimens that primarily target T cells in NHP: anti-CD4, anti-CD8, anti-CD8{beta}, and immunotoxin-conjugated anti-CD3. We evaluated these treatments in healthy unvaccinated and IV BCG-vaccinated NHP to measure the extent that vaccine-elicited T cells - which may be activated, increased in number, or resident in specific tissues - are depleted compared to resting populations in unvaccinated NHPs. We report quantitative measurements of in vivo depletion at multiple tissue sites providing insight into the range of cell types depleted by a given mAb. While we found substantial depletion of target cell types in blood and tissue of many animals, residual cells remained, often residing within tissue. Notably, we find that animal-to-animal variation is substantial and consequently studies that use these reagents should be powered accordingly.

immunology↗

bioRxiv2024

Adults patients with autoinflammation of unknown origin partially phenocopy the immune presentation of Still's disease

Autoinflammation of unknown origin remains amongst the most enigmatic of systemic autoinflammatory disorders (SAIDs), immunological disorders characterized by inappropriate activation of the innate immune response. Recent clinical research has identified multiple distinct disorders, although overlap in clinical characteristics and genetic drivers impede rapid and precise diagnosis, and the immunological underpinning of disease is poorly understood. Here we aimed to understand the immunological process behind patients with autoinflammation of unknown origin. In a multi-center European trial, we collected samples from 36 patients with recent disease activity, and used deep immunophenotyping and plasma proteomics to compare to 58 healthy controls and an additional demographically-similar 92 SAID patients. Key immunological changes were upregulation of CD38 and HLA across T cell subsets and upregulation of acute phase plasma proteins in autoinflammation of unknown origin patients. These previously poorly characterised patients partially phenocopied the Stills disease presentation. Together this study identifies potential biomarkers and disease-mediators in autoinflammation of unknown origin.

immunology↗

bioRxiv2025

SLAMF6 enables efficient attachment, synapse formation, and killing of HIV-1-infected CD4+ T cells by virus-specific CD8+ T cells

Efficient recognition and elimination of HIV-1-infected CD4+ T cells by cytotoxic CD8+ T cells (CTLs) require target cell engagement and the formation of a well-organized immunological synapse. Surface proteins belonging to the SLAM family are known to be crucial for stabilizing the immunological synapse and regulating antiviral responses during lymphotropic viral infections. In the context of HIV-1, there have been reports of SLAMF6 down-regulation in HIV-1-infected CD4+ T cells; however, the significance of this modulation for CTL function remains unclear. In this investigation, we used CTL lines from People living with HIV (PLWH) to examine the impact of SLAMF6 blockade on three pivotal processes: (1) the formation of CD8+-CD4+ T-cell conjugates, (2) the establishment of the immunological synapse, and (3) the killing and cytokine production capacity of HIV-1-specific CTLs during HIV-1 infection. Our findings reveal that the inability to form CD8+-CD4+ T-cell conjugates following incubation with an anti-SLAMF6 blocking antibody is primarily attributable to a defect in actin ring formation at the immunological synapse. Furthermore, SLAMF6 blockade leads to a reduction in the killing efficiency of HIV-1-infected CD4+ T cells by HIV-1-specific CTLs, underscoring the critical role of SLAMF6 in cytolytic function. This study highlights the importance of SLAMF6 receptors in modulating cytotoxic antiviral responses, shedding light on potential avenues for manipulation and enhancement of this pathway in the context of HIV and other lymphotropic viral infections.

immunology↗

bioRxiv2025

Selective targeting of IL-1RAP-dependent eosinophilic inflammation in allergic fungal airway disease

It is estimated that in excess of 10 million people around the globe are affected by severe asthma and fungal sensitisation (SAFS) or allergic bronchopulmonary aspergillosis (ABPA), severe asthma endotypes driven by hypersensitivity to environmentally ubiquitous fungal pathogens, primarily Aspergillus fumigatus. Here, we sought to define the immunological pathways underlying these allergic fungal airway diseases. To do so, we exploit the chronic exposure repeat challenge model using live A. fumigatus conidia to systematically define the key immunological pathways driving airway inflammation in allergic fungal airway disease. In response to daily intranasal challenge, we observed increased absolute numbers of neutrophils and eosinophils in bronchoalveolar lavage fluid (BALF), characteristic of human allergic fungal airway disease, with significant depletion of the alveolar macrophage population. Transcriptomic analysis of BALF cells identified increased expression of IL-1 family cytokines and receptors including IL-1{beta}, IL-1RL1, IL-1R2 and the IL-18 binding protein. Complementary proteomic analysis of BALF revealed increased levels of cell death related proteins calprotectin and IL-1 Receptor Accessory Protein (IL-1RAP). Targeting IL-1RAP, using knockout mice, led to selective reduction in eosinophilia, IL-5 and IL-13 in the airways without impairment of fungal killing. This study identifies a role for IL-1RAP in the generation of eosinophilia independent of neutrophil influx and highlights its potential as a novel immunotherapeutic target for the treatment of allergic fungal airway disease. Author SummaryAllergic bronchopulmonary aspergillosis (ABPA) is a form of lung disease primarily affecting those with asthma or cystic fibrosis induced by the ubiquitous pathogen Aspergillus fumigatus. Understanding the immunological mechanisms contributing to this airway disease is important for the development of novel treatments to improve quality of life and preserve lung function. In this study, we show that an Aspergillus fumigatus repeat challenge model phenocopies immunological features of allergic fungal airway disease and is hallmarked by increased IL-1 family signalling. We identify the IL-1RAP as a contributor to eosinophilia and the release of Type 2 cytokines during allergic fungal airway disease. This work represents major step in describing the molecular mechanisms of airway eosinophilia in response to fungal exposure and lays the groundwork for further dissection of inflammatory pathways to target with immunotherapeutic approaches.

immunology↗

bioRxiv2025

Minimal immune cell subset differences in a cohort of close contacts of tuberculosis index cases

Understanding the perturbations in immune response across the spectrum of TB infection is still unclear. In this study, we followed a cohort of close contacts of pulmonary TB patients with serial QFT testing at 0, 3, 6, and 12 months, and stratified them into six subgroups: QFT-increasing (low/high), QFT converters (QFT- to QFT+), QFT+ stable, and QFT- individuals. Despite these distinct QFT trajectories, we observed minimal differences in immune cell frequencies, activation profiles, and T helper subset distributions among the QFT subgroups, suggesting limited immunological stratification based on QFT dynamics alone. Ex vivo immune phenotyping, including analysis of CD4, CD8, and NKT cell frequencies, memory T cell subsets, and activated T cells (HLA-DRCD38), failed to distinguish between QFT subgroups. Antigen-specific CD4 T cell responses assessed by the activation-induced marker (AIM) assay were elevated in QFT+ compared to QFT- individuals. These findings suggest that blood-based immune profiling may not capture subtle immunological transitions among QFT converters or individuals with increasing QFT responses. In contrast, individuals with active TB (ATB) showed clear immune perturbations. ATB patients at diagnosis exhibited significantly elevated frequencies of antigen-specific CD4 T cells, increased activated T cells, and higher frequencies of intermediate monocytes and NK cells compared to QFT+/QFT- contacts. Many of these immune features declined with treatment, indicating therapy-associated immune resolution. Additionally, shifts in T helper subsets and effector memory populations were observed over the course of treatment. These results suggest that while ex vivo immune profiling can robustly distinguish active TB from non-diseased states, it lacks the resolution to differentiate QFT subgroups based on QFT dynamics alone. This could reflect either immunological similarity among close contacts regardless of QFT status or limitations of blood-based phenotyping in detecting early or subclinical immune shifts. Our study highlights the challenge of immunologically distinguishing QFT-defined subgroups within close contacts using conventional ex vivo profiling approaches.

immunology↗

bioRxiv2025

Decades-long elevation of interferon-alpha drives a Sjogren disease endotype: an interdisciplinary study

BACKGROUNDMechanistic heterogeneity is a major obstacle to the development of effective treatment for Sjogren disease (SjD) and there is a pressing need to stratify SjD according to precision medicine principles. Aberrant activation of the type I interferon (IFN) pathway represents a leading candidate pathway, but a causal role of elevated IFN- in driving a Sjogren disease endotype remains to be established. METHODSWe used ultrasensitive single molecule ELISA, and an oligoprotein interferon signature score (derived from broad capture proteomics), to study the role of IFN- in Sjogren disease. We analysed samples from the UK Primary Sjogren Syndrome Registry (UKPSSR, n=177) and UK Biobank Plasma Proteomics Project (n=47606 without Sjogren, n=257 with Sjogren, including 137 individuals sampled prior to diagnosis) to determine the timecourse and immune endotype associated with elevated IFN-. To address causality we created a new transgenic mouse model of IFN- overexpression to establish whether chronically elevated IFN- drives this immune endotype. FINDINGSOligoprotein interferon signatures can be detected at least 14 years prior to diagnosis of Sjogren disease in the UK Biobank-PPP. IFN- concentrations are elevated in 60% of Sjogren disease patients in the UKPSSR. Individuals with elevated IFN- display a distinct immunological endotype characterised by cytopenias, hypergammaglobulinaemia, multiple autoantibodies and autoimmunity against the Sjogren autoantigen TRIM21/Ro52. To address the key question of causal direction, we created a new mouse model of systemic chronic IFN- elevation, in which Ifn4 is overexpressed by conventional dendritic cells. This model recapitulates key features of the endotype and can be partially reversed by IFNAR1 blockade. INTERPRETATIONElevation of IFN- drives an immune endotype of Sjogren disease, originating over a decade prior to diagnosis. SjD patients with elevated IFN- concentrations are broadly clinically similar to those with normal IFN- concentrations, yet are immunologically distinct. This highlights the mechanistic heterogeneity of SjD and the need for immunological stratification along precision medicine principles, using high resolution biomarkers. As well as demonstrating causal direction, biological modelling shows that chronic IFN- elevation over the lifecourse has the potential to establish persistent immune dysregulation which responds only partially to interferon receptor blockade. These findings provide insights into SjD and other "interferonopathic" rheumatological disorders. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched MEDLINE for "Sjogrens Syndrome/Disease" and "interferon", including the terms "subsets", "sub-groups", "phenotypes", and "endotypes", filtering by "clinical trial", "stratification", and "immune-mediated inflammatory". We also included major review articles from noted experts. We identified reports of associations between IFN- and SjD, usually using indirect or imprecise measures of IFN-. None of these studies included prediagnostic samples and causal inference was limited. Added value of this studyThis study shows that IFN-, when measured directly using ultrasensitive single molecule ELISA approaches (uniquely optimised to determine healthy control concentrations), is elevated in a subset of people with SjD with a specific immunological endotype. Analysis of prediagnostic proteomics shows this elevation can be detected up to 14 years before diagnosis. We show that IFN- drives this endotype (as opposed to vice versa) by recapitulating key endotype features in a novel and unambiguous experimental mouse model of chronic IFN- elevation. We also show that the pathogenic consequences of IFN- elevation over long periods of time can only be partially reversed using IFNAR blockade. Implications of all the available evidenceThese data have important implications for future research, clinical practice, trial design, and therapeutic development. First, our findings provide clinical evidence, supported by unambiguous preclinical evidence, that decades-long elevated IFN can cause and drive a SjD endotype - and accurately defines the level of heterogeneity. Secondly, we provide biomarkers which may be of use in stratifying clinical trial design and also for early identification of at-risk individuals. Thirdly we provide biological proof of principle that longstanding and potentially undiagnosed elevation of IFN- can establish persistent immune dysregulation which may respond only partially to IFNAR blockade. Together these findings inform precision medicine approaches and future trial design.

immunology↗

bioRxiv2018

Comparative analysis of cellular immune responses in conventional and SPF Baboons (Papio spp.)

Baboons (papio spp.) have served as a successful model of human disease such as cardiac and respiratory, infectious, diabetes, genetics, immunology, aging, and xenotransplantation. The development of an immunologically defined specific-pathogen free (SPF) baboon model has further advanced research, especially with studies involving the immune system and immunosuppression. In this study, we compare normal immunological changes of peripheral blood mononuclear cell (PBMC) subsets, and their function in age-matched conventional and SPF baboons. Our results demonstrate that both groups have comparable numbers of different lymphocyte subsets, but there are phenotypic differences in central and effector memory T cells subsets that are more pronounced in the CD4+ T cells. Despite equal proportions of CD3+ T cells among the conventional and SPF baboon groups, PBMC show higher proliferative responses to mitogens PHA and PWM and higher IFN-{gamma} producing cells to Con A and PWM in the conventional group. Plasma levels of the inflammatory cytokine TNF- were significantly higher in SPF baboons. Exposure of PBMC from conventional baboons to various Toll like ligands (TLR ligands) TLR-3, TLR-4 and TLR-8 show higher IFN-{gamma} producing cells while PBMC from SPF baboons stimulated with TLR-5 and TLR-6 ligand show higher IFN-{gamma} producing cells. These findings suggest that while the lymphocyte subsets in conventional and SPF baboons share many phenotypic and functional similarities, specific differences exist in immune function of lymphocytes which could impact the quality and quantity of innate and adaptive immune responses. These differences should be considered for better experimental outcomes, specifically in studies measuring immunological endpoints.

immunology↗