Biology subjects

Wright, E.

Publications and source records attributed to Wright, E..

17 recordsLinked to original sources

bioRxiv2026

3D-genome impacts of TAD-boundary-disrupting ultra-rare structural variants identified in schizophrenia

Schizophrenia is a complex and multifactorial brain disorder that impacts ~1% of the U.S. population. The genetic architecture of schizophrenia includes 10 large rare structural variants (SVs) ~10 exonic variants, and over 250 common variants. Previously we combined whole genome sequencing (WGS) with brain-specific epigenomic data and found an excess of ultrarare SVs in schizophrenia localizing to the boundaries of topologically associated domains (TADs). Alterations in TAD boundaries (TAD-b) may lead to disarrangement of enhancer-promoter contacts and dysregulation of gene expression and have been associated with several human diseases. Our study sought to functionally characterize two of these TAD-b SVs using chromatin conformation capture (e.g., Hi-C) and RNA sequencing, to unveil mechanistic insight into the effects of these variants on 3D-genome organization and gene expression. To achieve this, we genetically engineered these two TAD-b SVs in isogenic induced pluripotent stem cells (iPSCs) using CRISPR/Cas9. iPSCs were differentiated into neuronal precursor cells, excitatory glutamatergic neurons, and medium spiny neurons. We found that these TAD-boundary-disrupting SVs could reshape the 3D-genome and transcriptional networks in a cell-type-specific manner.

genomics↗

bioRxiv2026

Quantitative imaging of schwannoma captures heterogeneity and accelerates preclinical testing, revealing distinct impacts of targeted therapies

Schwannomas are debilitating hallmarks of familial schwannomatoses and common sporadic tumors that form on spinal and cranial nerves. Drug-based therapies for schwannoma are desperately needed but their development has been extremely slow and disappointing, impeded particularly by the poorly understood and surprisingly complex and heterogeneous biology of schwannomas, and by the inefficient use of physiologically relevant in vivo preclinical models. We have addressed these gaps by developing a quantitative imaging-centered workflow that allows both a deep analysis of schwannoma development and accelerated preclinical testing in a widely used genetically engineered mouse model of neurofibromatosis type 2-related schwannomatosis (NF2-SWN). We deployed our workflow to study schwannoma development and to test two clinically relevant drugs (rapamycin and brigatinib) head-to-head. Our results uncovered the very early onset of heterogeneity and macrophage recruitment to initiating schwannomas, and the unexpectedly distinct impacts of the two drugs on both, highlighting the value of the pipeline for rapid, innovative future drug-testing.

cancer biology↗

bioRxiv2026

TALE and Hox Transcription Factors Control Adult Behaviors in Zebrafish

Behavioral dysfunction is a common characteristic of many mental health disorders. While the causes of these disorders vary, aberrant behaviors may arise from alterations in transcriptional regulation already during early neural development. Because transcription factors (TFs) often belong to families of closely related members, disruption of a single TF may indirectly influence the functionality of other family members. Consequently, mutations in TFs within the same family may lead to overlapping, yet distinct, phenotypes. This feature of TF function has important implications for understanding behavioral phenotypes, but detailed analyses across a single TF family are still lacking. In this study, we present a comprehensive behavioral analysis of adult zebrafish harboring mutations in individual members of the TALE and Hox TF families, that are essential for nervous system development. Using a battery of validated behavioral assays, we uncover elevated stress responses among all TF mutant lines, as well as TF-specific dysregulation in coping strategies, social interaction, learning/memory, and endurance and locomotion. The shared behavioral abnormalities across mutants suggests TF family members converge on core developmental pathways for stress-related behavioral regulation, while mutation-specific phenotypes indicate unique roles for individual TFs in fine-tuning neural function. Our findings provide a systematic behavioral characterization of TALE and Hox mutants in a vertebrate model and provide a framework for understanding how genetic variation within TF families may differentially contribute to vulnerability for mental health disorders.

animal behavior and cognition↗

bioRxiv2025

Cross-Neutralizing Monoclonal Antibodies with Broad Activity Against Human and Bat-Derived SARS-Related Coronaviruses

Effective therapeutics for severe cases of SARS-CoV-2 are still needed. As new variants of concern emerged an increase in hospitalizations was observed, especially in non-vaccinated individuals, immunocompromised individuals and the elderly, whereby treatment options became challenging. Several monoclonal antibodies (mAb) are being evaluated for approval due to their ability to neutralize the virus. Here, we report monoclonal antibodies targeting the Spike (S) with a strong neutralization profile against lentiviral and VSV pseudotypes displaying the Spikes of SARS-CoV-1, SARS-CoV-2 and variants of concern, in addition to two bat coronaviruses. We found several mAbs that were able to bind and neutralize a broad set of variants, with one mAb able to neutralize SARS-CoV-1, SARS-CoV-2, RaTG13 and WIV16. Their binding affinities were also characterized, and several mAbs were in the picomolar range against different variants. These results indicate that their use as a cocktail of monoclonal antibodies to treat patients infected with variants associated with severe disease and immune escape can be explored as an option. Furthermore, the cross reactivity observed by one mAb may reveal further insight into vulnerable portions of the Spike protein, which may become valuable future targets.

microbiology↗

bioRxiv2025

Ceudovitox: a novel pseudotyped-virus screening platform to identify cell entry factors for high consequence infections.

Development of scalable and highly adaptable platforms to characterise high consequence infections are essential for limiting the impact of future viruses with pandemic potential. As part of this, an understanding of the virus-host interactions is vital, with the cell entry mechanism being crucial for the development of therapeutics and vaccines. Current approaches in this field depend on assays with authentic (live) viruses that require high containment facilities. However, these are hindered by high costs, need for highly trained staff, slow processing times and limited scalability. Using pseudotyped viruses (PV) expressing the chikungunya (CHIKV) envelope protein as a proof-of-principle, we developed a novel screening platform, Ceudovitox, to identify cellular factors involved in viral entry. PVs were engineered to express the herpes simplex virus-1 thymidine kinase, which following addition of ganciclovir, can selectively kill infected cells. Then a heterogenous pool of knockout cells were produced using the CRISPR-Cas9 library. Infection of these cells with the "killer" PV system permitted positive selection of cells refractory to viral infection and, through next generation sequencing, identification of a number of factors involved in CHIKV entry. Matrix metalloproteinases were identified as novel entry factors and demonstrated that MMP-targeting drugs efficiently inhibit PV and authentic CHIKV infections. These results suggest this platform holds great promise as a pandemic-preparedness tool that increases the capacity and speed of screening for cell entry factors. It is also a safe platform able to dissect the gene network involved in virus entry. Ceudovitox will help identify new therapeutic targets, thereby aiding the development of treatments against future outbreaks or pandemic pathogens and making a significant contribution to the "100 days" mission. Author SummaryThe increased threat of the emergence of new viral pathogens with pandemic potential highlights the importance of developing scalable high-throughput screening platforms to quickly characterise new emergent viral pathogens. Improving understanding of virus-host interactions, including how viruses enter cells, can help fast development of new targeted therapeutics and reduce pandemic burdens. Current approaches rely on using live viruses, which are highly infectious and must be manipulated in high containment facilities, which are slow and cumbersome. Our new screening platform, Ceudovitox, is a safer, faster and more scalable alternative. Through using pseudotyped viruses, which can only undergo one replication cycle, we are able to distinguish virus entry factors of high containment viruses within highly abundant low containment facilities, allowing us to quickly characterise potential entry factors of high containment viruses. Within this study, Ceudovitox was shown to recognise both known and novel entry factors of Chikungunya virus; a virus which causes chronic arthralgia and arthritis. Matrix metalloproteinases were amongst novel entry factors identified and were seen to reduce virus infection in both pseudotyped and authentic virus assays, demonstrating how Ceudovitox can correctly discover virus entry factors of live high containment viruses. Ceudovitoxs utility as a screening platform for high containment viruses and new emerging pathogens, has the potential increase understanding and speed up the development of new therapeutics during pandemics, helping to reach the 100 Day Mission of pandemic preparedness.

molecular biology↗

bioRxiv2024

Inhibition of NFAT promotes loss of tissue resident uterine natural killer cells and attendant pregnancy complications in humans

Uterine natural killer cells (uNKs) are a tissue resident lymphocyte population that are critical for pregnancy success. Although mouse models have demonstrated that NK deficiency results in abnormal placentation and poor pregnancy outcomes, the generalizability of this knowledge to humans remains unclear. Here we identify uterus transplant (UTx) recipients as a human population with reduced uNK cells and altered pregnancy phenotypes. We show that the NK reduction in UTx correlates with impaired transcriptional programming of NK tissue residency arising from the inhibition of NFAT-mediated signaling. Our observations suggest that NFAT-dependent genes modulate multiple molecular tissue residency programs in uNKs. These include early residency programs involving AP-1-family transcription factors and TGF-{beta}-mediated upregulation of surface integrins. Collectively, our data identify a previously undescribed role for NFAT in uterine NK tissue residency and provide novel mechanistic insights into the biologic basis of pregnancy complications due to alteration of tissue resident NK subsets in humans. One Sentence SummaryRole of NFAT in uterine NK cell tissue residency

immunology↗

bioRxiv2024

Sequential Transcriptional Programs of Tissue Residency Drive Human Uterine NK Cell Development

Uterine natural killer cells are critical for pregnancy success, but the origin and development of these cells in humans remain unclear. Here we use various single cell approaches to identify the transcriptional programs governing uterine NK cell development in humans. These analyses suggest a developmental continuum which begins with seeding of the endometrium with blood immature CD56bright precursors, evolves through CD56bright endometrial founder NK cells, and ends with tissue resident decidual NK cells during pregnancy which possess non-cytotoxic functions. Our work identifies a role for sequential programs of tissue residency in the differentiation of these cells, as differentiating endometrial tissue resident NK (trNK) cells acquire early and late transcriptional programs of residency which coincide with acquisition of unique non-cytotoxic effector programs. Notably, we identified early residency programs in human endometrial trNKs by expression of NR4A2, AP-1 transcription factors, and other immediate early response genes that were shared with CD8 tissue resident memory T cells in mice, suggesting conservation of transcriptional programs of early tissue residency programs across species and cell types. Late residency programs were guided by TGF{beta}, which promoted expression of various integrins and trNK subset diversification within the non-pregnant endometrium. Altogether, these data identify the molecular foundations for endometrial trNK heterogeneity and suggest that the uterine NK diversity observed during pregnancy is established before embryo implantation and intimately tied to residency programming.

immunology↗

bioRxiv2023

Prediction of DNA i-Motifs Via Machine Learning

i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of putative iMs vary dramatically. Much previous research on iM has focused on assessing the iM folding properties using biophysical experiments. However, there are no dedicated computational tools for predicting the folding status and strength of iM structures. Here, we introduce a machine learning pipeline, iM-Seeker, to predict both folding status and structural stability of DNA iMs. The programme iM-Seeker incorporates a Balanced Random Forest classifier trained on genome-wide iMab antibody-based CUT&Tag sequencing data to predict the folding status and an Extreme Gradient Boosting regressor to estimate the folding strength according to both literature biophysical data and our in-house biophysical experiments. iM-Seeker predicts DNA iM folding status with a classification accuracy of 81% and estimates the folding strength with coefficient of determination (R2) of 0.642 on the test set. Model interpretation confirms that the nucleotide composition of the C-rich sequence significantly affects iM stability, with a positive correlation with sequences containing cytosine and thymine and a negative correlation with guanine and adenine. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/571121v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@11f4398org.highwire.dtl.DTLVardef@18eb7e9org.highwire.dtl.DTLVardef@cc49c6org.highwire.dtl.DTLVardef@1ff91a8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

Serological evidence of high pathogenicity virus infection in Eidolon helvum fruit bats in Nigeria

The Eidolon helvum fruit bat is the most widely distributed fruit bat in Africa and is known to be a reservoir for several pathogenic viruses that can cause disease in humans. To assess the risk of zoonotic spillover, we conducted a serological survey of 304 serum samples from E. helvum bats that were captured for human consumption in Makurdi, Nigeria. Using pseudotyped viruses, we screened the samples for neutralising antibodies against viruses from the Coronaviridae, Filoviridae, Orthomyxoviridae and Paramyxoviridae families. We report the presence of neutralising antibodies against henipavirus lineage GH-M74a virus (odds ratio 6.23; p<0.001), Nipah virus (odds ratio 4.04; p=0.00031), bat influenza H17N10 virus (odds ratio 7.25; p<0.001) and no significant association with Ebola virus (odds ratio 0.56; p=0.375) in the bat cohort. The data suggest a potential risk of zoonotic spillover including the possible circulation of highly pathogenic viruses in E. helvum populations. These findings highlight the importance of maintaining sero-surveillance of E. helvum to monitor changes in virus prevalence and distribution over time and across different geographic locations. Article summary lineThe detection of neutralizing antibodies against henipavirus GH-M74a virus, Nipah virus, and H17N10 virus in Eidolon helvum bat sera from Nigeria using pseudotyped viruses suggests a potential risk of zoonotic spillover.

microbiology↗

bioRxiv2022

Application and comparison of lyophilisation protocols to enhance stable long-term storage of filovirus pseudotypes for use in antibody neutralisation tests

Filoviruses encompass highly pathogenic viruses placing sporadic public health burden on countries affected. Efforts for improved diagnostics and surveillance are needed considering the recent Ebola outbreaks in Africa. The need for high containment facilities can be circumvented by the use of pseudotype viruses (PV), which can be handled in low containment, for tropism, drug screening, vaccine immunogenicity and serosurveillance studies. In this study we assessed stability and functionality after long-term storage of lyophilised filovirus pseudotypes for use in neutralisation assays. Lyophilised Ebola and Marburg PVs retained production titres for at least two years when stored at +4{degrees}C or less. Lyophilised Ebola PVs performed similarly to non-lyophilised PVs in neutralisation assays after reconstitution. When stored at high temperatures (+37{degrees}C), lyophilised PVs did not retain titres after one-month storage, however, when lyophilised using pilot scale facilities EBOV PVs retained titres and performed well in neutralisation assays after one-month storage at 37{degrees}C suggesting removing residual moisture might be crucial for avoiding cold-chain transportation. Lyophilisation could allow reagents to be transported more efficiently as well as reducing costs for a future serological kit.

microbiology↗

bioRxiv2021

SARS-CoV-2 variants of concern Alpha, Beta, Gamma and Delta have extended ACE2 receptor host-ranges

Following the emergence of SARS-CoV-2 in China in late 2019 a number of variants have emerged, with two of these - Alpha and Delta - subsequently growing to global prevalence. One characteristic of these variants are changes within the Spike protein, in particular the receptor binding domain (RBD). From a public health perspective these changes have important implications for increased transmissibility and immune escape; however, their presence could also modify the intrinsic host-range of the virus. Using viral pseudotyping we examined whether the variants of concern (VOCs) Alpha, Beta, Gamma and Delta have differing host ACE2 receptor usage patterns, focusing on a range of relevant mammalian ACE2 proteins. All four VOCs were able to overcome a previous restriction for mouse ACE2, with demonstrable differences also seen for individual VOCs with rat, ferret or civet ACE2 receptors, changes which we subsequently attribute to N501Y and E484K substitutions within the Spike RBD.

microbiology↗

bioRxiv2021

Effect of SFX-01 on proliferation of human glioblastoma cell lines

Glioblastoma (GBM) is the most aggressive and lethal of brain tumours and there is a clear need for novel therapies. SFX-01, a stabilised formu of sulforaphane (SFN) that is complexed with -cyclodextrin, is being investigated as a potential anticancer drug. And as part of this investigation we have determined its effect on the proliferation of a series of tumour cell lines. Growth-inhibitory concentrations (IC50 values) of SFX-01 and reference SFN were highly correlated but showed a divergence at higher drug concentrations that is likely to reflect drug binding to -cyclodextrin complexes. Because SFN is redox-sensitive, we also compared the effects of these drugs on four GBM lines that had been derived and cultured under physiological oxygen (5%) conditions. Comparisons were also made using a three-dimensional spheroid model, used to mimic the in vivo state of glioblastomas and to simulate barriers to drug delivery in vivo. SFX-01 and reference SFN and inhibited proliferation of four GBM cell lines in monolayers as well as in spheroids; -cyclodextrin alone had no significant effect. Our results are consistent with the hypothesis that SFN is liberated from SFX-01 at concentrations sufficient to inhibit cell growth. We envision that SFX-01 will have improved pharmacokinetic properties in vivo, warranting further pre-clinical investigation and clinical development.

cancer biology↗

bioRxiv2021

Reservoir host studies of Lloviu virus: first isolation, sequencing and serology in Schreiber's bats in Europe

IntroductoryFiloviruses are prime examples of emerging human pathogens that are transmitted to humans by zoonotic spillover events. Since their initial discovery, filovirus outbreaks have occured with increasing frequency and intensity. There is an urgent need to better understand their enzootic ecology and pathogenic potential, given recent zoonotic virus spillover events including the 2013-2016 West African Ebola virus (EBOV) epidemic. Several novel filoviruses have been discovered with a markedly wider geographic distribution than previously described. One of these novel filoviruses, Lloviu virus (LLOV), was first identified in 2002 in Schreibers bats (Miniopterus schreibersii) in Spain, Portugal, and southern France. Subsequently, in 2016, LLOV was detected during the passive monitoring of bats in Hungary. Here we report the first isolation of infectious Lloviu virus; from the blood of an asymptomatic Schreibers bat, subsequently cultivated in the Miniopterus sp. kidney cell line SuBK12-08. We also show that LLOV is able to infect monkey and human cells, suggesting that LLOV might have spillover potential. We performed a multi-year surveillance of LLOV and detected LLOV RNA in both deceased and asymptomatic live animals as well as in coupled ectoparasites from the families Nycteribiidae and Ixodidae. We present data on the natural infection and seropositivity of Schreibers bats and provide novel LLOV genomic sequence information from a bat host and an arthropod parasite. Our data support the role of bats, specifically Miniopterus schreibersii as natural reservoirs for the LLOV filovirus in Europe. We also suggest that bat-associated parasites might play a role in the natural ecology of filoviruses in temperate climate regions compared to filoviruses in the tropics. These results raise the possibility of cross-species transmission events via bat-human interactions.

microbiology↗

bioRxiv2020

Accelerating Prediction of Chemical Shift of Protein Structures on GPUs

Experimental chemical shifts (CS) from solution and solid state magic-angle-spinning nuclear magnetic resonance spectra provide atomic level information for each amino acid within a protein or protein complex. However, structure determination of large complexes and assemblies based on NMR data alone remains challenging due the complexity of the calculations. Here, we present a hardware accelerated strategy for the estimation of NMR chemical-shifts of large macromolecular complexes based on the previously published PPM_One software. The original code was not viable for computing large complexes, with our largest dataset taking approximately 14 hours to complete. Our results show that the code refactoring and acceleration brought down the time taken of the software running on an NVIDIA V100 GPU to 46.71 seconds for our largest dataset of 11.3M atoms. We use OpenACC, a directive-based programming model for porting the application to a heterogeneous system consisting of x86 processors and NVIDIA GPUs. Finally, we demonstrate the feasibility of our approach in systems of increasing complexity ranging from 100K to 11.3M atoms. Author summary

biophysics↗

bioRxiv2019

Isolation of an antimicrobial resistant, biofilm forming, Klebsiella grimontii isolate from a re-usable water bottle.

A re-usable water bottle was swabbed as part of the citizen science project Swab and Send and a Klebsiella grimontii isolate was recovered on chromogenic agar and designated SS141. Whole genome sequencing of SS141 showed it has the potential to be a human pathogen as it contains the biosynthetic gene cluster for the potent cytotoxin, kleboxymycin, and genes for other virulence factors. The genome also contains blaOXY-6-4 and fosA which is likely to explain the observed resistance to ampicillin, amoxicillin and fosfomycin. We have also shown that SS141 is a potent biofilm former, providing a reasonable explanation for its ability to colonise a re-usable water bottle. With the increasing use of re-usable water bottles as an alternative to disposables, and a strong forecast for growth in this industry over the next decade, this study highlights the need for cleanliness comparable to other re-usable culinary items.

microbiology↗

bioRxiv2017

Generation of Arctic-like Rabies Viruses Containing Chimeric Glycoproteins Enables Serological Potency Studies.

Rabies viruses have the highest case fatality rate of any known virus and are responsible for an estimated 60,000 deaths each year. This is despite the fact that there are highly efficacious vaccines and postexposure prophylaxis available. However, while it is assumed these biologics provide protection against all rabies virus isolates, there are certain subdivisions of RABV lineages, such as within the Arctic-like RABV (AL rabies virus lineage, where data is limited and thus the potency of existing biologics has not been thoroughly assessed. By fusing the Arctic-like rabies virus envelope glycoprotein ecto- and transmembrane domains with the vesicular stomatitis virus cytoplasmic domain, a high titre (7.7 x 105 - 6.1 x 106 RLU/ml) pseudotyped virus was generated that was subsequently used in a pseudotyped virus neutralisation assay. These results showed that Arctic-like rabies viruses are neutralised to human, canine and feline vaccines and human post-exposure prophylaxis and this was not influenced by the swapping of the cytoplasmic domains (CVS-11 vs CVS-11etmVSVc; r = 0.99, p < 0.0001). This study supports the concept that rabies virus vaccines and newly identified mAbs are able to neutralise rabies virus variants that cluster in a monophyletic clade, referred to as phylogroup I lyssaviruses.

microbiology↗

bioRxiv2016

Genome-Wide Fitness Analyses of the Foodborne Pathogen Campylobacter jejuni in In Vitro and In Vivo Models

Infection by Campylobacter is recognised as the most common cause of foodborne bacterial illness worldwide. Faecal contamination of meat, especially chicken, during processing represents a key route of transmission to humans. There is currently no licenced vaccine and no Campylobacter-resistant chickens. In addition, preventative measures aimed at reducing environmental contamination and exposure of chickens to Campylobacter jejuni (biosecurity) have been ineffective. There is much interest in the factors/mechanisms that drive C. jejuni colonisation and infection of animals, and survival in the environment. It is anticipated that understanding these mechanisms will guide the development of effective intervention strategies to reduce the burden of C. jejuni infection. Here we present a comprehensive analysis of C. jejuni fitness during growth and survival within and outside hosts. A comparative analysis of transposon (Tn) gene inactivation libraries in three C. jejuni strains by Tn-seq demonstrated that a large proportion, 331 genes, of the C. jejuni genome is dedicated to (in vitro) growth. An extensive Tn library in C. jejuni M1cam (~10,000 mutants) was screened for the colonisation of commercial broiler chickens, survival in houseflies and under nutrient-rich and-poor conditions at low temperature, and infection of human gut epithelial cells. We report C. jejuni factors essential throughout its life cycle and we have identified genes that fulfil important roles across multiple conditions, including maf3, fliW, fliD, pflB and capM, as well as novel genes uniquely implicated in survival outside hosts. Taking a comprehensive screening approach has confirmed previous studies, that the flagella are central to the ability of C. jejuni to interact with its hosts. Future efforts should focus on how to exploit this knowledge to effectively control infections caused by C. jejuni.\n\nAuthor SummaryCampylobacter jejuni is the leading bacterial cause of human diarrhoeal disease. C. jejuni encounters and has to overcome a wide range of \"stress\" conditions whilst passing through the gastrointestinal tract of humans and other animals, during processing of food products, on/in food and in the environment. We have taken a comprehensive approach to understand the basis of C. jejuni growth and within/outside host survival, with the aim to inform future development of intervention strategies. Using a genome-wide transposon gene inactivation approach we identified genes core to the growth of C. jejuni. We also determined genes that were required during the colonisation of chickens, survival in the housefly and under nutrient-rich and -poor conditions at low temperature, and during interaction with human gut epithelial tissue culture cells. This study provides a comprehensive dataset linking C. jejuni genes to growth and survival in models relevant to its life cycle. Genes important across multiple models were identified as well as genes only required under specific conditions. We identified that a large proportion of the C. jejuni genome is dedicated to growth and that the flagella fulfil a prominent role in the interaction with hosts. Our data will aid development of effective control strategies.

microbiology↗