Biology subjects

Williams, C. G.

Publications and source records attributed to Williams, C. G..

13 recordsLinked to original sources

bioRxiv2025

Aducanumab Binding to Aβ1-42 Fibrils Alters Dynamics of the N-Terminal Tail While Preserving the Fibril Core

Aducanumab, a human IgG1 antibody with plaque-clearing effects and modest clinical benefit, binds selectively to aggregated A{beta} via the N-terminal region. Yet, the molecular details of how the antibody engages A{beta}1-42 fibrils remain unresolved. Using magic-angle spinning nuclear magnetic resonance, we show that binding of aducanumab preserves the overall architecture of the A{beta}1-42 fibril core while inducing significant structural and dynamic perturbations in the N-terminal region. Antibody binding markedly reduces flexibility in this domain, with the appearance of sidechain resonances from residues D1, E3, and histidine (likely H6) in dipolar-based experiments. These sidechains--previously observed only in scalar-coupling spectra of the unbound state--indicate rigidification of residues that were dynamic. The interaction extends to S8 and Y10, indicating broader fibril engagement than the minimal epitope (residues 3-7) defined in fragment-based studies. Perturbations in the C-terminal segment (G37-A42) are consistent with its spatial proximity to the antibody-bound N-termini of neighboring monomers. Cryo-TEM images reveal fibrils bundling in the presence of aducanumab, consistent with lateral association via antibody cross-linking, supporting a model where surface coating and steric hindrance suppress secondary nucleation. This mode of action restricts monomer access to catalytic sites on fibril surface, resulting in partial inhibition ([~]three-fold reduction) of secondary nucleation. The effect depends on high avidity and relatively high stoichiometry, but is ultimately limited by antibody size relative to N-terminal spacing along the fibril. These findings provide atomic-level insights into aducanumabs binding mode and supply a structural framework for understanding antibody-mediated fibril recognition and for guiding next-generation therapies targeting A{beta} aggregates in Alzheimers disease. Significance StatementUnderstanding how therapeutic antibodies interact with amyloid-{beta} (A{beta}) fibrils is crucial for developing effective Alzheimers disease treatments. Magic angle spinning NMR provides atomic-level insights into the binding of aducanumab to mature A{beta}1-42 fibrils. Aducanumab binding preserves the fibrils core structure but slows the dynamics of the N-terminal domain of A{beta}. This interaction, which spans D1 to S8 and extends to Y10 on the fibril surface, is consistent with a mechanism in which N-terminal binding by the antibody interferes with aggregation steps like secondary nucleation. These findings detail how aducanumab engages its target fibril and provides insights relevant to other clinically approved antibodies and next-generation therapies that recognize the A{beta} N-terminal region.

biophysics↗

bioRxiv2025

Backbone Assignment of a 28.5 kDa Class A Extended Spectrum β-Lactamase by High-Field, Carbon-Detected Solid-State NMR

13C and 15N backbone chemical shift assignments are reported for the 28.5 kDa protein Toho-1 {beta}-lactamase, a Class A extended spectrum {beta}-lactamase. A very high level of assignment completeness (97% of the backbone) is enabled by the combined sensitivity and resolution gains of ultrahigh-field NMR spectroscopy (1.1 GHz), improved probe technology, and optimized pulse sequences. The assigned chemical shifts agree well with our previous solution-state NMR assignments, indicating that the secondary structure is conserved in the solid state. These assignments provide a foundation for future investigations of sidechain chemical shifts and catalytic mechanism.

biochemistry↗

bioRxiv2024

Temporally overlapping mechanisms diversify clonal B cell responses in vivo.

Naive B cells amplify and diversify their responses when activated by cognate antigen, via Myc-dependent clonal expansion, immunoglobulin class switch recombination (CSR), phenotypic variation, and somatic hypermutation (SHM). Whether these mechanisms act combinatorially in vivo to diversify clonal responses to a single pathogen remains unclear. Since diversity in the antigenic targets, functional classes, and production kinetics of parasite-specific antibodies influences immunity to malaria, we test here whether individual B cell clones diversify over time during Plasmodium infection and treatment. During the first week of infection, amid widespread Type I Interferon (IFN)-mediated bystander activation, CSR initiates soon after Myc up-regulation, and overlaps partially with clonal expansion, resulting in isotype variegation amongst clones. During the second week of infection, expanded clones that seed germinal centres (GC) bifurcate into extra-follicular plasmablasts, exhibit isotype variegation, and initiate SHM, revealing substantial intra-clonal diversification. Over the following month, GC clones exhibit SHM at approximately four mutations per week, with IgG mutational diversity and IgM+ cells also preserved in GCs over time. Anti-malarial intervention does not impede SHM, but instead exerts quantitative limits on GC size, plasma cell emergence, circulating IgG levels, and protection against re-infection. Finally, contemporaneous B cell development relocates from bone marrow to spleen during infection and treatment. Thus, multiple temporally overlapping mechanisms combine in vivo to amplify, diversify, and safeguard humoral immune responses. We present this data as a temporal, multi-parameter atlas of B cell differentiation in vivo: https://bcell-dynamics.science.unimelb.edu.au Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/628863v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@c57890org.highwire.dtl.DTLVardef@6e5936org.highwire.dtl.DTLVardef@a2e872org.highwire.dtl.DTLVardef@14abbac_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIPartial temporal overlap of CSR with clonal expansion leads to isotype variegation in clones. C_LIO_LIClones seeding GCs bifurcate into plasmablasts and exhibit isotype variegation. C_LIO_LIGC B cells accrue [~]4 mutations/week, a rate unaffected by anti-malarials. C_LIO_LIPlasmodium infection triggers antigen-independent Type I IFN-mediated bystander activation. C_LIO_LIB cell development is preserved in malaria by shifting from bone marrow to spleen. C_LI

immunology↗

bioRxiv2024

Metabolic immaturity of newborns and breast milk bile acids are the central determinants of heightened neonatal vulnerability to norovirus diarrhea

Noroviruses are the leading global cause of acute gastroenteritis, responsible for 685 million annual cases. While all age groups are susceptible to noroviruses, children are vulnerable to more severe infections than adults, underscored by 200 million pediatric cases and up to 200,000 deaths in children annually. Understanding the basis for the increased vulnerability of young hosts is critical to developing effective treatments. The pathogenic outcome of any enteric virus infection is governed by a complex interplay between the virus, intestinal microbiota, and host immune factors. A central mediator in these complex relationships are host- and microbiota-derived metabolites. Noroviruses bind a specific class of metabolites, bile acids, which are produced by the host and then modified by commensal bacterial enzymes. Paradoxically, bile acids can have both proviral and antiviral roles during norovirus infections. Considering these opposing effects, the microbiota-regulated balance of the bile acid pool may be a key determinant of the pathogenic outcome of a norovirus infection. The bile acid pool in newborns is unique due to immaturity of host metabolic pathways and developing gut microbiota, which could underlie the vulnerability of these hosts to severe norovirus infections. Supporting this concept, we demonstrate herein that microbiota and their bile acid metabolites protect from severe norovirus diarrhea whereas host-derived bile acids promote disease. Remarkably, we also report that maternal bile acid metabolism determines neonatal susceptibility to norovirus diarrhea during breastfeeding by delivering proviral bile acids to the newborn. Finally, directed targeting of maternal and neonatal bile acid metabolism can protect the neonatal host from norovirus disease. Altogether, these data support the conclusion that metabolic immaturity in newborns and ingestion of proviral maternal metabolites in breast milk are the central determinants of heightened neonatal vulnerability to norovirus disease.

microbiology↗

bioRxiv2023

CD4+ T cells display a spectrum of recall dynamics during re-infection with malaria parasites.

Children in malaria-endemic regions can experience multiple Plasmodium infections over a short period of time, with in vitro CD4+ T cell recall responses becoming more regulatory with increasing age and exposure. This suggests that repeated infection qualitatively changes CD4+ T cells, although the heterogeneity and dynamics of these responses await systematic analysis in vivo. Here, we examined TCR transgenic PbTII and polyclonal CD4+ T cells during Plasmodium re-infection in mice, in conjunction with scRNA-seq/TCR-seq and spatial transcriptomics at near single-cell resolution. PbTII cells gave rise to multiple antigen-experienced states in different areas of the spleen after primary infection and antimalarial treatment, including ongoing GC responses and T-cell zone memory. Upon re-infection, Th1-memory PbTII cells initiated a rapid effector response prior to proliferating, while GC Tfh cells of the same antigen specificity were entirely refractory within the same organ. Transcriptome dynamic modelling and network analysis of Th1 recall revealed a biphasic wave of RNA processing that firstly preceded immune effector transcription, and later accompanied cellular proliferation. Importantly, Th1 recall constituted a partial facsimile of primary Th1 responses, with no unique genes amongst the small subset of those upregulated upon re-infection. Finally, we noted a similar spectrum of antigen-experienced states and recall dynamics by polyclonal CD4+ T cells with diverse TCRs. Therefore, during re-infection with Plasmodium, persisting GC Tfh cells remained unaltered transcriptionally, Tcm/Tfh-like cells exhibited minimal proliferation, and Th1-memory cells displayed a rapid, proliferating IL-10-producing Tr1 response consistent with a shift towards immune-regulation. These data highlight a broad spectrum of simultaneous CD4+ T cell responses that occur in the spleen during re-infection with malaria parasites. HighlightsO_LISplenic TCR transgenic CD4+ T cells are highly heterogeneous prior to re-infection. C_LIO_LIPersisting GC Tfh cells are refractory to re-activation during re-infection. C_LIO_LITh1-memory cells rapidly upregulate RNA processing prior to effector function and proliferation. C_LIO_LITh1-recall is an imperfect but faithful facsimile of primary Th1 responses. C_LIO_LIA spectrum of recall states is observed in polyclonal CD4+ T cells with diverse TCRs. C_LI

immunology↗

bioRxiv2023

Spatial transcriptomics maps molecular and cellular requirements for CD4+ T cell-dependent immunity to malaria.

CD4+ T cells orchestrate adaptive immunity to circulating malaria parasites; yet cellular interactions and molecular mechanisms controlling Th1 and Tfh differentiation in the spleen remain to be fully defined in vivo. Here, using a murine model of CD4-dependent immunity, we tested if Slide-seqV2, a spatial transcriptomic method with near single-cell resolution, could determine the locations of multiple CD4+ T cell subsets and potentially interacting cellular partners in the spleen during infection. Firstly, Slide-seqV2 readily mapped splenic cellular structure and microanatomical change during infection. Next, computational integration with scRNA-seq reference datasets of splenocytes, stromal cells, and specifically of polyclonal CD4+ T cells and B cells, mapped the relative locations of multiple cell-types within this dense tissue. scRNA-seq of B cells over time mapped emergence of germinal centre B cells, red pulp-located plasmablasts and atypical B cells, and uncovered a prolonged CD4+ T-cell-independent, follicular bystander B cell response marked by Sca-1 and Ly6C upregulation. scRNA-seq of activated, polyclonal CD4+ T cells revealed their similarity to our previous TCR transgenic models. Importantly, spatial analysis revealed polyclonal Th1 cells co-localised with CXCL9/10-producing monocytes in the red pulp, while polyclonal Tfh-like cells were located close to CXCL13-expressing B cell follicles, consistent with our previous CXCR3/CXCR5 competition model of Th1/Tfh bifurcation. CRISPR/Cas9 disruption of either or both CXCR3 and CXCR5 in naive Plasmodium-specific CD4+ T cells had unexpectedly minor effects on Th1 differentiation in vivo. Instead, CXCR5 was essential for maximising clonal expansion, suggesting a role for splenic CXCL13+ cells in supporting CD4+ T cell proliferation in malaria. Thus, spatial transcriptomics at near single-cell resolution was feasible in densely packed secondary lymphoid tissue, providing multiple insights into mechanisms controlling splenic polyclonal CD4+ T cell and B cell differentiation during infection. HighlightsO_LISlide-seqV2 maps splenic microanatomy, including stromal and immune cell location. C_LIO_LIBystander activation of all follicular B cells occurs in malaria, marked by Sca-1/Ly6C upregulation. C_LIO_LISingle naive polyclonal CD4+ T cells differentiate mostly into Th1 and Tfh cells in malaria. C_LIO_LICell-cell colocalization analysis positions Th1 cells with monocytes in red pulp, and Tfh cells with Cxcl13+ B cell follicles. C_LIO_LICXCR5, but not CXCR3, supports parasite-specific CD4+ T cell clonal expansion. C_LI

immunology↗

bioRxiv2021

Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites

Maturation rate of malaria parasites within red blood cells (RBC) can be influenced by host nutrient status or circadian rhythm. Here, we observed in mice that systemic host inflammation, induced by lipopolysaccharide (LPS) conditioning or ongoing acute malaria infection, slowed the progression of a single cohort of parasites from one generation of RBC to the next. LPS-conditioning and acute infection both triggered substantial changes to the metabolomic composition of plasma in which parasites circulated. This altered plasma directly slowed parasite maturation in a manner that could not be rescued by supplementation, consistent with the presence of inhibitory factors. Single-cell transcriptomic assessment of mixed parasite populations, exposed to a short period of systemic host inflammation in vivo, revealed specific impairment in the transcriptional activity and translational capacity of trophozoites compared to rings or schizonts. Thus, we provide in vivo evidence of transcriptomic and phenotypic plasticity of asexual blood-stage Plasmodium parasites when exposed to systemic host inflammation.

microbiology↗

bioRxiv2021

Marburg and Ebola virus mRNA 3 untranslated regions contain negative regulators of translation that are modulated by ADAR1 editing

The filovirus family includes deadly pathogens such as Ebola virus (EBOV) and Marburg virus (MARV). A substantial portion of filovirus genomes encode 5 and 3 untranslated regions (UTRs) of viral mRNAs. Select viral genomic RNA sequences corresponding to 3UTRs are prone to editing by ADAR1. A reporter mRNA approach, in which different 5 or 3UTRs were inserted into luciferase encoding mRNAs, demonstrates that MARV 3UTRs yield different levels of reporter gene expression suggesting modulation of translation. The modulation occurs in cells unable to produce miRNAs and can be recapitulated in a minigenome assay. Deletion mutants identified negative regulatory regions at end of the MARV NP and L 3UTRs. Apparent ADAR1 editing mutants were previously identified within the MARV NP 3UTR. Introduction of these changes into the MARV nucleoprotein (NP) 3UTR or deletion of the region targeted for editing enhances translation, as indicated by reporter assays and polysome analysis. In addition, the parental NP 3UTR, but not the edited or deletion mutant NP 3UTRs, induce a type I interferon (IFN) response upon transfection into cells. Because some EBOV isolates from the West Africa outbreak exhibited ADAR1 editing of the VP40 3UTR, VP40 3UTRs with parental and edited sequences were similarly assayed. The EBOV VP40 3UTR edits also enhanced translation but neither the wildtype nor the edited 3UTRs induced IFN. These findings implicate filoviral mRNA 3UTRs as negative regulators of translation that can be inactivated by innate immune responses that induce ADAR1. ImportanceUTRs comprise a large percentage of filovirus genomes and are apparent targets of editing by ADAR1, an enzyme with pro- and antiviral activities. However, the functional significance of the UTRs and of ADAR1 editing have been uncertain. This study demonstrates that MARV and EBOV 3UTRs can modulate translation, in some cases negatively. ADAR1 editing or deletion of select regions within the translation suppressing 3UTRs, relieves the negative effects of the UTRs. These data indicate that filovirus 3UTRs contain translation regulatory elements that are modulated by activation of ADAR1, suggesting a complex interplay between filovirus gene expression and innate immunity.

microbiology↗

bioRxiv2021

Pulsed broad-spectrum UV light effectively inactivates SARS-CoV-2 on multiple surfaces

The ongoing SARS-CoV-2 pandemic has resulted in an increased need for technologies capable of efficiently disinfecting public spaces as well as personal protective equipment. UV light disinfection is a well-established method for inactivating respiratory viruses. Here, we have determined that broad-spectrum, pulsed UV light is effective at inactivating SARS-CoV-2 on multiple surfaces. For hard, non-porous surfaces we observed that SARS-CoV-2 was inactivated to undetectable levels on plastic and glass with a UV dose of 34.9 mJ/cm2 and stainless steel with a dose of 52.5 mJ/cm2. We also observed that broad-spectrum, pulsed UV light is effective at reducing SARS-CoV-2 on N95 respirator material to undetectable levels with a dose of 103 mJ/cm2. We included UV dosimeter cards that provide a colorimetric readout of UV dose and demonstrated their utility as a means to confirm desired levels of exposure were reached. Together, the results present here demonstrate that broad-spectrum, pulsed UV light is an effective technology for the inactivation of SARS-CoV-2 on multiple surfaces.

microbiology↗

bioRxiv2020

Non-canonical proline-tyrosine interactions with multiple host proteins regulate Ebola virus infection

The Ebola virus VP30 protein interacts with the viral nucleoprotein and with host protein RBBP6 via PPxPxY motifs. In these interactions the largely alpha-helical carboxy-terminal domain of the EBOV VP30 engages with the motif such that the prolines adopt non-canonical orientations, as compared to other proline-rich motifs. Affinity tag-purification mass spectrometry identified additional PPxPxY-containing host proteins, including hnRNP L, hnRNPUL1 and PEG10, as VP30 interactors. Of these, hnRNP L and PEG10, like RBBP6, inhibit viral RNA synthesis and EBOV replication, whereas hnRNPUL1 enhances. Further, double knockdown studies support additive effects of RBBP6 and hnRNP L. Binding studies demonstrate variable capacity of PPxPxY motifs to bind VP30 and the extended motif PxPPPPxY is demonstrated to confer optimal binding and to inhibit RNA synthesis, with the fifth proline and the tyrosine being most critical. Competition binding and hydrogen-deuterium exchange studies demonstrate that each protein binds a similar interface on VP30 and impacts VP30 phosphorylation. VP30 therefore represents a novel proline recognition domain that allows multiple host proteins to target a single viral protein-protein interface to modulate viral transcription.

microbiology↗

bioRxiv2020

Single-cell transcriptomics of allo-reactive CD4+ T cells over time reveals divergent fates during gut GVHD

Acute gastrointestinal Graft-versus-Host-Disease (GVHD) is a primary determinant of mortality after allogeneic hematopoietic stem-cell transplantation (alloSCT). It is mediated by alloreactive donor CD4+ T cells that differentiate into pathogenic subsets expressing IFN{gamma}, IL-17A or GM-CSF, and is regulated by subsets expressing IL-10 and/or Foxp3. Developmental relationships between T-helper states during priming in mesenteric lymph nodes (mLN) and effector function in the GI tract remain undefined at genome-scale. We used scRNA-seq and computational modelling to create an atlas of putative differentiation pathways during GVHD. Computational trajectory inference suggested emergence of pathogenic and regulatory states along a single developmental trajectory in mLN. Importantly, we identified an unexpected second trajectory, categorised by little proliferation or cytokine expression, reduced glycolysis, and high TCF1 expression. TCF1hi cells upregulated 4{beta}7 prior to gut migration and failed to express cytokines therein. Nevertheless, they demonstrated recall potential and plasticity following secondary transplantation, including cytokine or Foxp3 expression, but reduced TCF1. Thus, scRNA-seq revealed divergence of allo-reactive CD4+ T cells into quiescent and effector states during gut GVHD, reflecting putative heterogenous priming in vivo. These findings, the first at a single-cell level during GVHD over time, can now be used to interrogate T cell differentiation in patients undergoing alloSCT.

immunology↗

bioRxiv2019

Impact of Mengla virus proteins on human and bat innate immune pathways

M[e]ngla virus (MLAV), identified in Rousettus bats, is a phylogenetically distinct member of the family Filoviridae. Because filoviruses Ebola virus (EBOV) and Marburg virus (MARV) modulate host innate immune pathways, MLAV VP35, VP40 and VP24 proteins were compared with their EBOV and MARV homologs for innate immune pathway modulation. In human and Rousettus cells, MLAV VP35 behaved like EBOV and MARV VP35s, inhibiting virus-induced activation of the interferon (IFN)-{beta} promoter. MLAV VP35 inhibited IRF3 phosphorylation and interacted with PACT, a host protein engaged by EBOV VP35 to inhibit RIG-I signaling. MLAV VP35 also inhibited PKR activation. MLAV VP40 was demonstrated to inhibit type I IFN induced gene expression in human and bat cells. It blocked STAT1 tyrosine phosphorylation induced either by type I IFN or over-expressed Jak1, paralleling MARV VP40. MLAV VP40 also inhibited virus-induced IFN{beta} promoter activation, a property shared by MARV VP40 and EBOV VP24. The inhibition of IFN induction was preserved in the presence of a Jak kinase inhibitor, demonstrating that inhibition of Jak-STAT signaling is not sufficient to explain inhibition of IFN{beta} promoter activation. MLAV VP24 did not inhibit IFN-induced gene expression or bind karyopherin 5, properties of EBOV VP24. MLAV VP24 also differed from MARV VP24 in that it failed to interact with Keap1 or activate an antioxidant response element reporter gene, due to the absence of a Keap1-binding motif. These studies demonstrate similarities between MLAV and MARV in how they suppress IFN responses and differences in how MLAV VP24 interacts with host pathways.\n\nImportanceEBOV and MARV, members of the family Filoviridae, are highly pathogenic zoonotic viruses that cause severe disease in humans. Both viruses use several mechanisms to modulate the host innate immune response, and these likely contribute to severity of disease. Here, we demonstrate that MLAV, a filovirus newly discovered in a bat, suppresses antiviral type I interferon responses in both human and bat cells. Inhibitory activities are possessed by MLAV VP35 and VP40, which parallels how MARV blocks IFN responses. However, whereas MARV activates cellular antioxidant responses through an interaction between its VP24 protein and host protein Keap1, MLAV VP24 lacks a Keap1 binding motif and fails to activate this cytoprotective response. These data indicate that MLAV possesses immune suppressing functions that could facilitate human infection. They also demonstrate key differences in MLAV versus either EBOV or MARV engagement of host signaling pathways.

microbiology↗

bioRxiv2019

Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4+ T cells.

CD4+ T cells are repositories of immune memory, conferring enhanced immunity to many infectious agents. Studies of acute viral and bacterial infection suggest that memory CD4+ T cells develop directly from effectors. However, delineating these dynamic developmental pathways has been challenging. Here, we used high-resolution single-cell RNA-seq and temporal mixture modelling to examine the fate of Th1 and Tfh effector cells during non-lethal Plasmodium infection in mice. We observed linear Th1 and Tfh pathways towards memory, characterized by progressive halving in the numbers of genes expressed, and partial transcriptomic coalescence. Low-level persisting infection diverted but did not block these pathways. We observed in the Th1-pathway a linear transition from Th1 through a Tr1 state to TEM cells, which were then poised for Th1 re-call. The Tfh-pathway exhibited a modest Th1-signature throughout, with little evidence of Tr1 development, and co-expression of TCM and memory Tfh markers. Thus, we present a high-resolution atlas of transcriptome dynamics for naive to memory transitions in CD4+ T cells. We also defined a subset of memory-associated genes, including transcription factors Id2 and Maf, whose expression increased progressively against the background of transcriptomic quiescence. Single-cell ATAC-seq revealed substantial heterogeneity in chromatin accessibility in single effectors, which was extensively, though incompletely reset and homogenized in memory. Our data reveal that linear transitions from effector to memory occur in a progressive manner over several weeks, suggesting opportunities for manipulating CD4+ T cell memory after primary infection.\n\nHighlightsO_LIscRNA-seq reveals progressive transition from effector to memory in CD4+ T cells.\nC_LIO_LITranscriptome dynamics suggest linear not branching models for memory development.\nC_LIO_LIA subset of genes associates with gradual onset of CD4+ T cell memory.\nC_LIO_LITh1/Tfh predisposition varies among clonotypes with identical antigen-specificity.\nC_LIO_LIscATAC-seq uncovers non-coding \"memory\" elements in the genome.\nC_LI

immunology↗