bioRxiv Science⌕ Search

SEARCH · bioRxiv Science

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 343 records · Page 19Linked to original sources
bioRxiv2019

ADHD genetic liability and physical health outcomes - A two-sample Mendelian randomization study

ObjectiveAttention-deficit/hyperactivity disorder (ADHD) has been associated with a broad range of physical health problems, including cardiometabolic, neurological and immunological conditions. Determining whether ADHD plays a causal role in these associations is of great importance for treatment and prevention but also because comorbid health problems further increase the serious social and economic impacts of ADHD on individuals and their families.\n\nMethodsWe used a two-sample Mendelian randomization (MR) approach to examine the causal relationships between genetic liability for ADHD and previously implicated physical health conditions. 11 genetic variants associated with ADHD were obtained from the latest summary statistics. Consistent effects obtained from IVW, weighted median and MR Egger methods were taken forward for sensitivity analysis, including bidirectional MR and multivariable MR (MVMR).\n\nResultsWe found evidence of a causal effect of genetic liability for ADHD on childhood obesity (OR:1.29 (95% CI:1.02,1.63)) and coronary artery disease (CAD) (OR:1.11 (95% CI:1.03,1.19)) with consistent results across different MR approaches. There was further evidence for a bidirectional relationship between genetic liability for ADHD and childhood obesity. The effect of genetic liability for ADHD on CAD was independent of smoking heaviness but was attenuated when simultaneously controlling for childhood obesity. There was little evidence for a causal effect on other cardiometabolic, immunological, neurological disorders and lung cancer.\n\nConclusionOur findings strengthen the argument for early treatment and support for children with ADHD and their families and especially promoting physical activity and providing them with dietary advice to reduce future risk for developing CAD.\n\nKey Message O_LIEpidemiological studies have reported observational associations between ADHD and adult onset physical health outcomes.\nC_LIO_LIMendelian Randomization can be used to assess causal associations for ADHD on health outcomes that would traditionally require long term follow-up and may suffer confounding\nC_LIO_LIWe found that genetic liability for ADHD was associated with coronary artery disease and there was evidence for a bidirectional association between genetic liability for ADHD and childhood obesity\nC_LIO_LIMultivariable mendelian randomization suggests that the link between genetic liability and coronary artery disease might partially act through childhood obesity but was independent of smoking heaviness\nC_LIO_LIThere was little evidence of a causal of ADHD on other cardiometabolic and immunological diseases.\nC_LI

epidemiology↗
bioRxiv2019

Immune state networks of wild and laboratory mice

The mammalian immune system protects individuals from infection and disease. It is a complex system of interacting cells and molecules and extensive work, principally with laboratory mice, has investigated its function. Wild and laboratory animals lead very different lives, and this is reflected in there being substantial immunological differences between them. Here we use network analyses to study a unique data set of 120 immune measures of wild and laboratory mice, where immune measures define nodes and correlations of immune measures across individual mice define edges between immune measures. To date, there has only been very limited network analyses of the immune system, which is surprising because such analyses may be important to better understand its organisation and functionality. We found that the immunological networks of wild and laboratory mice were similar in some aspects of their mesoscale structure, particularly concerning cytokine response communities. However, we also identified notable differences in node membership of network communities between the wild and laboratory networks, pointing to how the same immune system acts and interacts differently in wild and in laboratory mice. These results show the utility of network analysis in understanding immune responses and also the importance of studying wild animals in additional to laboratory animals.\n\nAuthor summaryThe mammalian immune system is a complex system that protects individuals from infection and disease. Most of our understanding of the immune system comes from studies of laboratory animals, particularly mice. However, wild and laboratory animals lead very different lives, potentially leading to substantial immunological differences between them and so possibly limiting the utility of laboratory animals as informative model systems. As a complex interacting set of cells and molecules, the immune system is a biological network. Therefore, we used network analyses to study the immune system, specifically a unique data set of immune measures of wild and laboratory mice, where 120 different immune measures define nodes of the network. We found that the networks of wild and laboratory mice were similar in some aspects of their grouping structure, particularly concerning communities of nodes of cytokine responses. However, we also identified notable differences in node membership of communities between the wild and laboratory networks, pointing to how the same immune system behaves differently in wild and in laboratory mice. These results show the utility of network analysis in understanding immune responses and also the importance of studying wild animals in addition to laboratory animals.

systems biology↗
bioRxiv2025

A Falsifiable Framework for Testing Neutralityin T-Cell Receptor Repertoire Databases

BackgroundT-cell receptor (TCR) repertoire databases aggregate antigen-specific sequences from hundreds of studies, exhibiting heavy-tailed occurrence distributions commonly interpreted as signatures of selection or criticality. However, distinguishing genuine non-neutral dynamics from neutral drift with realistic biological constraints requires explicit computational null models--currently absent from repertoire immunology. MethodsWe developed a biologically calibrated neutral null model incorporating thymic output, negative selection, and peripheral homeostasis with parameters independently derived from immunology literature (Robins et al. 2009, naive repertoires). The model was validated against empirical repertoire statistics before generating predictions. We compared neutral predictions to occurrence patterns from 24,847 TCR-epitope combinations in VDJdb across four viral targets using multi-observable testing (power-law exponent, Shannon entropy, public clonotype fraction) with Bonferroni-corrected thresholds. ResultsThe neutral null model successfully reproduced three independent benchmarks. Public clonotype fraction in VDJdb (3.10%) significantly exceeded neutral predictions (1.47%{+/-}0.29%, 100th percentile, p < 0.001, Cohens d = 5.62), inconsistent with neutrality at stringent thresholds (Bonferroni ' = 0.0167). In contrast, power-law exponent ( = 2.450 vs. 2.391 {+/-} 0.177, p = 0.739, d = 0.33) and Shannon entropy (H = 12.10 vs. 12.34 {+/-} 1.17 bits, p = 0.838, d = -0.21) showed negligible deviations. This dissociation--public fraction deviates while diversity metrics remain neutral-consistent--is consistent with but does not prove selective enrichment for cross-individual TCR convergence. Supplementary analyses confirmed public enrichment is temporally stable (2009-2024, no significant trend p > 0.40) and universal across viral pathogens (CMV, EBV, Influenza, SARS-CoV-2, ANOVA p > 0.68), constraining plausible curation bias mechanisms. ConclusionsWe present a rigorous falsificationist framework for testing neutrality in TCR repertoires via pre-validated computational nulls, multi-observable comparisons, and honest power reporting. Application to VDJdb reveals public clonotype patterns suggestive of non-neutral processes (functional selection or curation bias), establishing testable hypotheses for experimental follow-up. The framework--emphasizing independent validation, pre-specified decision criteria, and effect size quantification--generalizes to antibody repertoires, microbiomes, and evolutionary systems requiring mechanistic discrimination between drift and selection. Author SummaryDetermining whether T-cell receptor occurrence patterns arise from random drift or functional selection is fundamental to understanding adaptive immunity, yet current approaches rely on descriptive statistics rather than rigorous hypothesis testing. We developed the first falsifiable framework for testing neutrality in TCR databases using a biologically realistic computational null model validated against independent empirical benchmarks. Applying this framework to VDJdb, we find that public clonotype frequencies (sequences appearing across many individuals) deviate significantly from neutral predictions, while overall repertoire diversity remains consistent with neutrality. This pattern suggests--but does not definitively prove--that selection or curation bias operates specifically on cross-individual TCR convergence. Our contribution is methodological: we demonstrate how to test mechanistic hypotheses rigorously rather than describe patterns phenomenologically. The framework is immediately applicable to ongoing debates in repertoire immunology and generalizes to other biological systems exhibiting heavy-tailed distributions.

bioinformatics↗
bioRxiv2026

Circadian regulators PER1 and PER2 regulate osteoclastogenesis by balancing competing activities of innate immunity genes

Bone remodeling is influenced by circadian rhythms as demonstrated by global gene expression patterns and the phenotypes of knockout mice of circadian regulators. However, the direct connections between circadian regulators and specific bone genes remain unclear. We previously found that a conditional knockout of Per1, a central circadian regulator, in osteoclasts increased osteoclastogenesis and decreased bone mass, whereas Per2 knockout did not cause these phenotypes. Here, we extended the research to Per1;Per2 conditional double knockout mice and observed different phenotypes and underlying mechanisms from individual knockouts. In contrast to Per1 knockout, the double knockout decreased osteoclastogenesis and increased bone mass. This was accompanied by downregulation of genes involved in innate immunity, including several known promoters and inhibitors of osteoclastogenesis. Chromatin immunoprecipitation and reporter assay suggested direct regulation of some of them by PER proteins. These results indicate that PER1 and PER2 are critical regulators of osteoclastogenesis through balancing multiple competing activities of osteoclastogenesis, rather than acting as simple promoters or inhibitors of osteoclastogenesis. Regulation of innate immunity genes by circadian regulators is widely observed across other monocyte/macrophage lineages. Our results extend this common mechanism to osteoclasts with therapeutic potential to treat inflammatory bone diseases. Lay summaryAlthough circadian rhythms regulate bone remodeling, direct links between circadian regulators and bone genes remain unclear. We previously demonstrated that depletion of Per1, a main circadian regulator, downregulates immunological genes, increases the number of osteoclasts, the main bone resorbing cells, and decreases bone mass in mice. Here, we showed the opposite effects with double depletion of Per1 and Per2 and identified a new set of downregulated immunological genes that promote or inhibit osteoclastogenesis. This study connects circadian rhythms to bone resorption through immunological genes with opposing activities in osteoclastogenesis, supporting therapeutic interventions targeting circadian regulators to treat inflammatory bone diseases.

cell biology↗
bioRxiv2026

Benchmarking generative scaffold design methods for peptide engineering in TCR-MHC complexes

De novo peptide design at T cell receptor-peptide-major histocompatibility complex (TCR-pMHC) interfaces is a central challenge in computational immunology, with direct implications for vaccine development, cancer immunotherapy, and autoimmune disease. Despite rapid advances in generative protein modeling, there is currently no systematic benchmark evaluating these methods in the highly constrained and immunologically relevant setting of peptide-MHC presentation and TCR recognition. Here, we present two complementary contributions. First, we introduce a multi-stage computational pipeline for peptide design in predefined TCR-pMHC contexts, integrating generative modeling with sequence optimization and structure-based filtering. Second, we establish a benchmark for evaluating generative peptide design methods in TCR-pMHC complexes. Using a curated dataset of high-quality crystal structures deposited after the AlphaFold3 training cutoff, we assess state-of-the-art generative approaches for peptide backbone generation, sequence design, and the enrichment of near-native solutions. We explicitly examine whether different backbone generation strategies respect the geometric constraints of the MHC binding groove and recover native-like peptide conformations. Our results reveal substantial method-dependent differences: some generative strategies fail systematically in the groove-bound peptide setting, whereas others generate physically plausible backbones with varying accuracy and conformational diversity. We further show that enforcing anchor constraints strongly influences peptide conformations at non-anchor positions, highlighting a trade-off between structural accuracy and conformational sampling. To enable fair and reproducible comparison, we introduce a standardized, multi-stage scoring protocol that integrates MHC binding prediction, physics-based energy evaluation, and independent structure prediction confidence metrics to enrich near-native designs from large candidate pools. Together, this work establishes the first comprehensive pipeline and benchmark for generative peptide design at TCR-pMHC interfaces and provides practical guidelines for developing peptide design workflows and evaluating generative models in immunologically constrained protein design settings.

bioinformatics↗
bioRxiv2026

A Structural Landscape of Fungal Allergens with Epitope-Level Resolution Reveals Cross-Kingdom Structural Similarity

The immunological properties of allergens are ultimately governed by three-dimensional protein structure, particularly the spatial organization of IgE-binding epitopes. Despite the need to capture global structural relationships and patterns of allergen diversity, most allergen classification and prediction strategies still rely predominantly on sequence-based approaches. Here, we present a structure-based framework that represents fungal allergens as elements embedded within a continuous structural manifold. Using AlphaFold-predicted full-length structures of 150 previously reported fungal allergens, we constructed a global structural distance space defined by TM-score-derived similarities. This manifold revealed a heterogeneous yet continuous landscape in which dense structural neighborhoods correspond to established allergen families, while more diffuse regions reflect gradual structural transitions. To directly link global protein architecture with immunologically relevant features, we extended this framework to epitope-level structural representations derived from predicted antibody-binding regions. Epitope-restricted structures preserved the relative organization of major allergen clusters, demonstrating that IgE-relevant features are embedded within conserved structural scaffolds. At the same time, epitope-level analysis demonstrated that high structural similarity can be observed at the epitope level even when global protein folds differ, highlighting the contribution of local structural features to immunologically relevant properties. We further applied a nearest-neighbor-based manifold inclusion analysis to screen nearly 20,000 fungal protein structures, identifying numerous allergen-related proteins occupying the same structural neighborhoods as known allergens, thereby extending allergen-associated architectures beyond current databases. Finally, structural screening of non-fungal allergens revealed cross-kingdom similarities to fungal allergens, suggesting convergent allergenic architectures across distant taxa. Together, this study establishes a unified structural manifold framework that integrates full-length protein and epitope-level information, providing a structure-based perspective on allergen diversity as a continuous space and on cross-reactivity.

bioinformatics↗
bioRxiv2026

Focused Ultrasound Thermal Ablation and CD40 Agonism Reprograms Breast Tumor Immunity to Drive Regression and Memory

Focused ultrasound thermal ablation (T-FUS) is a clinically accessible, non-invasive modality capable of inducing rapid tumor cytoreduction while mobilizing early immunologic danger signals. However, its capacity to synergize with potent co-stimulatory immunotherapies in breast cancer (BC) remains undefined. Here, we demonstrate that subtotal T-FUS cooperates with CD40 agonism to elicit durable, T cell-dependent tumor control across four immunologically and hormonally distinct murine BC models. Partial thermal ablation triggered canonical immunogenic cell-death signatures and acute remodeling of intratumoral myeloid populations, while expanding circulating CD4+ and CD8+ T cells. When layered onto this immunogenic milieu, CD40 markedly constrained tumor outgrowth, yielding significant reductions in tumor burden across all models and complete tumor eradication in 33% of E0771 tumors, with additional complete responses in BRPKP110 and EMT6. Efficacy required both CD4+ and CD8+ T cells, and complete responders mounted robust systemic immunity, rejecting contralateral tumor rechallenge with 100% protection and displaying persistent effector-memory T cell activation. Together, these findings establish T-FUS as an immune-potentiating partner for CD40 agonism, capable of driving durable, robust BC regression and immunological memory. This work positions T-FUS+CD40 agonism as a clinically scalable, in situ vaccination-like strategy with potential to benefit breast cancers, including luminal subtypes, that remain largely refractory to immune checkpoint blockade.

cancer biology↗
bioRxiv2026

Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone

Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems. ImportanceLaboratory mice are foundational models for immunology, yet their specific pathogen-free rearing and housing environments impose ecological constraints that reshape the gut microbiome and immune tone. This study introduces a scalable, pathogen-monitored Eco-tank system that restores environmental microbial complexity while preserving experimental control. By demonstrating that housing ecology reshapes microbiome functional potential and modulates baseline immune resistance without compromising vaccine responsiveness, this work highlights environmental context as a critical experimental variable in preclinical immunology and offers a tractable framework for improving translational relevance.

microbiology↗
bioRxiv2016

Profiling adaptive immune repertoires across multiple human tissues by RNA Sequencing

Assay-based approaches provide a detailed view of the adaptive immune system by profiling T and B cell receptor repertoires. However, these methods come at a high cost and lack the scale of standard RNA sequencing (RNA-seq). Here we report the development of ImReP, a novel computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data. We applied it to 8,555 samples across 544 individuals from 53 tissues from the Genotype-Tissue Expression (GTEx v6) project. ImReP is able to efficiently extract TCR- and BCR- derived reads from the RNA-Seq data and accurately assemble the complementarity determining regions 3 (CDR3s), the most variable regions of B- and T-cell receptors determining their antigen specificity. Using ImReP, we have created the systematic atlas of immunological sequences for B- and T-cell repertoires across a broad range of tissue types, most of which have not been studied for B and T cell receptor repertoires. We have also examined the compositional similarities of clonal populations between the GTEx tissues to track the flow of T- and B- clonotypes across immune-related tissues, including secondary lymphoid organs and organs encompassing mucosal, exocrine, and endocrine sites. The atlas of T- and B-cell receptor receptors, freely available at https://sergheimangul.wordpress.com/atlas-immune-repertoires/, is the largest collection of CDR3 sequences and tissue types. We anticipate this recourse will enhance future studies in areas such as immunology and advance development of therapies for human diseases. ImReP is freely available at https://sergheimangul.wordpress.com/imrep/.

immunology↗
bioRxiv2020

In silico characterization of mechanisms positioning costimulatory and checkpoint complexes in immune synapses

Integrin and small immunoglobulin superfamily (sIGSF) adhesion complexes function physiologically in human immunological synapses (IS) wherein sIGSF complexes form a corolla of microdomains around an integrin ring and secretory core. The corolla recruits and retains the major costimulatory and checkpoint complexes that regulate the response to T cell receptor (TCR) engagement, making forces that govern corolla formation of particular interest. We developed a phenomenological agent-based model in order to test different hypotheses concerning the mechanisms underlying molecular reorganization during IS formation. The model showed that sIGSF complexes are passively excluded to the distal aspect of the IS as long as their interaction with the ramified F-actin transport network is absent or weaker than that of integrins. An attractive force between sIGSF adhesion and costimulatory/checkpoint complexes relocates the latter from the centre of the IS to the corolla. The simulations suggest that size based sorting interactions with large glycocalyx components as well as a short-range self-attraction between sIGSF complexes explain the corolla "petals". These molecular and mechanistic features establish a general model that can recapitulate complex pattern formation processes observed in cell-bilayer and cell-cell interfaces. One Sentence SummaryComputer simulations of immunological synapses reveal the localization mechanisms of immunoglobulin superfamily adhesion and costimulatory/checkpoint complexes.

immunology↗
bioRxiv2020

Analysis of KSHV B lymphocyte lineage tropism in human tonsil reveals efficient infection of CD138+ plasma cells

Despite 25 years of research, the basic virology of Kaposi Sarcoma Herpesviruses (KSHV) in B lymphocytes remains poorly understood. This study seeks to fill critical gaps in our understanding by characterizing the B lymphocyte lineage-specific tropism of KSHV. Here, we use lymphocytes derived from 40 human tonsil specimens to determine the B lymphocyte lineages targeted by KSHV early during de novo infection in our ex vivo model system. We characterize the immunological diversity of our tonsil specimens and determine that overall susceptibility of tonsil lymphocytes to KSHV infection varies substantially between donors. We demonstrate that a variety of B lymphocyte subtypes are susceptible to KSHV infection and identify CD138+ plasma cells as a rare, but highly targeted cell type for de novo KSHV infection. Finally, we determine that the host immunological status influences the course of de novo infection in B lymphocytes. These results improve our understanding of KSHV transmission and the biology of early KSHV infection in a naive human host, and lay a foundation for further characterization of KSHV molecular virology in B lymphocyte lineages.

immunology↗
bioRxiv2020

The physical form of microbial ligands bypasses the need for dendritic cell migration to stimulate adaptive immunity

A central paradigm of immunology is that the innate immune system first detects infectious agents in peripheral tissues, shortly after a pathogen has breached an epithelial barrier. This detection event is mediated by pattern recognition receptors in phagocytes, which then migrate to draining lymph nodes (dLNs), where information of a microbial encounter is conveyed to T and B lymphocytes to generate adaptive immunity. Through the study of fungal moieties, we present data that challenge this model. We found that soluble fungal polysaccharides are immunosilent in the periphery, but become potent immunogens in the dLN. These ligands completely bypass the need of phagocyte migration and, instead, directly activate an immune response that is most similar to those that typify viral infections. These data establish a class of microbial products that violate a central tenet of the immunological lexicon and illustrate that the physical form (not just the chemical structure) impacts innate and adaptive immunity.

immunology↗
bioRxiv2020

Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Novel SARS coronavirus (SARS-CoV-2) has caused a pandemic condition world-wide and has been declared as public health emergency of International concern by WHO in a very short span of time. The community transmission of this highly infectious virus has severely affected various parts of China, Italy, Spain and USA among others. The prophylactic solution against SARS-CoV-2 infection is challenging due to the high mutation rate of its RNA genome. Herein, we exploited a next generation vaccinology approach to construct a multi-epitope vaccine candidate against SARS-CoV-2 with high antigenicity, safety and efficacy to combat this deadly infectious agent. The whole proteome was scrutinized for the screening of highly conserved, antigenic, non-allergen and non-toxic epitopes having high population coverage that can elicit both humoral and cellular mediated immune response against COVID-19 infection. These epitopes along with four different adjuvants were utilized to construct a multi-epitope vaccine candidate that can generate strong immunological memory response having high efficacy in humans. Various physiochemical analyses revealed the formation of a stable vaccine product having a high propensity to form a protective solution against the detrimental SARS-CoV-2 strain with high efficacy. The vaccine candidate interacted with immunological receptor TLR3 with high affinity depicting the generation of innate immunity. Further, the codon optimization and in silico expression show the plausibility of the high expression and easy purification of the vaccine product. Thus, this present study provides an initial platform of the rapid generation of an efficacious protective vaccine for combating COVID-19.

immunology↗
bioRxiv2020

Mobilization of tissue-resident memory CD4+ T lymphocytes and their contribution to a systemic secondary immune reaction

While it is generally accepted that tissue-resident memory T lymphocytes protect host tissues from secondary immune challenges, it is unclear whether, and if so, how they contribute to systemic secondary immune responses. Here we show that in human individuals with an established immune memory to measles, mumps and rubella viruses, when challenged with the measles-mumps-rubella (MMR) vaccine again, tissue-resident memory CD4+ T cells are mobilized into the blood within 16 to 48 hours after vaccination. These cells then leave the blood again, and apparently contribute to the systemic secondary immune reaction, as is evident from the representation of mobilized T cell receptor V{beta} clonotypes among newly generated circulating memory T lymphocytes, from day 7 onwards. Mobilization of the tissue-resident memory T cells is cognate, in that memory T lymphocytes recognizing other antigens, e.g. tetanus toxin, are not mobilized, unless they cross-react with the vaccine. These data originally demonstrate the essential contribution of tissue-resident memory T cells to secondary systemic immune responses, confirming that immunological memories to systemic pathogens are maintained (also) by tissue-resident memory T cells. In practical terms, the present work defines day 1 to 2 after antigenic challenge as a time window to assess the entire immunological T cell memory for a certain pathogen, including mobilized tissue-resident memory T cells, and its correlates of effectivity. Capsule summaryThe study demonstrates the rapid and cognate mobilization of tissue-resident memory CD4+ T cells into the blood upon antigenic rechallenge, and their contribution to secondary systemic immune responses.

immunology↗
bioRxiv2020

Inhibition of 2-Hydroxyglutrate Elicits Metabolic-reprograming and Mutant IDH1 Glioma Immunity

Mutant isocitrate-dehydrogenase-1 (IDH1-R132H; mIDH1) is a hallmark of adult gliomas. Lower grade mIDH1 gliomas are classified into two molecular subgroups: (i) 1p/19q co-deletion/TERT-promoter mutations or (ii) inactivating mutations in -thalassemia/mental retardation syndrome X-linked (ATRX) and TP53. This work, relates to the gliomas subtype harboring mIDH1, TP53 and ATRX inactivation. IDH1-R132H is a gain-of-function mutation that converts -ketoglutarate into 2-hydroxyglutarate (D-2HG). The role of D-2HG within the tumor microenvironment of mIDH1/mATRX/mTP53 gliomas remains unexplored. Inhibition of 2HG, when used as monotherapy or in combination with radiation and temozolomide (IR/TMZ), led to increased median survival (MS) of mIDH1 glioma bearing mice. Also, 2HG inhibition elicited anti-mIDH1 glioma immunological memory. In response to 2HG inhibition, PD-L1 expression levels on mIDH1-glioma cells increased to similar levels as observed in wild-type-IDH1 gliomas. Thus, we combined 2HG inhibition/IR/TMZ with anti-PDL1 immune checkpoint-blockade and observed complete tumor regression in 60% of mIDH1 glioma bearing mice. This combination strategy reduced T-cell exhaustion and favored the generation of memory CD8+T-cells. Our findings demonstrate that metabolic reprogramming elicits anti-mIDH1 glioma immunity, leading to increased MS and immunological memory. Our preclinical data supports the testing of IDH-R132H inhibitors in combination with IR/TMZ and anti-PDL1 as targeted therapy for mIDH1/mATRX/mTP53 glioma patients. Brief SummaryInhibition of 2-Hydroxyglutrate in mutant-IDH1 glioma in the genetic context of ATRX and TP53 inactivation elicits metabolic-reprograming and anti-glioma immunity.

immunology↗
bioRxiv2020

Immunoinformatic identification of B cell and T cell epitopes in the SARS-CoV-2 proteome

A novel coronavirus (SARS-CoV-2) emerged from China in late 2019 and rapidly spread across the globe, infecting millions of people and generating societal disruption on a level not seen since the 1918 influenza pandemic. A safe and effective vaccine is desperately needed to prevent the continued spread of SARS-CoV-2; yet, rational vaccine design efforts are currently hampered by the lack of knowledge regarding viral epitopes targeted during an immune response, and the need for more in-depth knowledge on betacoronavirus immunology. To that end, we developed a computational workflow using a series of open-source algorithms and webtools to analyze the proteome of SARS-CoV-2 and identify putative T cell and B cell epitopes. Using increasingly stringent selection criteria to select peptides with significant HLA promiscuity and predicted antigenicity, we identified 41 potential T cell epitopes (5 HLA class I, 36 HLA class II) and 6 potential B cell epitopes, respectively. Docking analysis and binding predictions demonstrated enrichment for peptide binding to HLA-B (class I) and HLA-DRB1 (class II) molecules. Overlays of predicted B cell epitopes with the structure of the viral spike (S) glycoprotein revealed that 4 of 6 epitopes were located in the receptor-binding domain of the S protein. To our knowledge, this is the first study to comprehensively analyze all 10 (structural, non-structural and accessory) proteins from SARS-CoV-2 using predictive algorithms to identify potential targets for vaccine development. Significance StatementThe novel coronavirus SARS-CoV-2 recently emerged from China, rapidly spreading and ushering in a global pandemic. Despite intensive research efforts, our knowledge of SARS-CoV-2 immunology and the proteins targeted by the immune response remains relatively limited, making it difficult to rationally design candidate vaccines. We employed a suite of bioinformatic tools, computational algorithms, and structural modeling to comprehensively analyze the entire SARS-CoV-2 proteome for potential T cell and B cell epitopes. Utilizing a set of stringent selection criteria to filter peptide epitopes, we identified 41 T cell epitopes (5 HLA class I, 36 HLA class II) and 6 B cell epitopes that could serve as promising targets for peptide-based vaccine development against this emerging global pathogen.

immunology↗
bioRxiv2020

PD-L1 expression in equine malignant melanoma and functional effects of PD-L1 blockade

Programmed death-1 (PD-1) is an immunoinhibitory receptor expressed on exhausted T cells during chronic illness. Interaction of PD-1 with its ligand PD-ligand 1 (PD-L1) delivers inhibitory signals and impairs proliferation, cytokine production, and cytotoxicity of T cells. We reported that the PD-1/PD-L1 pathway is closely associated with T-cell exhaustion and disease progression in bovine chronic infections and canine tumors. Moreover, we found that blocking antibodies targeting PD-1 and PD-L1 restore T-cell functions and may be used in immunotherapy in cattle and dogs. However, the immunological role of the PD-1/PD-L1 pathway remains unclear for chronic equine diseases, including tumors. In this study, we identified nucleotide sequences of equine PD-1 (EqPD-1) and PD-L1 (EqPD-L1) and investigated the role of anti-bovine PD-L1 monoclonal antibodies (mAbs) against EqPD-L1 using in vitro assays. We also evaluated the expression of PD-L1 in tumor tissues of equine malignant melanoma (EMM). The amino acid sequences of EqPD-1 and EqPD-L1 share a high identity and similarity with homologs from other mammalian species. Two clones of the anti-bovine PD-L1 mAbs recognized EqPD-L1 in flow cytometry, and one of these cross-reactive mAbs blocked the binding of equine PD-1/PD-L1. Importantly, PD-L1 expression was confirmed in EMM tumor tissues by immunohistochemistry. A cultivation assay revealed that PD-L1 blockade enhanced the production of Th1 cytokines in equine immune cells. These results suggest that our anti-PD-L1 mAbs may be useful for investigating the expression and role of the equine PD-1/PD-L1 pathway. Further research is required to discover the immunological role of PD-1/PD-L1 in chronic equine diseases and elucidate a future application in immunotherapy for horse.

immunology↗
bioRxiv2020

Mucosal immune stimulation with HSV-2 and polyICLC boosts control of viremia in SIVΔNef vaccinated rhesus macaques with breakthrough SIV infection

Development of an effective human immunodeficiency virus (HIV) vaccine is among the highest priorities in the biomedical research agenda. Adjuvants enhance vaccine efficacy, but in the case of HIV, strong or inappropriate immune activation may undermine protection by increasing HIV susceptibility. Co-infection with immunomodulatory pathogens may also impact vaccine efficacy. In the rhesus macaque rectal SIV{Delta}Nef live attenuated vaccine model, we utilized a low virulence HSV-2 infection and the double-stranded RNA viral mimic polyICLC as tools to probe the effects of distinct types of immune activation on HIV vaccine efficacy and explore novel correlates of protection from wild type SIV. Rectally administered HSV-2 and polyICLC impacted the protection conferred by mucosal SIV{Delta}Nef vaccination by favoring partial protection in animals with breakthrough infection following virulent SIV challenge ("Controllers"). However, SIV{Delta}Nef persistence in blood and tissues did not predict protection in this rectal immunization and challenge model. Non-controllers had similar SIV{Delta}Nef viremia as completely protected macaques, and while they tended to have less replication competent SIV{Delta}Nef in lymph nodes, controllers had no recoverable virus in the lymph nodes. Non-controllers differed from protected macaques immunologically by having a greater frequency of pro-inflammatory CXCR3+CCR6+ CD4 T cells in blood and a monofunctional IFN{gamma}-dominant CD8 T cell response in lymph nodes. Controller phenotype was associated with heightened IFN production during acute SIV infection and a greater frequency of CXCR5+ CD4 T cells in blood pre-challenge despite a lower frequency of cells with the T follicular helper (Tfh) cell phenotype in blood and lymph nodes. Our results establish novel correlates of immunological control of SIV infection while reinforcing the potential importance of T cell functionality and location in SIV{Delta}Nef efficacy. Moreover, this work highlights that triggering of mucosal immunity can aid mucosal vaccine strategies rather than undermine protection. AUTHOR SUMMARYAn efficacious HIV vaccine is essential to contain the HIV pandemic. Vaccine-mediated protection from HIV may be either enhanced or obstructed by mucosal immune activation; thus, the impact of adjuvants and underlying co-infections that lead to immune activation needs to be evaluated. Using the SIV macaque model, we set out to study the impact of underlying infection with HSV-2 or treatment with the adjuvant polyICLC on rectal immunization with the live attenuated vaccine SIV{Delta}Nef. We found that neither stimulus impacted complete protection from SIV; however, the combination of HSV-2 and polyICLC improved control of infection in animals that were not completely protected. Compared with non-controller macaques, controllers had less inflammatory T cells before SIV challenge as well as greater gene expression of IFN and more functional SIV-specific T cells after infection. The results add to our understanding of the mechanisms of SIV{Delta}Nef protection and demonstrate that mucosal immune activation does not necessarily undermine protection in mucosal vaccination against HIV.

immunology↗