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bioRxiv2025

Single-cell transcriptomics and machine learning reveal RNF144B and C5AR1 as immune-related biomarkers and therapeutic targets in myocardial infarction

BackgroundMyocardial infarction (MI) is a life-threatening cardiovascular disease characterized by high morbidity and mortality. Although advances in clinical management have improved patient outcomes, early diagnosis and effective immunomodulatory therapies remain limited. MethodsIn this study, we integrated multiple transcriptomic datasets and applied machine learning approaches, including LASSO regression, to identify a robust 13 key genes significantly associated with MI. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were subsequently performed to explore their potential biological functions. The immunological relevance of these genes was evaluated by analyzing their correlations with inflammation-related genes and those involved in immune cell migration. In addition, transcription factor (Johnson, Law et al.) and microRNA (miRNA) regulatory networks were constructed to elucidate upstream regulatory mechanisms. The expression levels of the 13 key genes were validated in MI mouse model. Furthermore, molecular docking was performed to identify candidate small molecules targeting core genes. ResultsAmong 11 cardiac cell populations identified, myeloid cells contributed most prominently to MI pathogenesis. A robust 13-gene predictive signature was established, with RNF144B and C5AR1 showing strong associations with immune modulation and disease severity. GSEA and GSVA further revealed that RNF144B was enriched in the neutrophil degranulation pathway, while C5AR1 was associated with the complement cascade. Correlation analysis demonstrated a significant positive relationship of RNF144B and C5AR1 with immunological roles. Both genes were also positively correlated with classical MI marker genes SERPINE1 and RUNX1. TF-gene and miRNA-mRNA regulatory networks supported the post-transcriptional regulation of these genes. In the MI mouse model, expression of the 13 genes was consistent with the risk-prediction model. Molecular docking identified CCX168 as a promising small-molecule candidate targeting RNF144B and C5AR1. ConclusionThis study reveals immune-related transcriptional signatures and signaling pathways that drive MI progression. The identified 13-gene signature, particularly RNF144B and C5AR1, holds promise as a diagnostic biomarker and therapeutic target, providing new insights for immunomodulatory and precision medicine strategies in MI. Keywords: Immune microenvironment, myeloid cells, inflammation, RNF144B, MI, immune-targeted therapy HighlightsO_LIA 13-gene signature was identified to predict MI risk C_LIO_LIRNF144B and C5AR1 are key immune regulators in MI progression C_LIO_LIGSEA and GSVA reveal immune-related pathways of RNF144B and C5AR1 C_LIO_LICCX168 is identified as a potential small-molecule therapy for MI C_LIO_LIMouse model validates gene expression consistent with the prediction model C_LI

cell biology↗

bioRxiv2025

Spatially organized lymphocytic microenvironments in high grade primary prostate tumors

The spatial arrangement of immune cells in the tumor microenvironment (TME) varies widely, from dispersed to clustered and tumor excluded to infiltrating. Multiplexed spatial profiling is an effective means of characterizing tumor-infiltrating lymphocytes (TILs) and immune complexes such as tertiary lymphoid structures (TLS) in the TME. However, few approaches have been described for objectively parametrizing patterns of immune organization and assessing their association with biological or clinical variables. This makes it difficult to evaluate whether a set of tumors is relatively immunologically cold or hot. Here we describe an intuitive set of statistical tools (available in the R package, tlsR) for characterizing lymphocyte patterns in the TME of solid cancers. We apply tlsR to primary prostate cancer (PCa), which is often described as immunologically cold. Using a cohort of 29 radical prostatectomy specimens stratified into low Gleason-grade (LGG; n=15) and high Gleason-grades (HGG; n =14) we show that HGG PCa is significantly more infiltrated than LGG PCa with lymphocytes organized into B cell or T cell enriched immune clusters (BICs and TICs). A subset of these ICs have the B and T cell zonation and follicular dendritic cells characteristic of a bona fide TLS. HGGs are also enriched with ICs containing precursor exhausted T cells (Tpex) and proliferating B cells and their tumor compartments harbor granzyme-B+ cytotoxic T cells in contact with cancer cells. Thus, far from being cold, a subset of HGG PCa has features associated with active immune surveillance, a finding with implications for emerging PCa immunotherapies.

cancer biology↗

bioRxiv2025

Antiviral and Anti-inflammatory Effects of Cannabidiol in HIV/SIV Infection

Persistent reservoirs and chronic immune activation are hallmarks of HIV, despite the effectiveness of antiretroviral therapy (ART) in suppressing viral replication. Here, we use rhesus macaques and primary and induced pluripotent stem cell (iPSC)-derived human immune cells to evaluate the virologic and immunologic consequences of cannabidiol (CBD) exposure during HIV/SIV infection. We show that CBD, in the absence of ART, suppresses viral replication and establishment of the viral reservoir to levels comparable with first-line therapies during acute SIV infection of rhesus macaques. This antiviral effect of CBD extended to in vitro HIV infection of human macrophages, T cells, and microglia. Immunologically, we observe CBD slowed CD4+ T cell decline and polarization, decreased CD14+CD16+ monocyte expansion, and reduced interferon-inducible cytokine release in rhesus macaques. We identify comparable effects on cytokine production with in vitro CBD treatment of human macrophages, T cells, and microglia. Importantly, we find CBD inhibits cytokines only when an immune response is elicited by HIV, suggesting it is not broadly immunosuppressive. Finally, we determine CBD regulates endocannabinoid receptors, modulators, and transporters and inhibits NF-{kappa}b and STAT1 activation when mediating its antiviral and anti-inflammatory effects. These findings show beneficial effects of CBD in laboratory models of untreated HIV, thus placebo-controlled clinical trials to evaluate the safety and effectiveness of adjunctive CBD use with ART is warranted.

microbiology↗

bioRxiv2025

Therapeutic Blockade of Type 2 Cytokines and PD1 Unleashes Anti-Tumor Immunity Through Coordinated Reprogramming of Innate and Adaptive Immune Surveillance

BackgroundCheckpoint inhibitors improve survival in patients with several types of tumors. However, resistance to checkpoint inhibitors creates an opportunity for patients to benefit from novel immunotherapies. The type 2 cytokines IL-4, IL-13 and TSLP have been implicated in suppressing anti-tumor immune responses through T and myeloid cells. Our current study tested whether combined therapeutic blockade of IL-4, IL-13 and TSLP improved anti-tumor immunity alone and in combination with PD1 antagonism. MethodsWe used in vitro experiments with primary cells to identify cell types likely to participate in controlling tumors upon IL-4, IL-13, TSLP and PD1 blockade. Therapeutic blockade in the subcutaneous CT26 model tested in vivo tumor growth inhibition and associated immunological changes. Bioinformatic analysis of human tumor bulk RNA sequencing data probed for survival associations with IL-4/IL-13 and TSLP transcriptional responses. ResultsIn vitro, IL-4 suppressed T cell-mediated tumor growth inhibition and reduced monocyte-derived dendritic cell expression of proteins associated with anti-tumor immunity. In vivo, blocking IL-4, IL-13, TSLP and PD1 improved tumor growth inhibition by creating "hotter" tumors. This was associated with repolarization of CD4 and CD8 T cells and shifts in monocyte, conventional type 1 and type 2 (or monocyte-derived) dendritic cell programs. Transcriptional responses to IL-4/IL-13 and TSLP were associated with poor survival outcomes across patients with several types of cancers. ConclusionTherapeutic blockade of IL-4, IL-13 and TSLP may drive immunological tumor growth inhibition in subsets of cancer patients alone and in combination with checkpoint inhibitors. Improved tumor growth inhibition was likely driven through augmented cytotoxic T cell priming in secondary lymphoid organs and improved reactivation by repolarized monocytes and dendritic cells in tumors.

cancer biology↗

bioRxiv2025

Citizen science gamers enable automated flow cytometry gating through machine learning

Manual flow cytometry gating requires up to one hour per sample with 32% inter-expert variability, creating critical bottlenecks in immunological research reproducibility. To address this, we developed flowMagic, a machine learning algorithm for automated gating that is trained on both expert-curated data (template data) and crowdsourced annotations from citizen science gaming. Through EVE Online, 839,199 players analyzed 52,178 bivariate plots from 37 studies, generating 31,703 quality-controlled training plots. Evaluated against 92,203 expert-validated files spanning 79 immune populations (i.e., a biologically defined cell subset within each bivariate plot), flowMagic achieved 90% accuracy for abundant populations and 65% for rare populations, outperforming existing methods. The algorithm reproduced biological patterns including neutrophil dynamics in COVID-19 patients and immune development in newborns. This gaming-based approach demonstrates that crowd-sourced pattern recognition generates robust training data for complex biomedical applications, offering transformative potential for standardizing flow cytometry analysis and accelerating immunological discovery.

bioinformatics↗

bioRxiv2025

AniMarkerDB: a comprehensive database for exploring cell types and marker genes in livestock and poultry at single-cell resolution

Single-cell RNA sequencing (scRNA-seq) has dramatically advanced the understanding of cellular heterogeneity. While numerous marker gene databases are available for humans and mice, a lack of systematic resources for livestock and poultry species remains, limiting progress in functional genomics, immunology, and breeding.. To address this challenge, we developed AniMarkerDB (https://animarkerdb.bio), a comprehensive and curated database dedicated to marker genes and immune-related epitopes in economically animals, including chicken, pig, and duck. AniMarkerDB integrates 7,010 marker gene across 37 tissues and 846 cell types, together with 71,442 immune epitope records from IEDB. All entries undergo rigorous literature curation, manual validation, and multi-level quality control, with standardized nomenclature and annotation to ensure data consistency and reusability. The platform supports flexible queries by species, tissue, cell type, or gene. It offers analytical tools for cross-species comparison model organisms such as human and mouse, interactive single-cell atlas visualization, and user-defined cell type annotation. Additionally, AniMarkerDB provides dynamic visualizations and export options, enabling researchers to efficiently obtain large-scale marker and epitope data for downstream applications such as infectious disease research, vaccine target design, and comparative immunology. Looking ahead, AniMarkerDB will expand species coverage and incorporate additional modalities, including single-cell atlases from healthy and disease models, establishing itself as a comprehensive and authoritative platform for animal cell biology, disease modeling, and translational research. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/682327v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@af7e7borg.highwire.dtl.DTLVardef@198d114org.highwire.dtl.DTLVardef@1c69ed2org.highwire.dtl.DTLVardef@e4fc43_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

FLASH Radiotherapy Mitigates Radiation-Induced Lymphopenia and Prevents Immunosuppression via Chk1-STAT3 Axis Modulation in a Preclinical Thoracic Irradiation Model

Background and AimsRadiation-induced lymphopenia (RIL) is a frequent side effect of conventional radiation therapy (CONV RT), due to the high radiosensitivity of circulating lymphocytes. Ultra-high dose rate "FLASH" RT may preferentially spare normal tissue while maintaining tumor control. This study evaluates the impact of single-fraction and multi-fraction thoracic FLASH RT on lymphocyte preservation, apoptosis, and immunosuppressive signaling in mice. MethodsWe compared the immunological impact of thoracic FLASH RT and CONV RT in C57BL/6 mice using single-fraction (17 Gy) and multi-fraction (2 Gy x 5) regimens using the Mobetron (IntraOp). Longitudinal blood sampling was performed at multiple time-points post-irradiation through facial vein bleed with flow cytometry analysis for CD4+, CD8+, CD19+, and NK cells to assess lymphocyte counts, apoptotic lymphocytes through Annexin V staining, and immune suppression by examining regulatory T cells (Tregs) and PD-1/PD-L1 expression. Mechanistic studies included immunofluorescence and Western blot analyses of splenic tissues to evaluate Chk1 and STAT3 signaling pathways. ResultsIn single-fraction RT, FLASH significantly reduced lung and heart fibrosis (p < 0.0001) at 28 weeks post-RT. The FLASH effect was also seen acutely on circulating immune cells, with significantly reduced lymphocyte apoptosis and accelerated recovery of CD4, CD8, CD3, NK, and B cell populations compared to CONV RT in both single-fraction and multi-fraction regimens. Conversely, CONV RT induced long-lasting increases in Tregs and sustained PD-1 and PD-L1 expression on T- and B-cells at 2- and 5-months post-irradiation in both fractionation regimens. Within the spleen, we also found CONV RT induced sustained activation of the Chk1-STAT3 pathway in CD45+ immune cells, which correlates with increased PD-1/PD-L1 expression. ConclusionFLASH RT mitigates RIL, reduces lymphocyte apoptosis, and prevents long-term immunosuppression by reduced activation of the Chk1-STAT3 pathway. These findings suggest FLASH RT may confer immunological advantages over CONV RT to enhance therapeutic efficacy.

cancer biology↗

bioRxiv2025

Cytokine and Immunoglobulin Dynamics in Phage Therapy: Insights from Clinical Cases

BackgroundBacteriophage therapy is increasingly used for antibiotic-refractory infections, yet its immunologic effects in humans remain poorly defined. We evaluated cytokine and immunoglobulin responses in nine compassionate-use cases of intravenous phage therapy, including solid organ transplant recipients and patients with device-associated or refractory bacterial infections. MethodsSerial serum samples were analyzed by multiplex Luminex immunology and isotyping assays, with results correlated to host immune status, infecting organism, and clinical outcome. ResultsCytokine patterns were heterogeneous and appeared to reflect the infecting pathogen more than phage exposure. Pseudomonas aeruginosa infections elicited broad pro-inflammatory cytokine increases (notably MCP-3 and TNF-{beta}), while Staphylococcus aureus infection was associated with overall cytokine reduction except for IL-6. Most immunocompetent patients exhibited an early IgM response within 1-2 weeks of phage initiation, whereas immunocompromised hosts demonstrated attenuated antibody levels. Neither cytokine nor humoral responses correlated with clinical outcome. In one case, serum neutralization developed against a specific phage but not against a subsequent, distinct phage cocktail targeting the same organism, suggesting variability in phage immunogenicity. ConclusionOverall, intravenous phage therapy frequently induces IgM responses, which are more pronounced in immunocompetent patients, while cytokine dynamics depend more on pathogen and immune status than on phage administration itself. These findings underscore the need for standardized immune profiling in clinical phage trials to delineate beneficial versus detrimental immune responses and to inform the design of phage formulations with optimized immunogenic profiles.

microbiology↗

bioRxiv2017

Genome-wide transcriptional responses of iron-starved Chlamydia trachomatis reveal prioritization of metabolic precursor synthesis over protein translation

Iron is essential for growth and development of Chlamydia. Its long-term starvation in cultured mammalian cells leads to production of aberrant non-infectious chlamydial forms, also known as persistence. Immediate transcriptional responses to iron limitation have not been characterized, leaving a knowledge gap of how Chlamydia regulates its response to changes in iron availability. We used the fast-chelating agent 2,2-Bipyridyl (BPDL) to homogeneously starve Chlamydia trachomatis serovar L2 of iron, starting at 6 or 12h post-infection. Immediate transcriptional responses were monitored after only 3 or 6h of BPDL-treatment, well before formation of aberrant Chlamydia. The first genome-wide transcriptional response of C. trachomatis to iron-starvation was subsequently determined utilizing RNA-sequencing. Only 7% and 8% of the genome was differentially expressed in response to iron-starvation at early and mid-stages of development, respectively. Biological pathway analysis revealed an overarching theme. Synthesis of macromolecular precursors (deoxynucleotides, amino acids, charged tRNAs, and acetyl-coA) was up-regulated, while energy-expensive processes (ABC transport and translation) were down-regulated. A large fraction of differentially down-regulated genes are involved in translation, including ribosome assembly, initiation and termination factors, which could be analogous to the translation down-regulation triggered by stress in other prokaryotes during stringent responses. Additionally, transcriptional up-regulation of DNA repair, oxidative stress, and tryptophan salvage genes reveals a possible coordination of responses to multiple antimicrobial and immunological insults. These responses of replicative-phase Chlamydia to iron-starvation indicate a prioritization of survival over replication, enabling the pathogen to \"stock the pantry\" with ingredients needed for rapid growth once optimal iron levels are restored.\n\nIMPORTANCEBy utilizing an experimental approach that monitors the immediate global response of Chlamydia trachomatis to iron-starvation, clues to long-standing questions in Chlamydia biology are revealed, including how Chlamydia adapts to this stress. We determined that this pathogen initiates a transcriptional program that prioritizes replenishment of nutrient stores over replication, possibly in preparation for rapid growth once optimal iron levels are restored. Transcription of genes for biosynthesis of metabolic precursors was generally up-regulated, while those involved in multiple steps of translation were down-regulated. We also observed an increase in transcription of genes involved in DNA repair and neutralizing oxidative stress, indicating that Chlamydia employs an \"all-or-nothing\" strategy. Its small genome limits its ability to tailor a specific response to a particular stress. Therefore, the \"all-or-nothing\" strategy may be the most efficient way of surviving within the host, where the pathogen likely encounters multiple simultaneous immunological and nutritional insults.

microbiology↗

bioRxiv2017

Non-parametric mixture models identify trajectories of childhood immune development relevant to asthma and allergy

Events in early life contribute to subsequent risk of asthma; however, the causes and trajectories of childhood wheeze are heterogeneous and do not always result in asthma. Similarly, not all atopic individuals develop wheeze, and vice versa. The reasons for these differences are unclear. Using unsupervised model-based cluster analysis, we identified latent clusters within a prospective birth cohort with deep immunological and respiratory phenotyping. We characterised each cluster in terms of immunological profile and disease risk, and replicated our results in external cohorts from the UK and USA. We discovered three distinct trajectories, one of which is a high-risk \"atopic\" cluster with increased propensity for allergic diseases throughout childhood. Atopy contributes varyingly to later wheeze depending on cluster membership. Our findings demonstrate the utility of unsupervised analysis in elucidating heterogeneity in asthma pathogenesis and provide a foundation for improving management and prevention of childhood asthma.

systems biology↗

bioRxiv2018

Placental-expanded, mesenchymal cells improve muscle function following hip arthroplasty

BackgroundNo regenerative approach has thus far been shown to be effective in skeletal muscle injuries, despite high frequency and associated functional deficits. We sought to address surgical trauma related muscle injuries using local intraoperative application of allogeneic placenta-derived, mesenchymal-like adherent cells (PLX-PAD), using hip arthroplasty as a standardized injury model, because of the high regenerative and immunomodulatory potency of this cell type.\n\nMethodsOur pilot phase I/IIa study was prospective, randomized, double blind and placebo-controlled. Twenty patients undergoing hip arthroplasty via a direct lateral approach were injected with 3.0x108 or 1.5x108 PLX-PAD or a placebo into the gluteus medius muscle.\n\nResultsWe did not observe any relevant PLX-PAD-related adverse events at the 2-year follow-up. Improved gluteus medius strength was noted as early as week 6 in the treatment-groups. Surprisingly, until week 26 the low-dose outperformed the high-dose group and reached significantly improved strength compared to placebo, mirrored by an increase in muscle volume. Histology indicated accelerated healing after cell therapy. Biomarker studies revealed that low-dose treatment reduced the surgery-related immunological stress reaction more than high-dose. Signs of late-onset immune reactivity after high-dose treatment corresponded to reduced functional improvement.\n\nConclusionAllogeneic PLX-PAD therapy improved strength and volume of injured skeletal muscle with a reasonable safety profile. Outcomes could be positively correlated with the modulation of early postoperative stress-related immunological reactions.\n\nTrial RegistrationClinicalTrials.gov (number NCT01525667) and EudraCT (number 2011-003934-16)\n\nFundingThe study was funded by the Sponsor, Pluristem Therapeutics, the Israeli innovation authority and the German Federal Ministry of Education and Research.\n\nConflict of interestT. Winkler, C. Perka and G.N. Duda are members of a clinical advisory board of Pluristem Ltd for future indications. T. Winkler, C. Perka, G.N. Duda, P. von Roth filed a patent together with Pluristem Ltd. E. Lukasiewicz Hagai, R. Ofir, L. Pinzur and E. Eyal are current or former employees of Pluristem Ltd. T. Winkler, P. Reinke and H.-D. Volk received in the past consulting fees from Pluristem Ltd. but not for this project.

clinical trials↗

bioRxiv2018

Resistant potato starch fuels beneficial host-microbe interactions in the gut

Interactions between diet, the microbiota, and the host set the ecological conditions in the gut and have broad implications for health. Prebiotics are dietary compounds that may shift these conditions towards health by promoting the growth of beneficial microbes. Pigs fed a diet amended with 5% resistant potato starch (RPS) exhibited alterations associated with gut health relative to swine fed an unamended diet (CON). RPS intake increased abundances of anaerobic Clostridia in feces and several tissues, as well as intestinal concentrations of butyrate. Functional gene amplicons suggested bacteria similar to Anaerostipes hadrus were stimulated by RPS intake. The CON treatment exhibited increased abundances of several genera of Proteobacteria (which utilize respiratory metabolisms) in several location. RPS intake increased the abundance of regulatory T cells in the cecum, but not periphery, and cecal immune status alterations were indicative of enhanced mucosal defenses. A network analysis of host and microbial changes in the cecum revealed that regulatory T cells positively correlated with butyrate concentration, luminal IgA concentration, expression of IL-6 and DEF1B, and several mucosa-associated bacterial taxa. Thus, the administration of RPS modulated the microbiota and host response, improved cecal barrier function, promoted immunological tolerance, and reduced the niche for bacterial respiration.\n\nImportanceThe gut microbiota is central to host health. Many disease states and disorders appear to arise from interactions between the gut microbial community and host immune system. As a result, methods and interventions to support the growth and activity of beneficial gut microbes are being actively pursued. Feeding the gut microbiota with dietary compounds, known as prebiotics, is one of the most promising ways to support gut health. Here we describe a successful prebiotic intervention in weaning swine, a relevant translational model for human health. This work unites microbial and immunological data and demonstrates one way a prebiotic intervention can play out for the benefit of the host.

systems biology↗

bioRxiv2019

Perturbation of the gut microbiota by antibiotics results in accelerated breast tumour growth and metabolic dysregulation

BackgroundBreast cancer is the second most prevalent cancer worldwide with around 1.7 million new cases diagnosed every year. Whilst prognosis is generally favourable in early stages, this worsens significantly in advanced disease. Therefore, it is pertinent to focus on mitigating factors that may slow growth or progression. Recently, the gut microbiome has been implicated in a wide-range of roles in tumour biology. Through modulation of immunity, the gut microbiota can improve the efficacy of several immunotherapies. However, despite the prevalence of breast cancer, there is still a lack of microbiota studies in this field, including exploring the influence of external microbiome-modulating factors such as antibiotics. We describe herein how disruption of the gut microbiota via antibiotics may be detrimental to patient outcomes through acceleration of tumour growth. ResultsSupplementing animals with a cocktail of antibiotics leads to gut microbiota alterations and is accompanied by significant acceleration of tumour growth. Surprisingly, and distinct from previous microbiome-tumour studies, the mechanism driving these effects do not appear to be due to gross immunological changes. Analysis of intratumoural immune cell populations and cytokine production are not affected by antibiotic administration. Through global tumour transcriptomics, we have uncovered dysregulated gene expression networks relating to protein and lipid metabolism that are correlated with accelerated tumour growth. Fecal metabolomics revealed a reduction of the microbial-derived short-chain fatty acid butyrate that may contribute to accelerated tumour growth. Finally, through use of a routinely administered antibiotic in breast cancer patients, Cephalexin, we have shown that tumour growth is also significantly affected. Metataxanomic sequencing and analysis highlighted significant antibiotic-associated reductions in the butyrate producing genera Odoribacter and Anaeotruncus, and increased abundance of Bacteroides. ConclusionsOur data indicate that perturbation of the microbiota by antibiotics may have negative impacts on breast cancer patient outcomes. This is of importance as antibiotics are regularly prescribed to breast cancer patients undergoing mastectomy or breast reconstruction. We have also shown that the metabolic impact of disruption to the microbiome should be considered alongside the potent immunological effects. We believe our work lays the foundation for improving the use of antibiotics in patients, and with further investigation could potentially inform clinical practice.

cancer biology↗

bioRxiv2019

Evaluation of the geographical utility of Eastern Russells viper (Daboia siamensis) antivenom from Thailand and an assessment of its protective effects against venom-induced nephrotoxicity

BackgroundDaboia siamensis (Eastern Russells viper) is a medically important snake species found widely distributed across Southeast Asia. Envenomings by this species can result in systemic coagulopathy, local tissue injury and/or renal failure. While administration of specific antivenom is an effective treatment for Russells viper envenomings, the availability of, and access to, geographically-appropriate antivenom remains problematic in many rural areas. In this study, we determined the binding and neutralizing capability of antivenoms manufactured by the Thai Red Cross in Thailand against D. siamensis venoms from three geographical locales: Myanmar, Taiwan and Thailand.\n\nMethodology/ Principle findingsThe D. siamensis monovalent antivenom displayed extensive recognition and binding to proteins found in D. siamensis venom, irrespective of the geographical origin of those venoms. Similar immunological characteristics were observed with the Hemato Polyvalent antivenom, which also uses D. siamensis venom as an immunogen, but binding levels were dramatically reduced when using comparator monovalent antivenoms manufactured against different snake species. A similar pattern was observed when investigating neutralization of coagulopathy, with the procoagulant action of all three geographical venom variants neutralized by both the D. siamensis monovalent and the Hemato Polyvalent antivenoms, while the comparator monovalent antivenoms were ineffective. Assessments of in vivo nephrotoxicity revealed that D. siamensis venom (700 {micro}g/kg) significantly increased plasma creatinine and blood urea nitrogen levels in anaesthetised rats. The intravenous administration of D. siamensis monovalent antivenom at three times higher than the recommended scaled therapeutic dose, prior to and 1 h after the injection of venom, resulted in reduced levels of markers of nephrotoxicity, although lower doses had no therapeutic effect.\n\nConclusions/SignificanceThis study highlights the potential broad geographical utility of the Thai D. siamensis monovalent antivenom for treating envenomings by the Eastern Russells viper. However, only the early delivery of high antivenom doses appear capable of preventing venom-induced nephrotoxicity.\n\nAuthor summarySnakebite is a major public health concern in rural regions of the tropics. The Eastern Russells viper (Daboia siamensis) is a medically important venomous snake species that is widely distributed in Southeast Asia and Southern China, including Taiwan. Envenoming by D. siamensis causes several systemic pathologies, most notably acute kidney failure and coagulopathy. The administration of antivenom is the mainstay therapeutic for treating snakebite, but in remote areas of Myanmar and Southern China access to antivenom is limited, and can result in the use of inappropriate, non-specific, antivenoms and treatment failure. Therefore, maximizing the utility of available efficacious antivenom is highly desirable. In this study, we investigated the utility of the widely available Thai Red Cross antivenoms for binding to and neutralizing D. siamensis venoms sourced from three distinct locales in Asia. Since the effectiveness and antivenom dose required to prevent D. siamensis venom-induced nephrotoxicity has been controversial, we also examined the preclinical efficacy of D. siamensis antivenom at preventing this pathology in experimentally envenomed anaesthetised animals. Our findings suggest that monovalent antivenom from Thailand, which is clinically effective in this country, has highly comparable levels of immunological binding and in vitro neutralization to D. siamensis venoms from Taiwan and Myanmar. We also show that the early administration of high therapeutic doses of antivenom are likely required to neutralize nephrotoxins and thus prevent acute renal failure following envenoming. Our findings suggest that certain Thai Red Cross antivenoms likely have wide geographical utility against D. siamensis venom and therefore may be useful tools for managing snakebite envenomings by this species in the absence of available locally manufactured therapeutics.

pharmacology and toxicology↗

bioRxiv2019

Identification of pathogen genomic differences that impact human immune response and disease during Cryptococcus neoformans infection

Patient outcomes during infection are due to a complex interplay between the quality of medical care, host immunity factors, and the infecting pathogens characteristics. To probe the influence of pathogen genotype on human immune response and disease, we examined Cryptococcus neoformans isolates collected during the Cryptococcal Optimal ART Timing (COAT) trial in Uganda. We measured human participants immunologic phenotypes, meningitis disease parameters, and survival. We compared this clinical data to whole genome sequences from 38 C. neoformans isolates of the most frequently observed sequence type (ST) ST93 in our Ugandan participant population, and an additional 18 strains from 9 other sequence types representing the known genetic diversity within the Ugandan Cryptococcus clinical isolates. We focused our analyses on 652 polymorphisms that: were variable among the ST93 genomes, were not in centromeres or extreme telomeres, and were predicted to have a fitness effect. Logistic regression and principal component analyses identified 40 candidate Cryptococcus genes and 3 hypothetical RNAs associated with human immunologic response or clinical parameters. We infected mice with 17 available KN99 gene deletion strains for these candidate genes and found that 35% (6/17) directly influenced murine survival. Four of the six gene deletions that impacted murine survival were novel. Such bedside-to-bench translational research provides important candidate genes for future studies on virulence-associated traits in human Cryptococcus infections.\n\nAuthor SummaryEven with the best available care, mortality rates in cryptococcal meningitis range from 20-60%. Disease is often due to infection by the fungus Cryptococcus neoformans and involves a complex interaction between the human host and the fungal pathogen. Although previous studies have suggested genetic differences in the pathogen impact human disease, it has proven quite difficult to identify the specific C. neoformans genes that impact the outcome of the human infection. Here, we take advantage of a Ugandan patient cohort infected with closely related C. neoformans strains to examine to role of pathogen genetic variants on several human disease characteristics. Using a pathogen whole genome sequencing approach, we showed that 40 C. neoformans genes are associated with human disease. Surprisingly, many of these genes are specific to Cryptococcus and have unknown functions. We also show deletion of these genes alters disease in a mouse model of infection, confirming their role in disease. These findings are particularly important because they are the first to identify C. neoformans genes associated with human cryptococcal meningitis and lay the foundation for future studies that may lead to new treatment strategies aimed at reducing patient mortality.

genetics↗

bioRxiv2019

Complement in human pre-implantation embryos: attack and defense

It is essential for early human life that immunological responses to developing embryos are tightly regulated. An imbalance in the activation and regulation of the human complement system occurs in pregnancy complications, such as pre-eclampsia and recurrent miscarriage. We hereby present the first full analysis of the expression and deposition of complement molecules in human pre-implantation embryos. Thus far, immunological imbalance has been considered in stages of pregnancy following implantation. We here show that complement activation and deposition takes place on developing human embryos already at the pre-implantation stage. Using confocal microscopy, we observed deposition of activation products such as C1q, C3 and C5 on healthy developing embryos, which highlights the need for strict complement regulation. The early embryos express the complement membrane inhibitors CD46, CD55 and CD59 and bind the soluble regulators C4bp and factor H. These findings show that complement targets human embryos, and indicate potential adverse pregnancy outcomes, if regulation of activation fails. In addition, single-cell RNA sequencing of embryos at oocyte, zygote, 4-cell and 8-cell stages showed expression of complement genes, e.g. C1s, C2, C3, C5, factor B and factor D. This shows that the embryonic cells themselves have the capacity to express C3 and C5, which may become activated and function as mediators of cellular signaling. The specific local embryonic expression of complement components, regulators, and deposition of activation products on the surface of embryos suggests that complement has immunoregulatory functions and may impact cellular homeostasis and differentiation at the earliest stage of human life.\n\nStatement of significanceWhile canonical functions of the complement system relate to pathogen-defence, it is known to drive certain immune pathologies. The work here described shows, for the first time, expression and localization of a full range of complement molecules in human pre-implantation embryos. We demonstrate complement attack against early embryos, and show presence of embryonic defence mechanisms. Furthermore, we reveal early embryonic production of complement activators, suggesting non-canonical roles in cell signalling and development. Our findings thus reveal a fundamental role for complement at the earliest stages of human embryogenesis. Our data opens up for future studies into the role of complement, both in relation to infertility and pregnancy complications, as well as basic cellular processes during early human development.

developmental biology↗

bioRxiv2019

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

BackgroundPlasmodium falciparum (Pf) whole-organism sporozoite vaccines have provided excellent protection against controlled human malaria infection (CHMI) and naturally transmitted heterogeneous Pf in the field. Initial CHMI studies showed significantly higher durable protection against homologous than heterologous strains, suggesting the presence of strain-specific vaccine-induced protection. However, interpretation of these results and understanding of their relevance to vaccine efficacy (VE) have been hampered by the lack of knowledge on genetic differences between vaccine and CHMI strains, and how these strains are related to parasites in malaria endemic regions.\n\nMethodsWhole genome sequencing using long-read (Pacific Biosciences) and short-read (Illumina) sequencing platforms was conducted to generate de novo genome assemblies for the vaccine strain, NF54, and for strains used in heterologous CHMI (7G8 from Brazil, NF166.C8 from Guinea, and NF135.C10 from Cambodia). The assemblies were used to characterize sequence polymorphisms and structural variants in each strain relative to the reference Pf 3D7 (a clone of NF54) genome. Strains were compared to each other and to clinical isolates from South America, Sub-Saharan Africa, and Southeast Asia.\n\nResultsWhile few variants were detected between 3D7 and NF54, we identified tens of thousands of variants between NF54 and the three heterologous strains both genome-wide and within regulatory and immunologically important regions, including in pre-erythrocytic antigens that may be key for sporozoite vaccine-induced protection. Additionally, these variants directly contribute to diversity in immunologically important regions of the genomes as detected through in silico CD8+ T cell epitope predictions. Of all heterologous strains, NF135.C10 consistently had the highest number of unique predicted epitope sequences when compared to NF54, while NF166.C8 had the lowest. Comparison to global clinical isolates revealed that these four strains are representative of their geographic region of origin despite long-term culture adaptation; of note, NF135.C10 is from an admixed population, and not part of recently-formed drug resistant subpopulations present in the Greater Mekong Sub-region.\n\nConclusionsThese results are assisting the interpretation of VE of whole-organism vaccines against homologous and heterologous CHMI, and may be useful in informing the choice of strains for inclusion in region-specific or multi-strain vaccines.

genomics↗

bioRxiv2019

Functionally overlapping variants control TB susceptibility in Collaborative Cross mice

Host genetics plays an important role in determining the outcome of Mycobacterium tuberculosis (Mtb) infection. We previously found that Collaborative Cross mouse strains differ in their susceptibility to Mtb, and that the CC042/GeniUnc (CC042) strain suffered from a rapidly progressive disease and failed to produce the protective cytokine, IFN{gamma}, in the lung. Here, we used parallel genetic and immunological approaches to investigate the basis of CC042 susceptibility. Using a population derived from a CC001/Unc (CC001) x CC042 intercross, we mapped four QTL underlying Tuberculosis ImmunoPhenotypes (Tip1-4). These included 2 major effect QTL on Chromosome 7 (Tip1 and Tip2) that were associated with bacterial burden. Tip2, along with Tip3 (Chromosome 15) and Tip4 (Chromosome 16) also correlated with IFN{gamma} production following infection, whereas Tip1 appeared to control an IFN{gamma}-independent mechanism of bacterial control. Further immunological characterization revealed that CC042 animals recruited relatively few antigen-specific T cells to the lung and these T cells failed to express the Integrin alpha L (L; i.e., CD11a), which contributes to T cell activation and migration. These defects could be explained by a CC042 private variant in the Itgal gene, which encodes CD11a, and is found within the Tip2 interval. This 15bp deletion leads to aberrant mRNA splicing and is predicted to result in a truncated protein product. The ItgalCC042 genotype was associated with all measured disease traits, indicating that this variant is a major determinant of susceptibility in CC042. The combined effect of functionally distinct Tip variants likely explains the profound susceptibility of CC042 and highlights the multigenic nature of TB control in the Collaborative Cross.\n\nImportance statementThe variable outcome of Mycobacterium tuberculosis infection observed natural populations is difficult to model in genetically homogenous small animal models. The newly-developed Collaborative Cross (CC) represents a reproducible panel of genetically-diverse mice that display a broad range of phenotypic responses to infection. We explored the genetic basis of this variation, focusing on a CC line that is highly susceptible to M. tuberculosis infection. This study identified multiple quantitative trait loci associated with bacterial control and cytokine production, including one that is caused by a novel loss-of-function mutation in the Itgal gene that is necessary for T cell recruitment to the infected lung. These studies verify the multigenic control of mycobacterial disease in the CC panel, identify genetic loci controlling diverse aspects of pathogenesis, and highlight the utility of the CC resource.

microbiology↗