Biology subjects

Gibson, C.

Publications and source records attributed to Gibson, C..

14 recordsLinked to original sources

bioRxiv2026

Proteolytic control of the SARS-CoV-2 furin cleavage site defines the phenotypic evolution from the pandemic to endemic state

The successive emergence of SARS-CoV-2 variants with altered tissue tropism has progressively decoupled transmissibility from lower respiratory tract pathogenicity. Omicron lineages transmit exceptionally well whilst limiting severe lung disease. Here, we demonstrate that this phenotype has evolved through two temporally distinct tissue-specific proteolytic controls at the Spike (S) furin cleavage site (FCS). At the virion level, cell-type-dependent furin-mediated FCS hyper-cleavage depletes S in lung but not nasal epithelial cells. At the infected cell membrane during cell-cell spread, TMPRSS2 mediates S FCS cleavage but is negatively regulated in the presence of ACE2. Tissue-specific solute carriers SLC6A19 and SLC6A20 sequester ACE2, thereby relieving inhibition of TMPRSS2 and enabling S FCS cleavage during cell-cell spread. Critically, whilst all SARS-CoV-2 lineages benefit from this latter pathway, Omicron variants have evolved exclusive dependence on it, a strategic consolidation that focuses S proteolytic activation to TMPRSS2 alone. The combined outcomes of S protein regulation across viral and cell membranes reveal how tissue-specific proteolytic optimisation drives Omicron's transmission fitness advantage in the upper respiratory tract but at the cost of heavy attenuation in the lower respiratory tract.

microbiology↗

bioRxiv2026

Pan-neutralization of parainfluenza viruses by a hemagglutinin-neuraminidase antibody

Human parainfluenza viruses (HPIVs) can cause severe respiratory illnesses, such as croup, bronchiolitis, and pneumonia, particularly in children, the elderly and immunocompromised individuals. No vaccines or specific therapeutics are available for use in humans. Here, we report the discovery of a human monoclonal antibody designated PVA269 that broadly and potently neutralizes all four HPIV subtypes, PIV5, and Sendai virus by targeting the hemagglutinin-neuraminidase (HN) glycoprotein. We show that PVA269 inhibits neuraminidase activity and hemagglutination of erythrocytes through insertion of a long heavy chain complementary-determining region 3 in the enzyme active site. We reveal that the antibody markedly remodels its interactions to accommodate distinct viral features across HPIV subtypes, such as HPIV2 N-linked glycans. These results define the molecular basis for the unique PVA269 pan-neutralizing activity of human and animal viruses spanning two genera. PVA269 provides potent prophylactic activity against HPIV3 replication in the upper and lower airways of the clinically predictive cotton rat model, thus supporting translation of its protective efficacy to humans. These data establish PVA269 as a best-in-class monoclonal antibody and a promising clinical candidate to prevent HPIV infection, transmission, and disease in vulnerable populations.

immunology↗

bioRxiv2024

Molecular basis of pathogenicity of the recently emerged FCoV-23 coronavirus

The ability of coronaviruses to recombine and cross species barriers affects human and animal health globally and is a pandemic threat. FCoV-23 is a recently emerged, highly pathogenic recombinant coronavirus responsible for a widespread outbreak of feline infectious peritonitis (FIP) likely linked to in-host viral evolution. Here, we report cryoEM structures of two FCoV-23 spike (S) isoforms explaining that the in-host loss of domain 0 observed in clinical samples enhances entry into cells and fusogenicity by facilitating protease access, leading to biotype switching and lethality. We show that FCoV-23 can use several aminopeptidase N (APN) orthologs as receptors and reveal the molecular determinants of receptor species tropism, including a glycan modulating human receptor utilization. We define antigenic relationships among alphacoronaviruses infecting humans and other mammalian species and identify a cross-reactive alphacoronavirus monoclonal antibody inhibiting FCoV-23 pseudovirus entry, paving the way for vaccine and therapeutic development targeting this highly pathogenic virus.

biochemistry↗

bioRxiv2024

pH-Controlled chemoselective rapid azo-coupling reaction (CRACR) enables global profiling of serotonylation proteome in cancer cells

Serotonylation has been identified as a novel protein post-translational modification for decades, where an isopeptide bond is formed between the glutamine residue and serotonin through transamination. Transglutaminase 2 (also known as TGM2 or TGase2) was proven to act as the main "writer" enzyme for this PTM and a number of key regulatory proteins (including small GTPases, fibronectin, fibrinogen, serotonin transporter, and histone H3) have been characterized as the substrates of serotonylation. However, due to the lack of pan-specific antibodies for serotonylated glutamine, the precise enrichment and proteomic profiling of serotonylation still remain challenging. In our previous research, we developed an aryldiazonium probe to specifically label protein serotonylation in a bioorthogonal manner, which depended on a pH-controlled chemoselective rapid azo-coupling reaction (CRACR). Here, we report the application of a photoactive aryldiazonium-biotin probe for the global profiling of serotonylation proteome in cancer cells. Thus, over 1,000 serotonylated proteins were identified from HCT 116 cells, many of which are highly related to carcinogenesis. Moreover, a number of modification sites of these serotonylated proteins were determined, attributed to the successful application of our chemical proteomic approach. Overall, these findings provided new insights into the significant association between cellular protein serotonylation and cancer development, further suggesting that to target TGM2-mediated monoaminylation may serve as a promising strategy for cancer therapeutics. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/593574v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@67e538org.highwire.dtl.DTLVardef@f9f722org.highwire.dtl.DTLVardef@cfe5fdorg.highwire.dtl.DTLVardef@104674f_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells

Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid residue of H3 (i.e., glutamine) and dopamine. In our previous studies, we discovered that the dynamics of this post-translational modification (including installation, removal, and replacement) were regulated by a single enzyme, transglutaminase 2 (TGM2), through reversible transamination. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of TGM2 in colon cancer cells. Due to the enzyme promiscuity of TGM2, non-histone proteins have also been identified as targets of dopaminylation on glutamine residues, however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of modification sites of these dopaminylated proteins were identified, attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that to block the installation of protein dopaminylation may become a promising anti-cancer strategy. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/591460v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a3e9dorg.highwire.dtl.DTLVardef@104ecddorg.highwire.dtl.DTLVardef@5ab948org.highwire.dtl.DTLVardef@3a5d8b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

AutoXAI4Omics: an Automated Explainable AI tool for Omics and tabular data

Machine learning (ML) methods have the potential of detailed insights of complex biological systems and today are increasingly used to analyse omics data for tasks such as the discovery of novel biomarkers and phenotype prediction. It can be extremely beneficial and powerful for scientists, domain experts, to easily run sophisticated, robust, and interpretable ML pipelines without the need for an in depth understanding of the code needed to train, tune, optimise ML algorithms. They can then focus on the biological interpretation and validation of the results and insights generated by ML models. Here, we present an entirely automated open-source explainable AI tool, AutoXAI4Omics, that performs classification and regression tasks from omics and tabular numerical data. AutoXAI4Omics accelerates scientific discovery by automating processes and decisions made by AI experts, e.g., selection of the best feature set, hyper-tuning of different ML algorithms and selection of the best ML model for a specific task and dataset. Prior to ML analysis AutoXAI4Omics incorporates feature filtering options that are tailored to specific omic data types. Moreover, the insights into the predictions that are provided by the tool through explainability analysis highlight associations between omic feature values and the targets under investigation e.g., predicted phenotypes, facilitating the discovery of actionable insights. AutoXAI4Omics is at: https://github.com/IBM/AutoXAI4Omics. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=188 HEIGHT=200 SRC="FIGDIR/small/586460v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@366327org.highwire.dtl.DTLVardef@a7b559org.highwire.dtl.DTLVardef@7319aforg.highwire.dtl.DTLVardef@9b5030_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Bioorthogonal labeling and enrichment of histone monoaminylation reveal its accumulation and regulatory function in cancer cell chromatin

Histone monoaminylation (i.e., serotonylation and dopaminylation) is an emerging category of epigenetic mark occurring on the fifth glutamine (Q5) residue of H3 N-terminal tail, which plays significant roles in gene transcription. Current analysis of histone monoaminylation is mainly based on site-specific antibodies and mass spectrometry, which either lacks high resolution or is time-consuming. In this study, we report the development of chemical probes for bioorthogonal labeling and enrichment of histone serotonylation and dopaminylation. These probes were successfully applied for the monoaminylation analysis of in vitro biochemical assays, cells, and tissue samples. The enrichment of monoaminylated histones by the probes further confirmed the crosstalk between H3Q5 monoaminylation and H3K4 methylation. Finally, combining the ex vivo and in vitro analyses based on the developed probes, we have shown that both histone serotonylation and dopaminylation are highly enriched in tumor tissues that overexpress transglutaminase 2 (TGM2) and regulate the three-dimensional architecture of cellular chromatin. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/586010v3_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1bee3f7org.highwire.dtl.DTLVardef@1687013org.highwire.dtl.DTLVardef@1960bd0org.highwire.dtl.DTLVardef@1e19a04_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Development of Ingenui-T, a Novel Vein-to-Vein Solution for Rapid Autologous CAR T-Cell Manufacturing Starting From Whole Blood, for the Treatment of Autoimmune Diseases

Apheresis, a conventional starting point for manufacturing chimeric antigen receptor (CAR) T-cell therapy, poses challenges due to the length and invasiveness of the procedure, the high demand for and limited quantity of apheresis beds, and additional resource constraints at collection centers. Furthermore, traditional CAR T-cell manufacturing often involves extended cell culture periods, leading to a final product that has progressed through the differentiation process and contains a higher frequency of cells with phenotypes that are indicative of lower functionality or potency.1 Here, we show that anti-CD19 CAR T-cells manufactured from fresh whole blood with minimal ex vivo expansion using Ingenui-T exhibit comparable or superior CAR-mediated and CD19-dependent functional activity compared to CAR T-cells manufactured from cryopreserved leukapheresis material following the a conventional manufacturing process. Anti-CD19 CAR T-cell production, manufactured from whole blood in less than 3 days of in vitro culture using Ingenui-T, yielded an average of about 40 million cells per 100 mL with high CD3 purity and viability. Furthermore, the final product was composed of cells with less differentiated phenotypes and sustained cytotoxic activity against CD19+ target cells at a lower dose than conventionally manufactured CAR T cells in preclinical in vitro assays. Ingenui-T is an innovative vein-to-vein solution, aimed at enhancing the patient experience, feasibility, and accessibility of CAR T-cell therapy by alleviating challenges linked to apheresis-based methods, with its patient-friendly nature, cost-effectiveness, and distinctive methodology.

immunology↗

bioRxiv2024

Human coronavirus HKU1 recognition of the TMPRSS2 host receptor

The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.

biochemistry↗

bioRxiv2023

The HCM-Linked Mutation Arg92Leu in TNNT2 Allosterically Alters the cTnC-cTnI Interface and Disrupts the PKA-mediated Regulation of Myofilament Relaxation

BackgroundImpaired left ventricular relaxation, high filling pressures, and dysregulation of Ca2+ homeostasis are common findings contributing to diastolic dysfunction in hypertrophic cardiomyopathy (HCM). Studies have shown that impaired relaxation is an early observation in the sarcomere-gene-positive preclinical HCM cohort which suggests potential involvement of myofilament regulators of relaxation. Yet, a molecular level understanding of mechanism(s) at the level of the myofilament is lacking. We hypothesized that mutation-specific, allosterically mediated, changes to the cardiac troponin C-cardiac troponin I (cTnC-cTnI) interface can account for the development of early-onset diastolic dysfunction via decreased PKA accessibility to cTnI. MethodsHCM mutations R92L-cTnT (Arg92Leu) and {Delta}160E-cTnT (Glu160 deletion) were studied in vivo, in vitro, and in silico via 2D echocardiography, western blotting, ex vivo hemodynamics, stopped-flow kinetics, time resolved fluorescence resonance energy transfer (TR-FRET), and molecular dynamics simulations. ResultsThe HCM-causative mutations R92L-cTnT and {Delta}160E-cTnT result in different time-of-onset of diastolic dysfunction. R92L-cTnT demonstrated early-onset diastolic dysfunction accompanied by a localized decrease in phosphorylation of cTnI. Constitutive phosphorylation of cTnI (cTnI-D23D24) was sufficient to recover diastolic function to Non-Tg levels only for R92L-cTnT. Mutation-specific changes in Ca2+ dissociation rates associated with R92L-cTnT reconstituted with cTnI-D23D24 led us to investigate potential involvement of structural changes in the cTnC-cTnI interface as an explanation for these observations. We probed the interface via TR-FRET revealing a repositioning of the N-terminus of cTnI, closer to cTnC, and concomitant decreases in distance distributions at sites flanking the PKA consensus sequence. Implementing TR-FRET distances as constraints into our atomistic model identified additional electrostatic interactions at the consensus sequence. ConclusionThese data indicate that the early diastolic dysfunction observed in a subset of HCM is likely attributable to structural changes at the cTnC-cTnI interface that impair accessibility of PKA thereby blunting {beta}-adrenergic responsiveness and identifying a potential molecular target for therapeutic intervention.

biophysics↗

bioRxiv2023

Antibiotic Resistance Gene Variant Sequencing is Necessary to Reveal the Complex Dynamics of Immigration from Sewers to Activated Sludge

Microbial community composition has increasingly emerged as a key determinant of antibiotic resistance gene (ARG) content. However, in activated sludge wastewater treatment plants (AS-WWTPs), a comprehensive understanding of the microbial community assembly process and its impact on the persistence of antimicrobial resistance (AMR) remains elusive. An important part of this process is the immigration dynamics (or community coalescence) between the influent and activated sludge. While the influent wastewater contains a plethora of ARGs, the persistence of a given ARG depends initially on the immigration success of the carrying population, and the possible horizontal transfer to indigenously resident populations of the WWTP. The current study utilised controlled manipulative experiments that decoupled the influent wastewater composition from the influent microbial populations to reveal the fundamental mechanisms involved in ARG immigration between sewers and AS-WWTP. A novel multiplexed amplicon sequencing approach was used to track different ARG sequence variants across the immigration interface, and droplet digital PCR was used to quantify the impact of immigration on the abundance of the targeted ARGs. Immigration caused an increase in the abundance of over 70 % of the quantified ARGs. However, monitoring of ARG sequence variants at the immigration interface revealed various immigration patterns such as (i) suppression of the indigenous mixed liquor variant by the immigrant, or conversely (ii) complete immigration failure of the influent variant. These immigration profiles are reported for the first time here and highlight the crucial information that can be gained using our novel multiplex amplicon sequencing techniques. Future studies aiming to reduce AMR in WWTPs should consider the impact of influent immigration in process optimisation and design.

microbiology↗

bioRxiv2023

Multiplexed Amplicon Sequencing Reveals High Sequence Diversity of Antibiotic Resistance Genes in Quebec Sewers

The United Nations Environment Assembly (UNEA-3) have recognised the importance of the environment in the development, spread and transmission of antimicrobial resistance (AMR) to humans and animals. Such recognition calls for wider surveillance of antimicrobial resistance genes (ARG) in wastewater and other environmental reservoirs. For ARG surveillance to be valuable to regulators, it must enable source tracking and risk assessment. Adequate surveillance also requires the processing of a large number of samples at a relatively low cost, and a low detection limit to allow quantification of the riskiest ARGs. However, current methods for tracking ARGs have various limitations. The current study presents a multiplexed targeted amplicon sequencing approach for the detection of sequence variants of ARGs in environmental samples. To demonstrate the application of this technique, wastewater samples collected from the inlet to 16 treatment plants located along a 440-km transect of the St-Lawrence river in the province of Quebec (Canada) were analysed. Among the ARGs examined, between 3 and 45 nucleic acid sequence variants were detected demonstrating the high sequence diversity that occurs within genes originating from a single sample type and the information that is missed using traditional techniques. Using the PLSDB and Comprehensive Antibiotic Resistance Database (CARD), the risk of ARG sequence variants was inferred based upon their reported mobility and detection in pathogens. Results suggest that sequence variants within a single ARG class present different risks to public health. In the future, targeted amplicon sequencing could be a valuable tool in environmental studies for both risk assessment purposes and in AMR source tracking.

microbiology↗

bioRxiv2023

Activated Sludge Microbial Community Assembly: The Role of Influent Microbial Community Immigration

Wastewater treatment plants (WWTPs) are host to diverse microbial communities and receive a constant influx of microbes from influent wastewater, however the impact of immigrants on the structure and activities of the activated sludge (AS) microbial community remains unclear. To gain insight on this phenomenon known as perpetual community coalescence, the current study utilised controlled manipulative experiments that decoupled the influent wastewater composition from the microbial populations to reveal the fundamental mechanisms involved in immigration between sewers and AS-WWTP. The immigration dynamics of heterotrophs were analysed by harvesting wastewater biomass solids from 3 different sewer systems and adding to synthetic wastewater. Immigrating influent populations were observed to contribute up to 25 % of the sequencing reads in the AS. By modelling the net growth rate of taxa, it was revealed that immigrants primarily exhibited low or negative net growth rates. By developing a protocol to reproducibly grow AS-WWTP communities in the lab, we have laid down the foundational principals for the testing of operational factors creating community variations with low noise and appropriate replication. Understanding the processes that drive microbial community diversity and assembly is a key question in microbial ecology. In the future, this knowledge can be used to manipulate the structure of microbial communities and improve system performance in WWTPs. ImportanceIn biological wastewater treatment processes, the microbial community composition is essential in the performance and stability of the system. To allow future process optimisation to meet new treatment goals, we need a better understanding of factors influencing the microbial community assembly in WWTPs. This study developed a reproducible protocol to investigates the impact of influent immigration (or perpetual coalescence of the sewer and activated sludge communities) with appropriate reproducibility and controls. We demonstrate herein that influent immigration contributed up to 25 % of the sequencing reads in the activated sludge under the studied conditions, highlighting the need to consider this process in future WWTP modelling and design.

microbiology↗

bioRxiv2022

Wastewater Influent Microbial Immigration and Contribution to Resource Consumption in Activated Sludge Using Taxon-Specific Mass-Flow Immigration Model

Wastewater influent microorganisms are part of the total chemical oxygen demand (COD) and affect the activated sludge (AS) microbial community. Precise modeling of AS processes requires accurate quantification of influent microorganisms, which is missing in many AS models (ASMs). In this study, influent microorganisms in COD unit were determined using a fast quantification method based on DNA yield and was compared with conventional respirometry method. The actively growing influent microorganisms were identified. A mass-flow immigration model was developed to quantify the influent-to-AS immigration efficiency (mi) of specific taxon i using mass balance and 16S rRNA gene high-throughput sequencing data. The modelled average m was 0.121-0.257 in site 1 (LaPrairie), and 0.050-0.126 in site 2 (Pincourt), which were corrected to 0.111-0.186 and 0.048-0.109 respectively using a constrain of mi [≤] 1. The model was further developed to calculate contributions to organic substrate consumption by specific taxa. Those genera with zero or negative net growth rates were not completely immigration dependent (mi < 1) and contributed to 2.4% - 5.4% of the substrate consumption. These results suggest that influent microbiome may be important contributors to AS microbiome assembly and system performance (substrate consumption), which may help to improve future AS process modelling and design. SynopsisInfluent microbial immigration lacks detailed taxon-specific quantification. This study presents quantitative methods and models for influent biomass, mass-flow immigration model, and resource consumption in activated sludge. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/504022v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1d6b43forg.highwire.dtl.DTLVardef@d3b7eborg.highwire.dtl.DTLVardef@1cfaef5org.highwire.dtl.DTLVardef@1e75bdb_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗