Biology subjects

Briggs, E.

Publications and source records attributed to Briggs, E..

9 recordsLinked to original sources

bioRxiv2026

Infection drives localised and individualised antibody repertoires, whereas immunisation promotes repertoire convergence in pig

Respiratory viruses elicit mucosal and systemic immunity, yet how tissue compartmentalisation and exposure route shape B cell repertoires remain unclear. Using the pig model, we characterised antibody repertoires in bronchoalveolar lavage, tracheobronchial lymph nodes, spleen, and blood following intranasal infection with pandemic influenza virus (pH1N1) or porcine respiratory coronavirus (PRCV), and after intramuscular PRCV immunisation. Infection induced highly compartmentalised responses, with antigen-associated clones enriched in lung, lymph nodes and spleen but with limited presentation in blood. These clones were largely private, indicating individualised responses, and displayed tissue-specific diversity. The similar tissue distributions between pH1N1 and PRCV infections suggest a conserved spatial organisation, although differential lymph node involvement indicates pathogen-specific effects. In contrast, intramuscular immunisation generated more convergent, public repertoires in blood, characterised by reduced clonal size diversity. Monoclonal antibody analysis revealed functional heterogeneity and limited overlap with bulk repertoires. Together, these findings show that despite stable germline usage, functional antibody responses are shaped by the route of antigen exposure, clonal selection, and host specific factors, resulting in distinct repertoire architectures between infection and immunisation. Author summaryRespiratory viruses such as influenza and coronaviruses infect the airways and lungs, where they trigger immune responses that help the body fight infection. Most studies of immunity rely on blood, although many immune cells function in tissues like the lungs. Therefore, we may be missing important parts of the immune response. We used pigs, a large animal model that closely resembles humans in respiratory biology and is naturally infected with influenzas and coronaviruses, to investigate how immune responses are shaped by infection compared with intramuscular vaccination. We examined B cells in lungs, nearby lymph nodes, spleen, and blood after infection with influenza or a porcine coronavirus and compared these with responses after vaccination. We found that infection generates distinct, individual immune responses in the lung and lymphoid organs. Vaccination by injection led to more similar responses across animals, mostly in the blood. This suggests the way the immune system encounters an antigen influences the response generated. We also showed that antibodies with similar binding properties can behave very differently in their ability to neutralise viruses. Our findings show that infection and vaccination shape immunity in fundamentally different ways, with important implications for designing vaccines that better protect against respiratory diseases.

immunology↗

bioRxiv2026

Pathogenesis and immune responses to Eurasian avian like H1N1 and influenza D virus in pigs.

Eurasian avian like H1N1 (EAavH1N1) and influenza D viruses (IDV) with their ongoing evolution and zoonotic potential are a serious threat to animal and human health. Using experimental infection of pigs, we characterized and compared their pathogenesis, and immune responses. EAavH1N1 induced rapid viral clearance, early immune activation, including robust systemic and mucosal antibody responses and increased IFN{gamma} and TNF production. This heightened immune response was associated with more severe pathology of the upper and lower respiratory tract. In contrast, IDV infection resulted in prolonged viral shedding and higher viral titres, with delayed and attenuated cellular immune responses. Single cell transcriptomic analysis of lung further indicated early and persistent suppression of antiviral and innate immune pathways during IDV infection. These findings demonstrate that EAavH1N1 and IDV exhibit distinct viral kinetics, immune activation profiles, and lung responses, providing insight into differences in transmission dynamics, disease severity, and immune control among influenza virus types in swine.

immunology↗

bioRxiv2025

Post-infection pig and ferret antisera show similar antigenic profiles for human influenza A(H1N1pdm09) viruses

BackgroundMonitoring antigenic drift in human influenza A viruses is essential for vaccine strain selection and ensuring protection against circulating strains. Antigenic drift is traditionally assessed using ferret antisera, which provide monospecific responses, and human vaccinee sera, which reflect exposure to multiple antigens. In this study we evaluated the pig as an alternative source of antisera to study antigenic drift compared to immune responses in ferrets and humans. We included seasonal influenza A(H1N1pdm09) human viruses that had shown different antigenic characteristics when using ferret or human antisera. MethodsPairs of pigs were inoculated with six human A(H1N1)pdm09 viruses circulating between 2019 and 2023, a period of marked antigenic drift. Pig and ferret antisera were analysed by hemagglutination inhibition (HI) and virus neutralization (VN) assays. ResultsPigs were successfully infected with all strains, shedding virus and producing antibody responses, confirming their susceptibility to human influenza A viruses. Antigenic reactivity of pig antisera was qualitatively comparable to ferret antisera in both HI and VN assays, although maximum homologous antibody titres were significantly higher in ferrets. The antisera raised against viruses in circulation in 2019 and before, exempified by A/Guangdong-Maonan/SWL1536/2019, clade 5a.1, were clearly differentiated by both ferret and pig antisera from those in clade 5a.2 and its derivatives that became predominant. ConclusionsFerrets and pigs showed comparable responses and both distinguished clade 5a.1 from clade 5a.2. However, neither model recognised antigenically drifted variants from 2019-2022, including subclades 5a.2-C, 5a.2a-C.1/C.1.9, and .5a.2a.1-C.1.1/D, which were distinguishable using human post-vaccination antisera.

immunology↗

bioRxiv2025

ADAR1 haploinsufficiency and sustained viral RdRp dsRNA synthesis synergize to dysregulate RNA editing and cause multi-system interferonopathy

Sensing of viral double-stranded RNA by MDA5 triggers abundant but transient interferon-stimulated gene (ISGs) expression. If dsRNA synthesis is made persistent by transgenically expressing a picornaviral RNA-dependent RNA polymerase (RdRp) in mice, lifelong MDA5-MAVS pathway activation and marked, global ISG upregulation result. This confers robust protection from viral diseases but in contrast to numerous other chronic MDA5 hyperactivation states, the mice suffer no autoimmune or other health consequences. Here we find they further confound expectations by being resistant to a strong autoimmunity (lupus) provocation. However, knockout of one allele of Adar breaks the autoinflammation-protected state of RdRptg mice and results in a severe disease that resembles interferonopathies caused by MDA5 gain-of-function protein mutations. Adar+/- mice are healthy but Adar+/- RdRptg mice have shortened lifespan, stunted growth, premature fur graying, poorly developed teeth, skeletal abnormalities, and extreme ISG elevations. A-to-I edits are both abnormally distributed and increased (numbers of genes and sites). These results, with a nucleic acid-triggered and MDA5-wild type model, illuminate the ADAR1-MDA5 axis in the regulation of innate immunity and establish that viral polymerase-sourced dsRNA can drive autoinflammatory disease pathogenesis. IMPORTANCERNA virus double-stranded RNAs are important pathogen associated molecular patterns that are sensed by the RIG-I like receptor MDA5, which triggers an acute innate immune response involving many ISGs. One key to a healthy innate immune system is that MDA5 not sense endogenous dsRNA. This is normally ensured by dsRNA duplex-disrupting ADAR1 editing of host dsRNAs. Picornavirus RdRptg mice have an unusual constitutive MDA5 activation state, with very high lifelong MDA5-mediated ISG expression that confers robust protection from diverse lethal viruses. Importantly, and in contrast to numerous other chronic MDA5 hyperactivation states, the mice develop no autoinflammatory consequences. If we delete one ADAR1 allele, however, which by itself is well tolerated, the mice develop a multisystem disease that resembles the human interferonopathy Singleton-Merten syndrome. In contrast to other MDA5/ADAR1 disease models, the MDA5 and ADAR1 proteins are both wild type in this dsRNA-driven model.

immunology↗

bioRxiv2024

Pathogenesis and immune response to respiratory coronaviruses in their natural porcine host

Porcine respiratory coronavirus (PRCV) is a naturally occurring pneumotropic coronavirus in the pig, providing a valuable large animal model to study acute respiratory disease. PRCV pathogenesis and the resulting immune response was investigated in pigs, the natural large animal host. We compared two strains, ISU-1 and 135, which induced differing levels of pathology in the respiratory tract to elucidate the mechanisms leading to mild or severe disease. The 135 strain induced greater pathology which was associated with higher viral load and stronger spike-specific antibody and T cell responses. In contrast, the ISU-1 strain triggered mild pathology with a more balanced immune response and greater abundance of T regulatory cells. A higher frequency of putative T follicular helper cells was observed in animals infected with strain 135 at 11 days post-infection. Single-cell RNA-sequencing of bronchoalveolar lavage revealed differential gene expression in B and T cells between animals infected with 135 and ISU-1 at 1 day post infection. These genes were associated with cell adhesion, migration, and immune regulation. Along with increased IL-6 and IL-12 production, these data suggest that heightened inflammatory responses to the 135 strain may contribute to pronounced pneumonia. Among BAL immune cell populations, B cells and plasma cells exhibited the most gene expression divergence between pigs infected with different PRCV strains, highlighting their potential role in maintaining immune homeostasis in the respiratory tract. These findings indicate the potential of the PRCV model for studying coronavirus induced respiratory disease and identifying mechanisms that determine infection outcomes. Author summaryUnderstanding how our immune system reacts to respiratory viruses, like SARS-CoV-2, is crucial to developing better treatments. While most COVID-19 infections are mild, some cases lead to severe lung damage, but we do not fully understand why. To study this, we used pigs, which respond more like humans compared to small animals, to explore how the immune system deals with respiratory coronaviruses. We tested two porcine respiratory coronavirus strains that caused different levels of lung damage. The more severe strain triggered a strong immune response and high inflammation, leading to lung pathology similar to that seen in severe COVID-19 cases. By contrast, the milder strain caused a balanced immune response, including more regulatory T cells that help control inflammation. We also found changes in genes related to antibody-producing cells, which may be important for controlling respiratory pathology. Interestingly, changes in immune responses and gene expression lasted long after the virus was cleared, potentially making individuals more vulnerable to future infections - similar to the "long COVID" symptoms seen in people. We propose that this pig model could help us study coronavirus-induced lung damage and test new therapies to prevent severe disease.

immunology↗

bioRxiv2019

Genome maintenance functions of Trypanosoma brucei DNA Polymerase N include telomere association and a role in antigenic variation

Maintenance of genome integrity is critical to guarantee transfer of an intact genome from parent to offspring during cell division. DNA polymerases (Pols) provide roles in both replication of the genome and the repair of a wide range of lesions. Amongst replicative DNA Pols, translesion DNA Pols play a particular role: replication to bypass DNA damage, often at the cost of mutation. All cells express a range of translesion Pols, but little work has examined their function in parasites, including whether the enzymes might contribute to host-parasite interactions. Here, we describe a dual function of translesion PolN in African trypanosomes. Previously we demonstrated that PolN is associated with telomeric sequences and now we show that RNAi-mediated depletion of PolN results in slowed growth, altered DNA content, changes in cell morphology, and increased sensitivity to DNA damaging agents. Depletion of PolN leads to chromosome segregation defects and accumulation of DNA damage. We also show that PolN displays discrete localisation at the nuclear periphery in the absence of exogenous DNA damage. In addition, we demonstrate that PolN depletion leads to deregulation of telomeric variant surface glycoprotein genes, linking the function of this translesion DNA polymerase to host immune evasion by antigenic variation.

microbiology↗

bioRxiv2019

Temporal Gut Microbial Changes Predict Recurrent Clostridium difficile in Patients with and without Ulcerative Colitis

BackgroundUlcerative colitis (UC) carries an increased risk of primary and recurrent Clostridium difficile infection (rCDI) and CDI is associated with UC flares. We hypothesized that specific fecal microbial changes associate with UC flare and rCDI.\n\nMethodsWe conducted a prospective observational cohort study of 57 patients with UC and CDI, CDI only, and UC flare only. Stool samples were collected at baseline, at the end of antibiotic therapy, and after reconstitution for 16S rRNA sequencing. The primary outcomes were recurrent UC flare and rCDI. Logistic regression and Lasso models were constructed for analysis.\n\nResultsThere were 21 (45.7%) patients with rCDI, while 11 (34.4%) developed UC flare. Patients with rCDI demonstrated significant inter-individual (P=.008) and intra-individual differences (P=.004 relative to baseline samples) in community structure by Jensen-Shannon distance (JSD) compared with non-rCDI. Two cross-validated models identified by Lasso regression predicted risk of rCDI: a baseline model with female gender, hospitalization for UC in the past year, increased Ruminococcaceae and Verrucomicrobia, and decreased Eubacteriaceae, Enterobacteriaceae, Lachnospiraceae, and Veillonellaceae (AuROC=0.94); and a model 14 days after completion of antibiotics with female gender, increased Shannon diversity, Ruminococcaceae and Enterobacteriaceae, and decreased community richness and Faecalibacterium (AuROC=0.9). Adding JSD between baseline and post-treatment samples to the latter model improved fit (AuROC=0.94). A baseline model including UC hospitalization in the past year and increased Bacteroidetes showed good fit characteristics for predicting increased risk of UC flare (AuROC=0.88).\n\nConclusionFecal microbial features at baseline and following therapy predict rCDI risk in patients with and without UC. These results may help risk stratify patients to guide management.

microbiology↗

bioRxiv2018

RibonucleaseH1-targeted R-loops in surface antigen gene expression sites can direct trypanosome immune evasion

Switching of the Variant Surface Glycoprotein (VSG) in Trypanosoma brucei provides a crucial host immune evasion strategy that is catalysed both by transcription and recombination reactions, each operating within specialised telomeric VSG expression sites (ES). VSG switching is likely triggered by events focused on the single actively transcribed ES, from a repertoire of around 15, but the nature of such events is unclear. Here we show that RNA-DNA hybrids, called R-loops, form preferentially within sequences termed the 70 bp repeats in the actively transcribed ES, but spread throughout the active and inactive ES in the absence of RNase H1, which degrades R-loops. Loss of RNase H1 also leads to increased levels of VSG coat switching and replication-associated genome damage, some of which accumulates within the active ES. This work indicates VSG ES architecture elicits R-loop formation, and that these RNA-DNA hybrids connect T. brucei immune evasion by transcription and recombination.\n\nAuthor summaryAll pathogens must survive eradication by the host immune response in order to continue infections and be passed on to a new host. Changes in the proteins expressed on the surface of the pathogen, or on the surface of the cells the pathogen infects, is a widely used strategy to escape immune elimination. Understanding how this survival strategy, termed antigenic variation, operates in any pathogen is critical, both to understand interaction between the pathogen and host and disease progression. A key event in antigenic variation is the initiation of the change in expression of the surface protein gene, though how this occurs has been detailed in very few pathogens. Here we examine how changes in expression of the surface coat of the African trypanosome, which causes sleeping sickness disease, are initiated. We reveal that specialised nucleic acid structures, termed R-loops, form around the expressed trypanosome surface protein gene and increase in abundance after mutation of an enzyme that removes them, leading to increased changes in the surface coat in trypanosome cells that are dividing. We therefore shed light on the earliest acting events in trypanosome antigenic variation.

microbiology↗

bioRxiv2018

Genome-wide mapping reveals conserved and diverged R-loop activities in the unusual genetic landscape of the African trypanosome genome

R-loops are stable RNA-DNA hybrids that have been implicated in transcription initiation and termination, as well as in telomere homeostasis, chromatin formation, and genome replication and instability. RNA Polymerase (Pol) II transcription in the protozoan parasite Trypanosoma brucei is highly unusual: virtually all genes are co-transcribed from multigene transcription units, with mRNAs generated by linked trans-splicing and polyadenylation, and transcription initiation sites display no conserved promoter motifs. Here, we describe the genome-wide distribution of R-loops in wild type mammal-infective T. brucei and in mutants lacking RNase H1, revealing both conserved and diverged functions. Conserved localisation was found at centromeres, rRNA genes and retrotransposon-associated genes. RNA Pol II transcription initiation sites also displayed R-loops, suggesting a broadly conserved role despite the lack of promoter conservation or transcription initiation regulation. However, the most abundant sites of R-loop enrichment were within the intergenic regions of the multigene transcription units, where the hybrids coincide with sites of polyadenylation and nucleosome-depletion. Thus, instead of functioning in transcription termination, most T. brucei R-loops act in a novel role, promoting RNA Pol II movement or mRNA processing. Finally, we show there is little evidence for correlation between R-loop localisation and mapped sites of DNA replication initiation.

genomics↗