Biology subjects

Deng, A.

Publications and source records attributed to Deng, A..

14 recordsLinked to original sources

bioRxiv2026

Molecular and Structural Characterisation of the MERS-Coronavirus Polymerase

MERS-CoV (Middle East respiratory syndrome coronavirus) belongs to the Betacoronavirus genus, which also includes SARS-CoV-2, the causative agent of the COVID-19 pandemic. MERS-CoV is the pathogen responsible for Middle East Respiratory Syndrome (MERS), a respiratory disease with a 36.5% case fatality rate. Given the capacity of coronaviruses for genetic recombination and mutation, MERS-CoV remains a pathogen of significant pandemic potential, with viral evolution potentially facilitating enhanced adaptation and transmission in humans. There are no approved treatments for MERS-CoV infection. The MERS-CoV replication-transcription complex (RTC), a multimeric protein complex key to genome amplification, has no cellular analogues and a highly conserved sequence, making it a useful target for antiviral compounds; however, structural and biochemical characterisation of the MERS-CoV RTC is limited. Here, we characterise the minimal MERS-CoV RTC using in vitro and single-molecule assays and show that it is susceptible to the RNA-dependent-RNA-polymerase inhibitor suramin. We present a structure of the minimal MERS-CoV RTC in complex with an RNA duplex, which shows strong structural similarity to the SARS-CoV-2 RTC. We use cross-subunit swapping experiments to show that the MERS-CoV NSP12 core can efficiently utilise SARS-CoV-2 cofactors NSP7 and NSP8, whereas SARS-CoV-2 NSP12 exhibits reduced in vitro activity with the MERS-CoV NSP8. This asymmetric cross-species compatibility highlights both the evolutionary conservation and virus-specific adaptation of coronavirus polymerase-cofactor interactions. Together, these findings provide a structural and mechanistic framework for understanding MERS-CoV RNA synthesis and establish its conserved RTC as a potential target for the development of broadly acting coronavirus antivirals.

microbiology↗

bioRxiv2026

Maternal E-cigarette Exposure Augments Murine Abdominal Aortic Aneurysm

Background: Smoking and family history are major risk factors for abdominal aortic aneurysm (AAA). Smoking and nicotine are modulators of DNA methylation, capable of causing heritable epigenetic alterations. Nicotine infusion and e-cigarette (e-cig) vaping augment murine AAA. We investigated the effects of murine maternal e-cig vaping on offspring experimental AAA, and impacts on transgenerational DNA methylation and accessibility. Methods: We performed perinatal e-cig nicotine vaping in two strains of adult female mice (ApoE-/- and C57BL/6J). Mice were mated to control males, and treated through gestation. A parallel group were instead sacrificed after treatment, for DNA analysis. Offspring were aged to adulthood, and AAAs were then induced by elastase (C57BL/6J) or angiotensin-II infusion (ApoE-/-), and ultrasound-tracked for 4 weeks. In a second cohort, parental and offspring aortic tissue and blood DNA underwent RRBS and ATAC-seq analysis respectively. Offspring abdominal aortic anatomy was examined, and stiffness was assessed with ex vivo arterial myography. Results: Maternal e-cig exposure increased offspring AAA growth in both models and genders. AAA incidence was increased in ApoE-/- males, and observed effects were overall more pronounced in males. Maternal vape exposure altered aortic DNA methylation and blood DNA accessibility in mothers and offspring, with differential sites in numerous genes identified, including AAA-related genes and pathways. Pathways were enriched for transcription factors, inflammation/immune-related genes, and angiogenesis genes, with similar changes identified in exposed mothers. Male offspring displayed more differential genes. Significant changes were located in genes known to harbor AAA risk loci in humans, and overlapped with published epigenetic alterations in human smokers. Differences also occurred in offspring aortic structure and stiffness. Conclusions: Maternal e-cig nicotine exposure augments AAA growth in multiple models across generations. These effects are accompanied by broad epigenetic DNA reprogramming of key AAA modulator genes and pathways.

genomics↗

bioRxiv2026

SETD3 ACTIN HISTIDINE METHYLTRANSFERASE REGULATES INTESTINAL EPITHELIAL BARRIER INTEGRITY AND MUCOSAL INFLAMMATION

Intestinal epithelial barrier is a key feature of the healthy gut, and disruption of this barrier is a driver of mucosal inflammation. Integrity of the intestinal epithelial barrier is controlled by tight junctions (TJs) and adherens junctions (AJs) associated with the underlying actin cytoskeleton. Posttranslational modifications of actins affect the cytoskeletal assembly and dynamics, however whether such modifications regulate epithelial barriers remains unknown. SETD3 methyltransferase methylates actins at the His73 residue, thereby enhancing filamentous (F)-actin polymerization and turnover. This study examines the role of SETD3 in regulating structure and function of normal intestinal epithelial barrier, as well as its involvement in barrier disruption during mucosal inflammation. siRNA mediated knockdown of SETD3 in DLD-1 and HCA-7 human intestinal epithelial cells (IEC) resulted in several functional and morphological cell abnormalities. These include increased permeability of the IEC barrier, diminished assembly of the perijunctional F-actin belt, increased cell size, and delayed TJ reassembly during calcium switch. Consistently, SETD3 knockout (KO) mice displayed increased intestinal permeability and decreased labeling intensity of apical {beta}-actin as compared to wildtype controls. Furthermore, SETD3 KO mice showed increased cell stemness and proliferation in colonic epithelium without defects in AJ/TJ assembly and secretory cell differentiation. In addition, SETD3 KO mice developed more severe disease symptoms during dextran sodium sulfate (DSS)-induced colitis, which were accompanied by accelerated mucosal erosion and increased macrophage, T cell and neutrophil infiltration into colonic tissue. Overall, our data suggests that SETD3 acts as a novel positive regulator of the intestinal epithelial barrier and plays a protective role during intestinal mucosal damage and inflammation.

cell biology↗

bioRxiv2025

Structural and functional characterisation of the Crimean-Congo Haemorrhagic Fever Virus RNA Dependent RNA Polymerase

Crimean-Congo Haemorrhagic Fever Virus (CCHFV) is found across Africa, Asia, and the Middle East where it can cause Haemorrhagic outbreaks with high case fatality rates. Central to the viral life cycle is the viral L-protein, a crucial and multifunctional protein which both transcribes and replicates the viral genome. Here, we present the cryoEM structures of an RNA free and a 5 promoter bound complex, describing the core catalytic RNA-dependent RNA polymerase (RdRp). We observe an RdRp that is substantially larger than related L-proteins and contains domain insertions unique to the nairovirus family. The 5 RNA promoter is found in a tight RNA hairpin stabilised by a single base pair, with 5 binding triggering the closure of protein over the RNA. Functional analysis of the endonuclease and RdRp activities reveals an enzyme which is capable of both activities and demonstrate RdRp inhibition by known antiviral nucleosides. These data advance our understanding of the molecular mechanisms behind genome replication and transcription, that will help inform future antiviral development.

microbiology↗

bioRxiv2025

Deep learning reveals functional archetypes in the adult human gut microbiome that underlie interindividual variability and confound disease signals

Understanding the functional diversity of the gut microbiome is essential for decoding its roles in health and disease. Using a deep-learning framework, we identified three functional archetypes defining healthy adult gut microbiomes, each characterized by specific metabolic potentials: sugar metabolism with branched-chain amino acid and cell wall synthesis (Archetype 1), fatty acid and TCA cycle metabolism (Archetype 2), and amino acid and nitrogen metabolism (Archetype 3). Archetype proximity is linked to stability, with Archetype 2 representing the most resilient state, likely due to its metabolic flexibility. Functional diversity emerged as a confounder in disease-associated microbial signatures. In inflammatory bowel disease, we observed archetype-specific shifts, including increased carbohydrate metabolism in Archetype 1-dominant samples and inflammatory pathways in Archetype 3-dominant samples, suggesting distinct opportunities for microbiome-targeted interventions. This framework addresses key challenges in microbiome research, including inter-individual variability and confounding, while providing robust insights into disease-associated functional shifts and microbial ecosystem dynamics. HighlightsO_LIAdult gut microbiomes are defined by three functional archetypes C_LIO_LIArchetypes reveal distinct metabolic potentials and inform on microbiome stability C_LIO_LIArchetype-specific functional profiles confound disease associations and reveal therapeutic targets C_LIO_LIA deep-learning framework enables robust characterization of microbial functional ecosystems C_LI

microbiology↗

bioRxiv2024

De novo design and structure of a peptide-centric TCR mimic binding module

T cell receptor (TCR) mimics offer a promising platform for tumor-specific targeting of peptide-MHC in cancer immunotherapy. Here, we designed a de novo -helical TCR mimic (TCRm) specific for the NY-ESO-1 peptide presented by HLA-A*02, achieving high on-target specificity with nanomolar affinity (Kd = 9.5 nM). The structure of the TCRm/pMHC complex at 2.05 [A] resolution revealed a rigid TCR-like docking mode with an unusual degree of focus on the up-facing NY-ESO-1 side chains, suggesting the potential for reduced off-target reactivity. Indeed, a structure-informed in silico screen of 14,363 HLA-A*02 peptides correctly predicted two off-target peptides, yet our TCRm maintained a wide therapeutic window as a T cell engager. These results represent a path for precision targeting of tumor antigens with peptide-focused -helical TCR mimics.

immunology↗

bioRxiv2024

Mechanistic insights into the activity of SARS-CoV-2 RNA polymerase inhibitors using single-molecule FRET

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has resulted in significant global mortality and disruption. Despite extensive research, the precise molecular mechanisms underlying SARS-CoV-2 replication remain unclear. To address this, we developed a single-molecule Forster resonance energy transfer (smFRET) assay to directly visualize and analyse in vitro RNA synthesis by the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). We purified the minimal replication complex, comprising nsp12, nsp7, and nsp8, and combined it with fluorescently labelled RNA substrates, enabling real-time monitoring of RNA primer elongation at the single-molecule level. This platform allowed us to investigate the mechanisms of action of key inhibitors of SARS-CoV-2 replication. In particular, our data provides evidence for remdesivirs mechanism of action, which involves polymerase stalling and subsequent chain termination dependent on the concentration of competing nucleotide triphosphates. Our study demonstrates the power of smFRET to provide dynamic insights into SARS-CoV-2 replication, offering a valuable tool for antiviral screening and mechanistic studies of viral RdRp activity.

microbiology↗

bioRxiv2024

A mRNA Vaccine Encoding for a 60-mer G Glycoprotein Nanoparticle Elicits a Robust Neutralizing Antibodies Response Against the Nipah Virus

The Nipah virus is a zoonotic pathogen causing encephalitis and acute respiratory illness in humans with very high fatality rates. Here we report a novel messenger RNA vaccine that directly encodes for a nanoparticle displaying 60 head domains of the Nipah virus G (NiV G) glycoprotein that acts as a highly effective antigen. A vaccine encoding for the NiV G nanoparticle elicits high antibody titers against NiV G and a robust neutralizing antibody response with a pseudotyped Nipah virus system. We ultimately find that the proposed mRNA NiV G nanoparticle (mRNA NiV G-NP) provides a flexible platform for the development of vaccines that will likely be of great value in combatting future Nipah virus outbreaks.

immunology↗

bioRxiv2024

A conserved genetic basis for commensal-host specificity through live imaging of colonization dynamics

Animals throughout the metazoa selectively acquire specific symbiotic gut bacteria from their environment that aid host fitness. Current models of colonization suggest these bacteria use weakly specific receptors to stick to host tissues and that colonization results when they stick in a region of the host gut that overlaps with their nutritional niche. An alternative model is that unique receptor-ligand binding interactions provide specificity for target niches. Here we use live imaging of individual symbiotic bacterial cells colonizing the gut of living Drosophila melanogaster to show that Lactiplantibacillus plantarum specifically recognizes a distinct physical niche in the host gut. We find that recognition is controlled by a colonization island that is widely conserved in commensals and pathogens from the Lactobacillales to the Clostridia. Our findings indicate a genetic mechanism of host specificity that is broadly conserved. One-Sentence SummaryHost-symbiont specificity is encoded by a conserved colonization island that provides molecular precision to host niche access.

microbiology↗

bioRxiv2024

Spatial characterization of interface dermatitis in cutaneous lupus reveals novel chemokine ligand-receptor pairs that drive disease

BackgroundChemokines play critical roles in the recruitment and activation of immune cells in both homeostatic and pathologic conditions. Here, we examined chemokine ligand-receptor pairs to better understand the immunopathogenesis of cutaneous lupus erythematosus (CLE), a complex autoimmune connective tissue disorder. ObjectivesOur objectives were to (1) characterize the cellular and proteomic constitution of interface dermatitis in CLE using blister biopsies, (2) map chemokine:ligand receptor pairs that govern recruitment of immune cells to form interface dermatitis in CLE, and (3) perform unbiased analyses in tandem on different clinical subtypes to identify novel genes and proteins underlying discoid versus subacute CLE. MethodsWe used suction blister biopsies to measure cellular infiltrates with spectral flow cytometry in the interface dermatitis reaction, as well as 184 protein analytes in interstitial skin fluid using 96-plex immunoassay targeted proteomics. Flow and 96-plex immunoassay data concordantly demonstrated significant increases in T cells and antigen presenting cells (APCs). We also performed spatial transcriptomics and spatial proteomics of punch biopsies using digital spatial profiling (DSP) technology on CLE skin and healthy margin controls to examine discreet locations within the tissue. ResultsSpatial and 96-plex immunoassay data confirmed elevation of interferon (IFN) and IFN-inducible CXCR3 chemokine ligands. Comparing involved versus uninvolved keratinocytes in CLE samples revealed upregulation of essential inflammatory response genes in areas near interface dermatitis, including AIM2. 96-plex immunoassay data confirmed upregulation of Caspase 8, IL-18 which is the final product of AIM2 activation, and induced chemokines including CCL8 and CXCL6 in CLE lesional samples. Chemotaxis assays using PBMCs from healthy and CLE donors revealed that T cells are equally poised to respond to CXCR3 ligands, whereas CD14+CD16+ APC populations are more sensitive to CXCL6 via CXCR1 and CD14+ are more sensitive to CCL8 via CCR2. ConclusionsTaken together, our data map a pathway from keratinocyte injury to lymphocyte recruitment in CLE via AIM2-Casp8-IL-18-CXCL6/CXCR1 and CCL8/CCR2, and IFNG/IFNL1-CXCL9/CXCL11-CXCR3, and identify potential novel biomarkers of disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/574422v2_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1e86dbeorg.highwire.dtl.DTLVardef@7d0208org.highwire.dtl.DTLVardef@1108aa8org.highwire.dtl.DTLVardef@ff255f_HPS_FORMAT_FIGEXP M_FIG C_FIG Model of chemokine systems governing recruitment of immune cell subsets to form interface dermatitis in cutaneous lupus. A. Summary of fresh tissue blister biopsy studies demonstrating increases in HLADR+ cells in nonlesional lupus biopsies as assessed by flow cytometry, and increased CXCL6 and CCL8 as assessed by 96 plex immunoassay. Lesional lupus biopsies also demonstrated significant increases in T cells and CXCL9/10/11 production. B. Model of chemokine-directed formation of interface dermatitis in cutaneous lupus. 1. Whole transcriptome atlas (WTA) digital spatial profiling (DSP) revealed increased AIM2 in keratinocytes proximal to inflammation, which is reported to be induced by environmental triggers including UV light and toxins. We also noted increased Caspase 8 (Casp8) and IL18 at the protein level, which can be induced downstream of AIM2. Chemokines including CXCL6 and CCL8 can be induced downstream of IL18, explaining how CCL8 and CXCL6 might be induced. 2. Recruitment of myeloid cell first responders by CCL8 and CXCL6. CD14+CD16+ myeloid cells, which were recently described in nonlesional lupus skin, express CXCR1 and migrate towards CXCL6, whereas CD14+CD16-myeloid cells express more CCR2 and migrate towards CCL8. 3. The CXCR3 ligands CXCL9/10/11 are expressed by keratinocytes, but more strongly in CD45+ immune cell and T cell regions of interest (ROIs). 4. T cells express CXCR3 and migrate towards CXCL9 and to a greater extent CXCL11. 5. The recruited HLADR+ myeloid populations and T cells contribute to formation of interface dermatitis. Thus, we propose a model in which keratinocyte/myeloid crosstalk can reinforce chemokine systems to optimally recruit lymphocytes and other immune cells to form interface dermatitis. Created with Biorender.com. Plain language summaryLupus skin rashes arise during flares, after exposure to medications or sunlight, or in response to other triggers of inflammation. To understand how white blood cells enter the skin to cause these rashes, we used new technologies to look at proteins that attract them into the skin. We found proteins that are expressed by skin cells in lesions that can recruit specific types of white blood cells that are thought to be the initiators of skin rashes. Once in the skin, these and other white blood cells can make additional proteins that bring in more and more cells. We hope that our findings will be used to test new topical treatments for lupus and other autoimmune skin rashes.

immunology↗

bioRxiv2023

TransGeneSelector: A Transformer-based Approach Tailored for Key Gene Mining with Small Plant Transcriptomic Datasets

Gene mining, particularly from small sample sizes such as in plants, remains a challenge in life sciences. Traditional methods often omit significant genes, while deep learning techniques are hindered by small sample constraints and lack specialized gene mining approaches. This paper presents TransGeneSelector, the first deep learning method tailored for key gene mining in small transcriptomic datasets, ingeniously integrating data augmentation, sample filtering, and a Transformer-based classifier. Tested on Arabidopsis thaliana seeds germination classification using just 79 samples, it not only achieves classification performance on par with, if not superior to, Random Forest and SVM but also excels in identifying upstream regulatory genes that Random Forest might miss, and these pinpointed genes more accurately reflect the metabolic processes inherent in seed germination. TransGeneSelectors ability to mine vital genes from limited datasets signifies its potential as the current state-of-the-art in gene mining in small sample scenarios, providing an efficient and versatile solution for this critical research area.

bioinformatics↗

bioRxiv2022

Structural characterization of a breast cancer-associated mutation in caveolin-1

Caveolin-1 (CAV1) is a membrane sculpting protein that oligomerizes to generate flask-shaped invaginations of the plasma membrane known as caveolae. Mutations in CAV1 have been linked to multiple diseases in humans. Such mutations often interfere with oligomerization and the intracellular trafficking processes required for successful caveolae assembly, but the molecular mechanisms underlying these defects have not been structurally explained. Here, we investigate how a breast cancer-associated mutation in one of the most highly conserved residues in CAV1, P132L, affects CAV1 structure and oligomerization. We show that P132 is positioned at a major site of protomer-protomer interactions within the CAV1 complex, providing a structural explanation for why the mutant protein fails to homo-oligomerize correctly. Using a combination of computational, structural, biochemical, and cell biological approaches, we find that despite its homo-oligomerization defects P132L is capable of forming mixed hetero-oligomeric complexes with wild type CAV1 and that these complexes can be incorporated into caveolae. These findings provide insights into the fundamental mechanisms that control the formation of homo- and hetero-oligomers of caveolins that are essential for caveolae biogenesis, as well as how these processes are disrupted in human disease.

biophysics↗

bioRxiv2022

A mRNA vaccine encoding for a RBD 60-mer nanoparticle elicits neutralizing antibodies and protective immunity against the SARS-CoV-2 delta variant in transgenic K18-hACE2 mice

Two years into the COVID-19 pandemic there is still a need for vaccines to effectively control the spread of novel SARS-CoV-2 variants and associated cases of severe disease. Here we report a messenger RNA vaccine directly encoding for a nanoparticle displaying 60 receptor binding domains (RBDs) of SARS-CoV-2 that acts as a highly effective antigen. A construct encoding the RBD of the delta variant elicits robust neutralizing antibody response with neutralizing titers an order of magnitude above currently approved mRNA vaccines. The construct also provides protective immunity against the delta variant in a widely used transgenic mouse model. We ultimately find that the proposed mRNA RBD nanoparticle-based vaccine provides a flexible platform for rapid development and will likely be of great value in combatting current and future SARS-CoV-2 variants of concern.

immunology↗

bioRxiv2020

Transmission dynamics of 2019 novel coronavirus (2019-nCoV)

RationaleSeveral studies have estimated basic production number of novel coronavirus pneumonia (NCP). However, the time-varying transmission dynamics of NCP during the outbreak remain unclear. ObjectivesWe aimed to estimate the basic and time-varying transmission dynamics of NCP across China, and compared them with SARS. MethodsData on NCP cases by February 7, 2020 were collected from epidemiological investigations or official websites. Data on severe acute respiratory syndrome (SARS) cases in Guangdong Province, Beijing and Hong Kong during 2002-2003 were also obtained. We estimated the doubling time, basic reproduction number (R0) and time-varying reproduction number (Rt) of NCP and SARS. Measurements and main resultsAs of February 7, 2020, 34,598 NCP cases were identified in China, and daily confirmed cases decreased after February 4. The doubling time of NCP nationwide was 2.4 days which was shorter than that of SARS in Guangdong (14.3 days), Hong Kong (5.7 days) and Beijing (12.4 days). The R0 of NCP cases nationwide and in Wuhan were 4.5 and 4.4 respectively, which were higher than R0 of SARS in Guangdong (R0=2.3), Hongkong (R0=2.3), and Beijing (R0=2.6). The Rt for NCP continuously decreased especially after January 16 nationwide and in Wuhan. The R0 for secondary NCP cases in Guangdong was 0.6, and the Rt values were less than 1 during the epidemic. ConclusionsNCP may have a higher transmissibility than SARS, and the efforts of containing the outbreak are effective. However, the efforts are needed to persist in for reducing time-varying reproduction number below one. At a Glance CommentaryO_ST_ABSScientific Knowledge on the SubjectC_ST_ABSSince December 29, 2019, pneumonia infection with 2019-nCoV, now named as Novel Coronavirus Pneumonia (NCP), occurred in Wuhan, Hubei Province, China. The disease has rapidly spread from Wuhan to other areas. As a novel virus, the time-varying transmission dynamics of NCP remain unclear, and it is also important to compare it with SARS. What This Study Adds to the FieldWe compared the transmission dynamics of NCP with SARS, and found that NCP has a higher transmissibility than SARS. Time-varying production number indicates that rigorous control measures taken by governments are effective across China, and persistent efforts are needed to be taken for reducing instantaneous reproduction number below one.

systems biology↗