Biology subjects

Bishop, C. R.

Publications and source records attributed to Bishop, C. R..

11 recordsLinked to original sources

bioRxiv2026

ApolipoproteinE drives inflammation resolution pathways essential for recovery from Japanese encephalitis

Effective control of viral encephalitis requires immune responses that clear infection without causing damaging neuroinflammation, yet the mechanisms governing resolution and recovery remain unclear. Using a Japanese encephalitis virus mouse model spanning asymptomatic, symptomatic, and lethal trajectories, together with single-cell spatial transcriptomics and RNA-seq, we identify apolipoprotein E (ApoE) as a driver of neuroinflammation resolution. Apoe was upregulated in microglia and infiltrating myeloid cells of symptomatic survivors, where Apoe-Trem2-Tyrobp signalling promoted a phagocytic, anti-inflammatory program. In contrast, immune cells in lethal disease failed to induce Apoe and remained pro-inflammatory. ApoE-deficient mice were unable to recover following encephalitis onset, demonstrating that ApoE signalling is essential for resolution and recovery. Analysis of cerebrospinal fluid from acute encephalitis patients linked APOE isoforms to neuroinflammation resolution, with APOE{varepsilon}2 carriers exhibiting reduced neutrophils and shorter hospitalisation. These findings identify ApoE as a critical driver of neuroinflammation resolution and a promising therapeutic target for viral encephalitis.

microbiology↗

bioRxiv2025

Characterisation and phylogenetic analysis of Murray Valley encephalitis virus (MVEV) from the Ralph Doherty collection.

Murray Valley encephalitis virus (MVEV) is a zoonotic flavivirus endemic to Australia and Papua New Guinea. A recent outbreak of MVEV has prompted renewed concerns regarding the potential for MVEV to generate disease outbreaks. Currently, nine full length sequences of MVEV are publicly available, divided into four genotypes (G1-G4). Herein, we sequenced MVEV isolates from the Ralph Doherty Virus Collection, a virus bank with Australian field isolates dating between the 1950s-1980s, and determined their phylogenetic relationship with existing isolates to provide insights into virus evolution and genetic diversity. Additionally, we characterised isolates from different genotypes both in vitro using human neuronal cells, and in vivo using C57BL/6J mice, to provide additional insight into MVEV pathogenicity and establish models of MVEV disease that recapitulate MVEV human disease. We found 15 new full length sequences of MVEV, which primarily clustered into the dominant genotype, G1. Additionally, we show MVEV can be lethal and neuroinvasive in C57BL/6J mice, recapitulating histological lesions identified in human infection. Overall, our study contributes significant genomic sequences to the current MVEV database and establishes mouse models of disease and infection which can be used for mechanistic studies and evaluation of new interventions.

microbiology↗

bioRxiv2024

The effects of iron deficient and high iron diets on SARS-CoV-2 lung infection and disease

The severity of Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often dictated by a range of comorbidities. A considerable literature suggests iron deficiency and iron overload may contribute to increased infection, inflammation and disease severity, although direct causal relationships have been difficult to establish. Here we generate iron deficient and iron loaded C57BL/6J mice by feeding low and high iron diets, with mice on a normal iron diet representing controls. All mice were infected with a primary omicron XXB SARS-CoV-2 isolate and lung inflammatory responses were analyzed by histology, immunohistochemistry and RNA-Seq. Compared with controls, iron deficient mice showed no significant changes in lung viral loads or histopathology, whereas, iron loaded mice showed slightly, but significantly, reduced lung viral loads and histopathology. Transcriptional changes were modest, but illustrated widespread dysregulation of inflammation signatures for both iron deficient vs. controls, and iron loaded vs. controls. Some of these changes could be associated with detrimental outcomes, whereas others would be viewed as beneficial. Diet-associated iron deficiency or overload thus induced modest modulations of inflammatory signatures, but no significant histopathologically detectable disease exacerbations. Author summaryA diet deficient in iron can lead to anemia, a widespread problem worldwide. A diet with excessive iron is less common, but can be associated with excessive consumption of iron supplements. We investigate herein using a mouse model, whether low or high iron diets predispose to detrimental outcomes in the lungs after infection with SARS-CoV-2. A considerable literature suggests iron dysregulation would promote infection and inflammation. However, we found, although inflammatory responses showed modest modulations, viral loads were unaffected or slightly reduced, and lung histopathology was either unaffected or indicated slightly less severe disease. These findings do not support a view that low or high iron diets represent comorbidities predisposing to overt detrimental outcomes for acute COVID-19 lung disease.

pathology↗

bioRxiv2024

TMEM106B-mediated SARS-CoV-2 infection allows for robust ACE2-independent infection in vitro but not in vivo

Angiotensin converting enzyme 2 (ACE2) serves as the primary entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, ACE2-independent entry has been observed in vitro for SARS-CoV-2 strains containing the E484D amino acid substitution in the spike protein. In this study, we conducted a whole genome CRISPR-Cas9 knockout screen using a SARS-CoV-2 strain containing the spike-E484D substitution (SARS-CoV-2MA1) to identify the ACE2-independent entry mechanisms. Our findings revealed that SARS-CoV-2MA1 infection in HEK293T cells relied on heparan sulfate and endocytic pathways, with TMEM106B emerging as the most significant contributor. While SARS-CoV-2MA1 productively infected human brain organoids and K18-hACE2 mouse brains, it did not infect C57BL/6J or Ifnar-/- mouse brains. This suggests that ACE2-independent entry via TMEM106B, which is a protein that is predominantly expressed in the brain, did not overtly increase the risk of SARS-CoV-2 neuroinvasiveness in wild-type mice. Importantly, SARS-CoV-2MA1 did not replicate in Ace2-/- mouse respiratory tracts. Overall, this suggests that robust ACE2-independent infection by SARS-CoV-2E484D is likely a phenomenon specific to in vitro conditions, with no apparent clinical implications.

microbiology↗

bioRxiv2024

Tracking inflammation resolution signatures in lungs after SARS-CoV-2 omicron BA.1 infection of K18-hACE2 mice

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes Coronavirus Disease 2019 (COVID-19), which can result in severe disease, often characterised by a cytokine storm and the associated acute respiratory distress syndrome. However, many infections with SARS-CoV-2 are mild or asymptomatic throughout the course of infection. Although blood biomarkers of severe disease are well studied, less well understood are the inflammatory signatures in lung tissues associated with mild disease or silent infections, wherein infection and inflammation are rapidly resolved leading to sequelae-free recovery. Herein we described RNA-Seq and histological analyses of lungs over time in an omicron BA.1/K18-hACE2 mouse infection model, which displays these latter features. Although robust infection was evident at 2 days post infection (dpi), viral RNA was largely cleared by 10 dpi. Acute inflammatory signatures showed a slightly different pattern of cytokine signatures compared with severe infection models, and where much diminished 30 dpi and absent by 66 dpi. Cellular deconvolution identified significantly increased abundance scores for a number of anti-inflammatory pro-resolution cell types at 5/10 dpi. These included type II innate lymphoid cells, T regulatory cells, and interstitial macrophages. Genes whose expression trended downwards over 2 - 66 dpi included biomarkers of severe disease and were associated with cytokine storm pathways. Genes whose expression trended upward during this period were associated with recovery of ciliated cells, AT2 to AT1 transition, reticular fibroblasts and innate lymphoid cells, indicating a return to homeostasis. Very few differentially expressed host genes were identified at 66 dpi, suggesting near complete recovery. The parallels between mild or subclinical infections in humans and those observed in this BA.1/K18-hACE2 mouse model are discussed with reference to the concept of "protective inflammation".

immunology↗

bioRxiv2023

Microplastics dysregulate innate immunity in the SARS-CoV-2 infected lung

Global microplastic (MP) pollution is now well recognized, with humans and animals consuming and inhaling MPs on a daily basis. Herein we described the effects of azide-free, 1 {micro}m polystyrene MP beads co-delivered into lungs with a SARS-CoV-2 omicron BA.5 inoculum using a mouse model of mild COVID-19. Lung virus titres and viral RNA levels were not significantly affected by MPs, with overt clinical or histopathological changes also not observed. However, RNA-Seq of infected lungs revealed that MP exposure suppressed innate immune responses at 2 days post infection (dpi) and increased pro-inflammatory signatures at 6 dpi. The cytokine profile at 6 dpi showed a significant correlation with the cytokine release syndrome signature seen in some severe COVID-19 patients. This study adds to a growing body of literature suggesting that MPs can dysregulate inflammation in specific disease settings. Graphical Abstract HIGHLIGHTSO_LIA single inoculation of microplastics dysregulated SARS-CoV-2 lung inflammation C_LIO_LIAt the peak of SARS-CoV-2 infection microplastics decreased early innate responses C_LIO_LILater post infection microplastics promoted a "cytokine release syndrome" signature C_LIO_LIA key mechanism may involve the inhibition of the phagocytosis of infected cells C_LIO_LIAzide-free microplastics were used, with no elevated ROS responses identified C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/567745v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@73eefborg.highwire.dtl.DTLVardef@14eb683org.highwire.dtl.DTLVardef@b0638aorg.highwire.dtl.DTLVardef@571512_HPS_FORMAT_FIGEXP M_FIG Postulated mechanisms whereby microplastics might decrease the proinflammatory responses 2 days after SARS-CoV-2 infection, yet promote the proinflammatory cytokine release syndrome signature at 6 days post infection. C_FIG

microbiology↗

bioRxiv2023

Characterization of an Australian outbreak Japanese Encephalitis virus genotype 4 isolate in mice and human cortical brain organoids

BackgroundHuman infections with Japanese encephalitis virus (JEV) are a leading cause of viral encephalitis. An unprecedented outbreak of JEV genotype 4 was recently reported in Australia, with an isolate (JEVNSW/22) obtained from a stillborn piglet brain. MethodsHerein we compared the neuropathology of JEVNSW/22, JEVFU (genotype 2) and JEVNakayama (genotype 3) in adult C57BL/6J wild-type mice, mice deficient in interferon regulatory factor 7 (Irf7-/-), and mice deficient in type I interferon receptor (Ifnar-/-), as well as in human cortical brain organoids (hBOs). Using human serum post-Imojev vaccination, we performed neutralisation assays to determine JEVNSW/22 susceptibility to vaccine responses. FindingsIn C57BL/6J and Irf7-/- mice with lethal outcomes, brain infection and histopathological lesions recapitulated those seen in humans and primates. JEV was universally lethal in Ifnar-/- mice by day 3 with histological signs of brain hemorrhage, but produced no other detectable brain infection or lesions, with viral protein detected in blood vessels but not neurons. We thus describe a new Irf7-/- mouse model for JEVNSW/22, which had increased viremia compared to C57BL/6J mice, allowing for lethal neuroinvasive infection in one mouse. Overall, JEVNSW/22 was less neurovirulent than other JEV isolates in C57BL/6J and Irf7-/- mice, and was more sensitive to type I interferon. All JEV isolates showed robust cytopathic infection of human cortical brain organoids, albeit lower for JEVNSW/22. We also show that Imojev vaccination in humans induced neutralizing antibodies against JEVNSW/22, with the level of cross-neutralisation related to the conservation in envelope protein amino acid sequences for each isolate. InterpretationOur study establishes JEVNSW/22 mouse models of infection, allowing for possible lethal neuroinvasive infection that was rarer than for other JEV genotypes. JEV vaccination regimens may afford protection against this newly emerged JEV genotype 4 strain, although neutralizing antibody responses are sub-optimal. FundingQIMRB received a generous philanthropic donation from the Brazil Family Foundation awarded to D.J.R. to support Japanese Encephalitis virus research at QIMRB. A.S. holds an Investigator grant from the National Health and Medical Research Council (NHMRC) of Australia (APP1173880). We also acknowledge the intramural grant from QIMR Berghofer awarded to R.S. and D.J.R. for purchase of the CelVivo Clinostar incubator for producing human cortical brain organoids. The project "Japanese encephalitis vaccine via the intradermal route in children and adults (JEVID-2): A clinical trial comparing the immunogenicity and safety of Japanese encephalitis vaccine administered by subcutaneous and intradermal routes" being conducted by G.D., N.G., and N.W. was funded by the Sydney Childrens Hospitals Network and New South Wales Health. Research in context Evidence before the studyJEV from the historically rare genotype 4 recently emerged in Australia, causing an unprecedented outbreak, with 44 human cases and 7 fatalities. While a range of JEV mouse models have been reported, none of them infect adult mice with a genotype 4 isolate. The efficacy of current vaccines for this JEV genotype are also unclear. Added value of this studyWe establish well characterised adult and subcutaneously infected mouse models for JEV which recapitulate many aspects of human disease including lethal neuroinvasive infection and severe histopathological lesions. Prolonged viremia was significantly associated with lethal neuroinvasiveness in Irf7-/-mice. We demonstrate that a genotype 4 Australian isolate, JEVNSW/22, exhibited markedly diminished lethal neuroinvasion compared to other JEV genotypes. Using serum from Imojev vaccine recipients, neutralizing antibodies against JEVNSW/22 were present, albeit at sub-optimal titers. Implications of all the available evidenceThe establishment of well characterised adult mouse models of JEVNSW/22 with rare neuropenetrance after peripheral inoculation that recapitulate human disease is an important tool that can now be deployed in pre-clinical studies and to understand disease pathogenesis. Our study suggests that new vaccines should be developed against circulating JEV strains for optimal neutralizing antibody responses.

microbiology↗

bioRxiv2022

Omicron BA.5 infects human brain organoids and is neuroinvasive and lethal in K18-hACE2 mice

The reduced pathogenicity of the omicron BA.1 sub-lineage compared to earlier variants is well described, although whether such attenuation is retained for later variants like BA.5 and XBB remains controversial. We show that BA.5 and XBB isolates were significantly more pathogenic in K18-hACE2 mice than a BA.1 isolate, showing increased neuroinvasiveness, resulting in fulminant brain infection and mortality, similar to that seen for original ancestral isolates. BA.5 also infected human cortical brain organoids to a greater extent than the BA.1 and original ancestral isolates. In the brains of mice, neurons were the main target of infection, and in human organoids neuronal progenitor cells and immature neurons were infected. Although fulminant brain infection is not a feature of COVID-19, evidence for brain infection and brain damage in some COVID-19 patients with severe disease is becoming compelling, with the results herein suggesting that evolving omicron variants may have increasing intrinsic neuropathogenic potential.

microbiology↗

bioRxiv2022

Analysis of Aedes aegypti microRNAs in response to Wolbachia wAlbB infection and their potential role in mosquito longevity

The mosquito Aedes aegypti is the primary vector of a range of medically important viruses including dengue, Zika, West Nile, yellow fever, and chikungunya viruses. The endosymbiotic bacterium Wolbachia pipientis wAlbB strain is a promising biocontrol agent for blocking viral transmission by Ae. aegypti. To predict the long-term efficacy of field applications, a thorough understanding of the interactions between symbiont, host, and pathogen is required. Wolbachia influence host physiology in a variety of ways including reproduction, immunity, metabolism, and longevity. MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that regulate gene expression in eukaryotes and viruses. A number of miRNAs are known to regulate biological processes in Drosophila and mosquitoes, including facilitating Wolbachia maintenance. We generated the first chromosomal map of Ae. aegypti miRNAs, and compared miRNA expression profiles between a wAlbB-transinfected Ae. aegypti mosquito line and a tetracycline cleared derivative, using deep small RNA-sequencing. We found limited modulation of miRNAs in response to wAlbB infection. Several miRNAs were modulated in response to age, some of which showed greater upregulation in wAlbB-infected mosquitos than in tetracycline cleared ones. By selectively inhibiting some differentially expressed miRNAs, we identified miR-2946-3p and miR-317-3p as effecting mosquito longevity. ImportanceWolbachia is an endosymbiotic bacterium found in about 65% of insect species. It is mostly known for reproductive manipulations of the host, and also blocking replication of positive sense RNA viruses. Transinfection of Wolbachia into Aedes aegypti mosquitoes, which transmit a variety of arboviruses, including dengue virus, has provided a novel biological approach in reducing transmission of arboviruses. To gain a better understanding of Wolbachia-mosquito interactions, we investigated the impact of Wolbachia on the microRNA profile of Ae. aegypti mosquitoes. We produced the first chromosome-level map of Ae. Aegypti miRNAs. We found modulation of microRNAs in mosquitoes due to age, with two miRNAs, 317-3p and 2946-3p, showing significant increase with age. Inhibition of 317-3p and 2946-3p led to reduced mosquito life span in wAlbB-infected mosquitoes. The outcomes provide insights into underlying molecular mechanisms involved in Wolbachia-host interactions.

microbiology↗

bioRxiv2022

Mouse models of COVID-19 recapitulate inflammatory pathways rather than gene expression

BACKGROUNDHow well mouse models recapitulate the transcriptional profiles seen in humans remains debatable, with both conservation and diversity identified in various settings. The K18-hACE2 mouse model has been widely used for evaluation of new interventions for COVID-19. METHODHerein we use RNA-Seq data and bioinformatics approaches to compare the transcriptional responses in the SARS-CoV-2 infected lungs of K18-hACE2 mice with those seen in humans. RESULTSOverlap in differentially expressed genes was generally poor ({approx}20-30%), even when multiple studies were combined. The overlap was not substantially improved when a second mouse model was examined wherein hACE was expressed from the mouse ACE2 promoter. In contrast, analyses of immune signatures and inflammatory pathways illustrated highly significant concordances between the species. CONCLUSIONAs immunity and immunopathology are the focus of most studies, these hACE2 transgenic mouse models can thus be viewed as representative and relevant models of COVID-19.

molecular biology↗

bioRxiv2021

Microplastic consumption induces inflammatory signatures in the colon and prolongs a viral arthritis

Global microplastic (MP) contamination and the effects on the environment are well described. However, the potential for MP consumption to affect human health remains controversial. Mice consuming {approx}80 {micro}g/kg/day of 1 {micro}m polystyrene MPs via their drinking water for a month showed no weight loss, nor were MPs detected in organs. The microbiome was also unchanged. MP consumption did lead to small transcriptional changes in the colon suggesting plasma membrane perturbations and mild inflammation. Mice were challenged with the arthritogenic chikungunya virus, with MP consumption leading to a significantly prolonged arthritic foot swelling that was associated with elevated Th1, NK cell and neutrophil signatures. Immunohistochemistry also showed a significant increase in the ratio of neutrophils to monocyte/macrophages. The picture that emerges is reminiscent of enteropathic arthritis, whereby perturbations in the colon are thought to activate innate lymphoid cells that can inter alia migrate to joint tissues to promote inflammation.

immunology↗