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Results for “immunology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 325 records · Page 18Linked to original sources

bioRxiv2021

Miltefosine enhances infectivity of miltefosine-resistant Leishmania infantum by attenuating innate immune recognition

Miltefosine (MIL) is currently the only oral drug available to treat visceral leishmaniasis but its use as first-line monotherapy has been compromised by an increasing treatment failure. Despite the scarce number of resistant clinical isolates, MIL-resistance by mutations in a single aminophospholipid transporter gene can easily be selected in a laboratory environment. These mutations result in a reduced survival in the mammalian host, which can partially be restored by exposure to MIL, suggesting a kind of drug-dependency. To enable a combined study of the infection dynamics and underlying immunological events for differential in vivo survival, firefly luciferase (PpyRE9) / red fluorescent protein (DsRed) double-reporter strains were generated of MIL-resistant (MIL-R) and syngeneic MIL-sensitive (MIL-S) Leishmania infantum. Results in C57Bl/6 and BALB/c mice show that MIL-R parasites induce an increased innate immune response that is characterized by enhanced influx and infection of neutrophils, monocytes and dendritic cells in the liver and elevated serum IFN-{gamma} levels, finally resulting in a less efficient establishment in liver macrophages. The elevated IFN-{gamma} levels were shown to originate from an increased response of hepatic NK and NKT cells to the MIL-R parasites. In addition, we demonstrated that MIL could increase the in vivo fitness of MIL-R parasites by lowering NK and NKT cell activation, leading to a reduced IFN-{gamma} production. These data provide an immunological basis for the MIL-R-associated attenuated phenotype and for the peculiar drug-dependency that may constitute one of the mechanisms of treatment failure. ImportanceRecently, our laboratory demonstrated an in vivo fitness loss of experimentally selected MIL-R parasites in both the sand fly vector and vertebrate host. These findings could explain the scarce number of MIL-R clinical isolates. Surprisingly, MIL-R parasites developed a MIL-dependency which could partially rescue their fitness loss and which may constitute a mechanism of treatment failure. This research aimed to better understand the immunological basis of the attenuated phenotype and the effect of MIL on infectivity traits. Together, this study provides new insights into the complex interplay between the parasite, drug and host and discloses an immune-related mechanism of treatment failure.

microbiology↗

bioRxiv2021

A lipid nanoparticle RBD-hFc mRNA vaccine protects hACE2 transgenic mice against lethal SARS-CoV-2 infection

The current global COVID-19 pandemic led to an unprecedented effort to develop effective vaccines against SARS-CoV-2. mRNA vaccines were developed very rapidly during the last year, and became the leading immunization platform against the virus, with highly promising phase-3 results and remarkable efficacy data. Since most animal models are not susceptible to SARS CoV-2 infection, pre-clinical studies are often limited to infection-prone animals such as hamsters and non-human primates. In these animal models, SARS-CoV-2 infection results in viral replication and a mild disease disease. Therefore, the protective efficacy of the vaccine in these animals is commonly evaluated by its ability to elicit immunologic responses, diminish viral replication and prevent weight loss. Our lab recently reported the design of a SARS-CoV-2 human Fc-conjugated receptor-binding domain (RBD-hFc) mRNA vaccine delivered via lipid nanoparticles (LNPs). These experiments demonstrated the development of a robust and specific immunologic response in RBD-hFc mRNA-vaccinated BALB/c mice. In the current study, we evaluated the protective effect of this RBD-hFc mRNA vaccine by employing the K18-hACE2 mouse model. We report that administration of RBD-hFc mRNA vaccine to K18-hACE2 mice led to a robust humoral response comprised of both binding and neutralizing antibodies. In accordance with the recorded immunologic immune response, 70% of vaccinated mice were protected against a lethal dose (3000 plaque forming units) of SARS-CoV-2, while all control animals succumbed to infection. To the best of our knowledge, this is the first non-replicating mRNA vaccine study reporting protection of K18-hACE2 against a lethal SARS-CoV-2 infection.

microbiology↗

bioRxiv2021

The Immune landscape of solid pediatric tumors.

BackgroundImmunotherapy is quickly coming to the forefront of cancer treatment; however, the implementation of immunotherapy in solid pediatric cancers, which classically display a low mutational load, is hindered by insufficient understanding of the determinants of cancer immune responsiveness in children. In order to better understand tumor-host interplay, we sought to characterize solid pediatric cancers based on immunological parameters using analytes extracted from gene expression data. MethodsWe used RNAseq data from the publicly available TARGET studies for five pediatric solid tumor types (408 patients): Wilms tumor (WT), neuroblastoma (NBL), osteosarcoma (OS), clear cell sarcoma of the kidney (CCSK) and rhabdoid tumor of the kidney (RT). We assessed the performance of previously identified immune signatures like the Immunologic Constant of Rejection (ICR), which captures an active Th1/cytotoxic response associated with favorable prognosis and responsiveness to immunotherapy. We also performed gene set enrichment analysis (ssGSEA) and clustering, using more than 100 immune signatures to define immune subtypes in pediatric tumors and compared the overall survival across subtypes. The expression of immune checkpoints and enrichment of oncogenic pathways were also assessed across the immune subtypes. ResultsThe five tumor types showed distinct ICR score distributions. A higher ICR score was associated with better survival in OS and NBL-HR-MYCN_NA, but with poorer survival in WT. The clustering of immune signatures revealed the same five principal modules observed in adult solid tumors: Wound Healing, TGF-B signaling, IFN-G signaling, Macrophages, and Lymphocytes. These modules clustered pediatric patients into six immune subtypes (S1-S6) with distinct survival outcomes. The S2 cluster showed the best overall survival and was characterized by low enrichment of the wound healing signature, high Th1, low Th2. Conversely, cluster S4 showed the worst survival and highest enrichment of wound healing signature, low Th1, and high Th2. Furthermore, the upregulation of the WNT/Beta-catenin pathway is associated with unfavorable outcomes and lack of T-cell infiltration in OS. ConclusionsWe demonstrated that extracranial solid pediatric tumors could be classified according to their immune disposition, unveiling similarity with adults tumors. Immunological parameters might be explored to refine diagnostic and prognostic biomarkers and to identify potential immune-responsive tumors.

cancer biology↗

bioRxiv2021

Spontaneous control of SIV replication does not prevent immune dysregulation and bacterial dissemination in animals co-infected with M. tuberculosis

Individuals infected with both HIV and Mycobacterium tuberculosis (Mtb) are more likely to develop severe Tuberculosis (TB) disease than HIV-naive individuals. To understand how a chronic pre-existing Simian immunodeficiency virus (SIV) infection impairs the early immune response to Mtb, we used the Mauritian cynomolgus macaque (MCM) model of SIV/Mtb co-infection. We examined the relationship between peripheral viral control and Mtb burden, Mtb dissemination, and immunological function between SIV+ spontaneous controllers, SIV+ non-controllers, and SIV-naive MCM who were challenged with a barcoded Mtb Erdman strain and necropsied six weeks post infection. Mycobacterial burden was highest in the SIV+ non-controllers in all assessed tissues. In lung granulomas, we found the frequency of CD4+ T cells producing TNF was reduced in all SIV+ MCM, but CD4+ T cells producing IFN{gamma} were only lower in the SIV+ non-controllers. Further, while all SIV+ MCM had more PD1+ and TIGIT+ T cells in the lung granulomas relative to SIV-naive MCM, SIV+ controllers exhibited the highest frequency of cells expressing these markers. To measure the effect of SIV infection on within-host bacterial dissemination, we sequenced the molecular barcodes of Mtb present in each tissue and characterized the complexity of the Mtb populations. While Mtb population complexity was not associated with infection group, lymph nodes had increased complexity when compared to lung granulomas across all groups. These results provide evidence SIV+ animals, independent of viral control, exhibit dysregulated immune responses and enhanced dissemination of Mtb, likely contributing to the poor TB disease course across all SIV/Mtb co-infected animals. ImportanceHIV and TB remain significant global health issues, despite the availability of treatments. Individuals with HIV, including those who are virally suppressed, are at an increased risk to develop and succumb to severe TB disease when compared to HIV-naive individuals. Our study aims to understand the relationship between SIV replication, mycobacterial growth, and immunological function in the tissues of co-infected Mauritian cynomolgus macaques during the early phase of Mtb infection. Here we demonstrate that increased viral replication is associated with increased bacterial burden in the tissues and impaired immunologic responses, and that the damage attributed to virus infection is not fully eliminated when animals spontaneously control virus replication.

microbiology↗

bioRxiv2022

Generating an in vitro gut model with physiologically relevant biophysical mucus properties

IntroductionGastrointestinal (GI) in vitro models have received lasting attention as an effective tool to model drug and nutrient absorption, study GI diseases, and design new drug delivery vehicles. A complete model of the GI epithelium should at a minimum include the two key functional components of the GI tract: mucus and the underlying epithelium. Mucus plays a key role in protecting and lubricating the GI tract, poses a barrier to orally administered therapies and pathogens, and serves as the microenvironment for the GI microbiome. These functions are reliant on the biophysical material properties of the mucus produced, including viscosity and pore size. MethodsIn this study, we generated in vitro models containing Caco-2 enterocyte-like cells and HT29-MTX goblet-like cells and determined the effects of coculture and mucus layer on epithelial permeability and biophysical properties of mucus using multiple particle tracking (MPT). ResultsWe found that mucus height increased as the amount of HT29-MTX goblet-like cells increased. Additionally, we found that increasing the amount of HT29-MTX goblet-like cells within culture corresponded to an increase in mucus pore size and mucus microviscosity, measured using MPT. When compared to ex vivo mucus samples from mice and pigs, we found that a 90:10 ratio of Caco-2:HT29-MTX coculture displayed similar mucus pore size to porcine jejunum and that the mucus produced from 90:10 and 80:20 ratios of cells shared mechanical properties to porcine jejunum and ileum mucus. ConclusionsGI coculture models are valuable tools in simulating the mucus barrier and can be utilized for a variety of applications including the study of GI diseases, food absorption, or therapeutic development. BiographyDr. Maisel joined the University of Maryland in January 2019 having done interdisciplinary training in nanotechnology, mucosal immunology, lymphatic immunology, and immunoengineering. She completed her PhD in Biomedical Engineering at the Johns Hopkins University in 2014 after which she was an NIH postdoctoral fellow at the University of Chicago in Molecular Engineering and Immunology. The Maisel Lab uses in vitro modeling, nanotechnology, and immunoengineering approaches to study and develop treatments for diseases at mucosal surfaces. They are interested in designing nanoparticles to take advantage of and study the interface between biological barriers, particularly the lymphatics, interstitial tissue, and mucosal surfaces, and nanoparticles. Dr. Maisel has won a number of awards, including NSF GRFP and NIH F32 fellowships as a trainee, the American Lung Association Dalsemer Award, LAM Foundation Career Development Award, an NSF CAREER Award, and an NIH NIGMS Maximizing Investigator Research Award. Her work has led to numerous high-impact publications, particularly in the field of drug delivery and mucosal immunoengineering, and several patents.

bioengineering↗

bioRxiv2022

Gut microbial disruption in critically ill patients with COVID-19 associated pulmonary aspergillosis

ObjectivesCOVID-19 disease can be exacerbated by Aspergillus superinfection (CAPA). The causes of CAPA are not yet fully understood. Recently, alterations in the gut microbiome have been associated with a complicating course and increasing severity of COVID-19 disease, most likely via immunological mechanisms. Aim of this study was to investigate a potential association between severe CAPA and alterations in the gut and bronchial microbiota. MethodsWe performed 16S rRNA gene amplicon sequencing of stool and bronchial samples from a total of 16 COVID-19 patients with CAPA and 26 patients without CAPA. All patients were admitted to the intensive care unit. Results were carefully tested for potential influences on the microbiome during hospitalization. ResultsWe found that late in COVID-19 disease, CAPA patients exhibited a trend towards reduced gut microbial diversity. Furthermore, late stage CAPA disease showed an increased presence of Staphylococcus epidermidis in the gut. This is not found in late non-CAPA cases or early disease. The analysis of bronchial samples did not show significant results. ConclusionsThis is the first study showing alterations in the gut microbiome accompany severe CAPA and possibly influence the hosts immunological response. In particular, an increase of Staphylococcus epidermidis in the intestine could be of importance. SummaryThe composition of intestinal bacteria in severe CAPA disease is altered with an increase in Staphylococcus epidermidis in the gut. Alterations in the composition of intestinal bacteria in severe CAPA may indicate immunologic involvement of the gut in the disease.

microbiology↗

bioRxiv2023

Multimodal profiling of chordoma immunity reveals distinct immune contextures

Chordomas are cancers from the axial skeleton presenting immunological hallmarks of unknown significance. In recent years, some clinical trials demonstrated that chordomas can respond to immunotherapy. We present a comprehensive characterisation of immunological features of 76 chordomas through application of a multimodal approach comprising transcriptional profiling, multidimensional immunophenotyping and TCR profiling. Chordomas generally presented an immune "hot" microenvironment in comparison to other sarcomas, as indicated by the immunologic constant of rejection transcriptional signature. We identified two distinct groups of chordomas based on T cell infiltration. The highly infiltrated group was further characterised by high dendritic cell infiltration and the presence of multicellular immune aggregates in tumours, whereas low T cell infiltration was associated with lower overall cell densities of immune and stromal cells. Interestingly, patients with higher T cell infiltration displayed a more pronounced clonal enrichment of the T cell receptor repertoire compared to those with low T cell counts. Furthermore, we observed that the majority of chordomas maintained HLA class I expression. Our findings shed light on the natural immunity against chordomas. Understanding their immune landscape could guide the development and application of immunotherapies in a tailored manner, ultimately leading to an improved clinical outcome for chordoma patients.

cancer biology↗

bioRxiv2023

Safety Assessment of Intravenous Injection of Rat Embryonic Proteome Extract for in-vivo Regenerative Therapies

Back groundTissue differentiation and organogenesis are exclusively embryonic-phase activities, and these two activities are strictly under the control of the embryonic proteome, the developing embryo is a prime source of molecules for regenerative therapy. Many ex-vivo rudimentary organoid culture studies confirmed the inherent biological function of embryonic factors. Before using embryonic proteins for in vivo therapies, their safety should be confirmed first. Hence, we aimed for an in vivo study to inject rat embryonic proteome extract (EPE) through the intravenous route and investigate the impact on immunological, biochemical, and hematological parameters in the adult rats. MethodsIn this study, we isolated rat embryonic proteins from the 14th, 16th, and 19th embryonic days by homogenization of embryos and isolated protein extracts through ultra-centrifugation. Six pairs of rats have been taken; six are allotted for control, and six are for the embryonic extract injection. The isolated embryonic protein extract was injected intravenously into the treatment group of rats and the normal saline into the control group. After the injections, blood samples are collected from both the treated and control groups to analyse immunological markers Il6, CRP, biochemical parameters creatinine, urea, sugar, proteins, albumin, globulin, and hematological parameters total leucocyte count, neutrophils, and lymphocyte percentage ResultAfter the EPE injection, biochemical parameters, immunological markers, and hematological parameters were analyzed in both control and treated groups. All the above mentioned parameters are within normal limits. Statistical analyses were done using the t-test for unequal variance (p< 0.05). We observed no significant difference between the control and treated groups, so in vivo injections of embryonic protein extract is safe for the use of in vivo regenerative therapies. ConclusionDespite extensive in vitro studies confirmed the biological function of embryonic growth factors for organ differentiations and rudimentary organoids, but in vivo clinical applications are not yet started because of immunogenicity, heterogeneity, and tumorigeniety. In our study we injected EPE intravenously and showed that EPE is non-immunogenic, non-heterogeneic, and non-tumorigenic. This study concludes that EPE is safe for in vivo injection, so that further studies can be continued for intra-organ injections for organ regenerative therapy.

developmental biology↗

bioRxiv2024

Establishment of an easy-to-construct liver injury mouse model for longitudinal analysis by drinking-water administration of 4,4'-methylenedianiline

Background & AimsLongitudinal animal models are essential for understanding the temporal dynamics of liver injury and recovery. While drinking water-based administration is ideal for sustained exposure in high feasibility, available compounds are limited, with thioacetamide (TAA) being the primary option. Here, we aimed to establish a novel drinking water-induced mouse model of cholestatic liver injury using 4,4-methylenedianiline (MDA), and to characterize its pathological trajectory in comparison to the TAA model. MethodsMice were administered MDA via drinking water for 28 Days. To elucidate the early events that give rise to chronic pathological divergence, we conducted a multi-layered analysis comprising plasma biochemical assays, immune cell profiling by flow cytometry, and hepatic transcriptomics at five time points during the early phase. The MDA model was evaluated against the established TAA model. ResultsMDA administration induced sustained ALT elevation, peribiliary fibrosis, and spatially irregular focal hepatocellular necrosis, distinguishing it from the centrilobular injury observed with TAA. Additionally, the MDA model showed significant elevations in ALP, TBIL, and TCHO, indicating cholestatic liver dysfunction. Early-phase analyses revealed model-specific differences in immunological and molecular responses, including increased CD8 T cell populations and enrichment of fibrinolysis-related gene expression in MDA-DW mice. ConclusionsWe present the MDA-DW model as a novel, longitudinally tractable liver injury model that complements existing systems by capturing alternative spatial, immunological, and transcriptional patterns of injury. This model offers a valuable platform for dissecting the temporal dynamics of liver disease progression in experimental settings. Significance StatementWe developed a cost-effective, non-invasive mouse model of cholestatic liver injury using drinking-water administration of 4,4-methylenedianiline (MDA). This model exhibits periportal-predominant damage, peribiliary fibrosis, and spatially irregular focal hepatocellular necrosis, distinct from conventional centrilobular models. Early-phase multi-omics analysis revealed immunological and transcriptomic differences, including increased CD8 T cells and activation of fibrinolysis-related pathways. The low mortality rate and ease of implementation enable long-term studies and cross-sectional comparisons across time points or interventions. This study provides not only a practical model for investigating chronic liver injury, but also a rich time-series, multi-view dataset, offering a valuable resource for advancing research on liver pathophysiology and toxicological mechanisms.

pharmacology and toxicology↗

bioRxiv2024

Parent-specific transgenerational immune priming enhances offspring defense - unless heat-stress negates it all

Trans-generational immune priming (TGIP) adjusts offspring immune responses based on parental immunological experiences - a form of trans-generational plasticity predicted to be adaptive when parent-offspring environmental conditions match. In contrast, mis-matches between environmental conditions negate those advantages, rendering TGIP costly when mismatched immunological offspring phenotypes are induced. Particularly maternal TGIP was thought to shape offspring immunological preparedness: mothers eggs contain more substance than sperm and, in viviparous species, pregnancy provides additional avenues for immune priming of developing offspring. The syngnathids (pipefishes and seahorses) unique male pregnancy provides an unusual perspective to the ecological relevance of TGIP in a system where egg production and pregnancy occur in different sexes. We simulated parental bacteria exposure in broad nosed pipefish, Syngnathus typhle, through vaccinations with heat-killed Vibrio aestuarianus before mating the fish to each other or control individuals. Resulting offspring were raised, and some exposed to V. aestuarianus, in a control or heat-stress environment, after which transcriptome and microbiome compositions were investigated. Transcriptomic TGIP effects were only observed in Vibrio-exposed offspring at control temperatures, arguing for low costs of TGIP in non-matching environments. Transcriptomic phenotypes elicited by maternal and paternal TGIP had only limited overlap and were not additive. Both transcriptomic responses were significantly associated to immune functions, and specifically the paternal response to the innate immune branch. TGIP of both parents reduced the relative abundance of the experimental Vibrio in exposed offspring, showcasing its ecological effectiveness. Despite its significance in matching biotic environments, no TGIP-associated phenotypes were observed for heat-treated offspring. Heat-spikes caused by climate change thus threaten TGIP benefits, potentially increasing susceptibility to emerging marine diseases. This highlights the urgent need to understand how animals will cope with climate-induced changes in microbial assemblages by illustrating the importance - and limits - of TGIP in mitigating the impacts of environmental stressors on offspring vulnerability.

evolutionary biology↗

bioRxiv2024

A mathematical description of non-self for biallelic genetic systems in pregnancy, transfusion, and transplantation.

A central issue in immunology is the immunological response against non-self. The prerequisite for a specific immunological response is the exposure to the immune system of a non-self-antigen. Mathematical equations are presented, that define the fraction of all outcomes with a non-self-allele in biallelic systems at the population level in pregnancy and transfusion/transplantation medicine. When designing assays, the mathematical descriptions can be used for estimating the number of genetic markers necessary to obtain a predetermined probability level in detecting non-self-alleles of a given frequency. For instance, the equations can be helpful in the design of assays, where the non-self-allele can be detected by analysis of cfDNA in plasma from pregnant women, to estimate fetal fraction or to monitor changes in cfDNA in plasma of transplantation patients. The equations give exact, quantitative descriptions of all non-self-situations in pregnancy and transfusion/transplantation.

genetics↗

bioRxiv2024

Elucidating immune-related gene transcriptional programs via factorization of large-scale RNA-profiles

Recent developments in immunotherapy, including immune checkpoint blockade (ICB) and adoptive cell therapy, have encountered challenges such as immune-related adverse events and resistance, especially in solid tumors. To advance the field, a deeper understanding of the molecular mechanisms behind treatment responses and resistance is essential. However, the lack of functionally characterized immune-related gene sets has limited data-driven immunological research. To address this gap, we adopted non-negative matrix factorization on 83 human bulk RNA-seq datasets and constructed 28 immune-specific gene sets. After rigorous immunologist-led manual annotations and orthogonal validations across immunological contexts and functional omics data, we demonstrated that these gene sets can be applied to refine pan-cancer immune subtypes, improve ICB response prediction and functionally annotate spatial transcriptomic data. These functional gene sets, informing diverse immune states, will advance our understanding of immunology and cancer research.

bioinformatics↗

bioRxiv2024

Replicating dynamic immune responses at single-cell resolution within a microfluidic human skin equivalent

The intricate immunological functions of human skin involve the interplay between multiple different cell types as well as dynamic trafficking of leukocytes in and out the tissue, both of which are extremely challenging to replicate in vitro. To enable in vitro investigation of human skin immunology, we developed a microfluidic human skin equivalent (HSE) that supports the delivery of circulating immune cells via a vascular microchannel embedded within the dermis of a full-thickness construct. We demonstrated that stimulation of keratinocyte inflammation with lipopolysaccharide and nigericin promoted rapid monocyte recruitment out of the vascular channel and into the epidermal layer within 24 hours, followed by a second wave of monocyte migration into the dermis over a period of six days. Single-cell transcriptomic analysis of the tissue-resident and recruited cell populations revealed dynamic and cell-specific patterns of gene expression that were characteristic of acute activation and resolution of an inflammatory immune response. Moreover, comparison of the gene signatures of the monocyte-derived cells to in vivo populations provided molecular level validation of the model and indicated a differentiation trajectory of the monocytes through to mature dermal macrophages. To extend the microfluidic platform to additional applications, we also modelled age-associated immune dysfunction by the inclusion of senescent fibroblasts, which promoted increased monocyte recruitment into the HSE, replicating previous in vivo human studies. Thus, the microfluidic HSE presented here replicates key aspects of dynamic inflammatory immune responses within the skin and represents a tractable experimental tool for interrogating mechanisms of human skin immunology.

bioengineering↗

bioRxiv2025

Bridging Gaps in Antibody Responses and Animal Welfare: Assessing Blood Collection Methods and Vaginal Immunity in Mice Immunized with Intranasal Gonococcal Vaccines

Assessing antibody titers and functional responses is essential for evaluating vaccine efficacy, yet the impact of blood collection methods on these immunological assessments remains unclear. Retro-orbital (RO) blood collection is commonly used but significant complications can occur. Increasingly, investigators have adopted alternative blood collection approaches, such as saphenous vein (SV) sampling to improve laboratory animal welfare. This study compared RO and SV sampling in the development of a Neisseria gonorrhoeae (Ng) vaccine, evaluating Adhesin Complex Protein (ACP) and multiple transferable resistance (Mtr) E protein (MtrE) as antigen candidates. Epitope mapping revealed that ACP and MtrE possess multiple, highly accessible B-cell and T-cell epitope clusters, reinforcing their immunological potential. Following intranasal immunization with rACP, rACP+CpG, and rMtrE+CpG, we assessed the specificity, magnitude, kinetics, and functional quality of immune responses elicited by the immunization regimens. Out of 45 comparisons, only eight significant differences were detected in antibody titers, while the human serum bactericidal assays revealed no differences between RO and SV in antigen-immunized groups. However, antibodies elicited by rACP alone or ACP+CpG in SV samples restored 30.05% and 75.2% of human lysozyme hydrolytic activity compared to 19.3 and 59.9 % in RO, respectively suggesting that SV sampling may be more reliable for assessing functional antibody responses. Beyond its immunological advantages, SV sampling reduces stress, minimizes ocular trauma, and improves animal welfare, making it a viable alternative to RO collection. Given its widespread use in vaccine research, standardizing SV sampling could improve data reliability, ethical compliance, and translational relevance in preclinical studies.

microbiology↗

bioRxiv2025

Investigating Factors Driving Shifts in Subtype Dominance within H5Nx Clade 2.3.4.4b High-Pathogenicity Avian Influenza viruses

H5Nx clade 2.3.4.4b high-pathogenicity avian influenza viruses (HPAIVs) have decimated wild bird and poultry populations globally since the autumn of 2020. In the United Kingdom (UK) and in continental Europe, the H5N8 subtype predominated during the first epizootic wave of 2020/21, with few detections of H5N1. However, during the second (2021/22) and third (2022/23) epizootic waves, H5N1 was the dominant subtype. The rapid shift in dominance from H5N8 to H5N1 was likely driven by a combination of virological, immunological, and/or host-related factors. In this study, we compared viral fitness and immunological responses in ducks, a key reservoir species, using dominant genotypes of H5N1 (genotype AB) and H5N8 (genotype A) from the second wave. While viral shedding dynamics were similar for both viruses, H5N8 was more pathogenic. Antigenic analysis of post-infection duck sera revealed that the haemagglutinin (HA) protein was antigenically similar across clade 2.3.4.4b H5 HPAIVs, but neuraminidase (NA) proteins displayed different patterns of cross-reactivity. We also modelled a scenario where ducks were pre-exposed to H5N1 (genotype C) or H5N8 (genotype A) from the first wave and subsequently challenged with either homologous or heterologous subtypes from the second wave (genotype AB or A). Despite the absence of seroconversion, pre-exposure to different subtypes resulted in varying clinical outcomes following challenge. These findings indicate that both viral and immunological factors likely played significant roles in the emergence and spread of H5Nx HPAIVs in wild bird populations.

microbiology↗

bioRxiv2025

cytoGPNet: Enhancing Clinical Outcome Prediction Accuracy Using Longitudinal Cytometry Data in Small Cohort Studies

Cytometry data, including flow cytometry and mass cytometry, are now standard in numerous immunological studies, such as cancer immunotherapy and vaccine trials. These data enable the monitoring of an individuals peripheral immune status over time, providing detailed insights into immune cells and their role in clinical outcomes. However, traditional analyses relying on summary statistics, such as cell subset proportions and mean fluorescence intensity, may overlook critical single-cell information. To address this limitation, we introduce cytoGPNet, a novel approach that harnesses extensive cytometry data to predict individual-level outcomes. cytoGPNet is designed to address four key challenges: (1) accommodating varying numbers of cells per sample; (2) analyzing the longitudinal cytometry data to understand temporal relationships; (3) maintaining robustness under the constraints of limited individual samples in immunological studies; and (4) ensuring interpretability to facilitate biomarker identification. We apply cytoGPNet to data from multiple diverse studies, each with unique characteristics. Despite these differences, cytoGPNet consistently outperforms other popular methods in terms of prediction accuracy. Moreover, cytoGPNet provides interpretable results at multiple levels, offering valuable insights. Our findings underscore the effectiveness and versatility of cytoGPNet in enhancing the analysis of cytometry data and its potential to advance immunological research.

bioinformatics↗

bioRxiv2025

EVA: a Foundation Model Advancing Translational Drug Development in Immuno-Inflammation

Drug development is a lengthy and high-risk process, with most investigational drug candidates failing in phase II randomized clinical trials (RCT) due to insufficient efficacy. It makes early prediction of trial outcomes crucial for reducing attrition and guiding strategic decisions, especially in immunology and inflammation (I&I) diseases. Herein, we present EVA, the first pre-trained foundation model in complex inflammatory diseases tailored to support drug development. EVA learns generalizable patterns from large-scale data of cell biology and immunology, enabling superior predictive performance and generalization compared to traditional approaches. EVA is pre-trained on tens of millions of single-cell RNA-seq samples and tens of thousands of bulk RNA-seq samples from I&I diseases patients, enabling it to learn disease-relevant transcriptomic patterns in this therapeutic area. By fine-tuning EVA in few-shot settings on both preclinical (mouse) and clinical (human) data and harnessing its wide pre-training knowledge, EVA predicts drug responses in I&I with high precision at both cohort and patient levels, as illustrated by accurate forecasting of anti-TNF therapeutic activity in ulcerative colitis. By deciphering its decision process, we further highlight that EVAs ability to stratify patients based on predicted drug response can also be leveraged to discover drug response biomarkers as early as preclinical stages. EVAs applications in precision immunology encompass therapeutic target validation prior to clinical entry, identification of patient subpopulations most likely to benefit from treatment, and comparative efficacy analysis against competitor compounds. EVAs versatility makes it an invaluable tool for strategic decision-making throughout the drug development pipeline: by leveraging it to prioritize the most promising drug candidates and optimize RCT designs, it can contribute to reduce late-stage failures and accelerate the delivery of effective therapies. Overall, this work represents a significant advancement in utilizing a pre-trained foundation model for precision drug development in complex inflammatory diseases. Graphical abstractEVA is a pre-trained foundation model specific to immune-mediated inflammatory diseases. It enables the prediction of therapeutic efficacy in patients leveraging data from preclinical disease models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/651839v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@1c783f1org.highwire.dtl.DTLVardef@1a760d9org.highwire.dtl.DTLVardef@1c7748aorg.highwire.dtl.DTLVardef@1b44f82_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Exploratory Statistical Analysis of Rheumatoid Factor Based Subgroups in Sjögren's Syndrome.

This method describes a computational pipeline for stratifying autoimmune patient groups using exclusively binary autoantibody data. Our method addresses a methodological gap in computational immunology by providing a standardized framework for analyzing categorical serological data commonly found in electronic health records and resource-limited settings. The pipeline integrates three complementary analytical modules: O_LIModule 1: Exploratory screening using statistical association tests. C_LIO_LIModule 2: Quantification of overall immunological similarity and un-certainty. C_LIO_LIModule 3: Prediction modeling and validation against chance. C_LI We demonstrate the methods utility by applying it to two autoimmune disorders. We were successful in recapitulating established clinical relationships in these two closely linked diseases. The pipeline is implemented in Python and includes detailed configuration options for custom disease groups, autoanti-body panels and stratification variables. This method enables researchers to extract meaningful immunological patterns from underutilized binary clinical data, serving as a hypothesis-generation tool to help drive impactful exploration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/670596v4_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@7c6df3org.highwire.dtl.DTLVardef@116ac5eorg.highwire.dtl.DTLVardef@18e76dcorg.highwire.dtl.DTLVardef@1d6b71_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗