Biology subjects

Chiu, C.

Publications and source records attributed to Chiu, C..

At least 19 recordsLinked to original sources

bioRxiv2026

Cholinergic and adrenergic modulation sculpts parallel inhibition of SST-INs in visual cortex

GABAergic interneurons are fundamental to the normal function of neuronal circuits in the neocortex. A growing literature has highlighted the role of somatostatin-expressing interneurons (SST-INs) in regulating cortical activity, and inhibition of SST-INs by other interneurons has emerged as a circuit motif leading to disinhibition of pyramidal neurons. However, the diversity and regulation of GABAergic inputs to SST-INs are only partially understood. Here, we combined widefield and 2-photon optogenetic stimulation of parvalbumin (PV)- and vasoactive intestinal peptide (VIP)-expressing interneurons with recordings from fluorescently identified SST-INs in layer 2/3 of primary visual cortex (V1). Our results show that both PV- and VIP-INs form inhibitory inputs onto SST-INs but with varying functional properties. PV-INs evoke strong, fast inhibition onto perisomatic regions of their target cells, while VIP-INs evoke slower inhibition onto target cell dendrites that is partially mediated by alpha subunit-containing GABA receptors. Cholinergic modulation through muscarinic receptors strongly suppresses PV-IN output while adrenergic modulation through beta receptors enhances VIP-IN output. Computational modeling suggests that these parallel inhibitory pathways can differentially regulate circuit gain and network stability across different inputs and arousal conditions. Thus, the diversity of disinhibitory GABAergic circuits in the neocortex provides a mechanism for state-dependent flexibility in circuit function.

neuroscience↗

bioRxiv2026

Systematic Evaluation of Nasal Immune Cell Sampling and Antigen-specific T cell Detection using Cryopreserved Nasal Swabs

The upper respiratory tract is a key entry point for pathogens, yet local tissue-resident memory T cells (Trm) remain underexplored compared to peripheral blood. We systematically compared nasal curettes and 8 different swab types for immune cell collection, assessing yield, operator variability, and T cell phenotypes across the three turbinates and nasopharynx. The use of flocked swabs yielded higher immune cell numbers while being similarly tolerated, especially with reduced sampling duration. Nasal Trm subsets were consistent across the turbinates, whereas nasopharyngeal Trm displayed a more recently recruited phenotype. Multiple cryopreservation media were evaluated and all demonstrated high viability after thawing. Antigen-specificity was assessed using the activation induced marker (AIM) assay, peptideHLA tetramers and bulk TCR-sequencing following expansion. Notably, influenza-specific T cell frequencies were reliably detected by AIM and correlated between fresh and cryopreserved nasal samples. Downregulation of the CD3/TCR complex was observed in nasal samples. These findings establish a robust approach for nasal Trm profiling, demonstrating that cryopreservation preserves functional antigen-specific T cells. This work enables centralized, minimally invasive nasal T cell analysis for multicenter studies, including mucosal vaccination trials and controlled human infection models.

immunology↗

bioRxiv2026

Inhibition of integrin αvβ8-mediated TGFβ activation and active-TGFβ blockade promote anti-tumor immunity through distinct biological mechanisms

Transforming Growth Factor {beta} (TGF{beta}) is a potent immunosuppressor and a primary driver of resistance to cancer immunotherapy. While preclinical models have long suggested that TGF{beta} inhibition could synergize with immune checkpoint inhibitors, these effects have proven difficult to replicate in clinical settings. The highly regulated TGF{beta} pathway can be inhibited through various mechanisms, including neutralizing activated ligands or inhibiting upstream activators, such as integrins. Recent structural data demonstrated that integrin v{beta}8 can enable TGF{beta}1/3 signaling without releasing the active cytokines from their Latency-Associated Peptides, suggesting that ligand-blocking antibodies may have limited access to their epitopes. Here, we show that integrin v{beta}8 blockade, while achieving anti-tumor responses similar to those of anti-TGF{beta} antibodies, does so through a distinct mechanism of action. Anti-v{beta}8 is 3 orders of magnitude more potent at inhibiting v{beta}8-mediated TGF{beta} activity than a commonly used antibody against the mature form of the cytokine. Whereas TGF{beta} ligand inhibition has little effect on TGF{beta} signaling in tumor-draining lymph nodes (tdLN) and requires IFN{gamma} for its anti-tumor effects, v{beta}8 blockade strongly inhibits TGF{beta} signaling in tdLN and, in combination with PD-L1 blockade, drives tumor control through an IFN{gamma} -independent mechanism that strictly requires T cell egress from tdLN. Combined v{beta}8 and anti-PD-L1 blockade enhances antigen presentation in dendritic cells (DCs) and, unlike TGF{beta} ligand blockade, improves the efficiency of DC-induced T cell activation in response to cross-presented antigen. These findings suggest that v{beta}8 blockade can disable an immunologically critical source of TGF{beta} signaling that is not addressed by antibodies targeting TGF{beta} ligands, suggesting a promising new approach to TGF{beta} pathway modulation. One Sentence SummaryUnlike ligand-neutralizing antibodies, v{beta}8 blockade suppresses TGF{beta} in tdLN and boosts DC-T cell activation, a differentiated immunotherapy strategy.

immunology↗

bioRxiv2026

A Co-culture Cell-Based Reporter Assay for Quantitative Measurement of Integrin αvβ8-Mediated Activation of Latent TGF-β1

Integrin v{beta}8 is a major activator of latent transforming growth factor-{beta} (TGF-{beta}) and an emerging therapeutic target in cancer and immune regulation. However, functional assays that directly measure v{beta}8-mediated activation of latent TGF-{beta} in a physiologically relevant context remain limited. Here, we report a co-culture cell-based reporter assay for quantitative measurement of v{beta}8-mediated activation of latent TGF-{beta}1. NIH/3T3 reporter cells were engineered to express a SMAD-responsive NanoLuc reporter, constitutive firefly luciferase for internal normalization, and cell-surface GARP-latent TGF-{beta}1. When co-cultured with v{beta}8-expressing LN-229 cells, reporter cells produced a robust signal that directly reflected localized latent TGF-{beta}1 activation. The assay demonstrated stable expression of the required biological components, reproducible signal-to-background performance, and sensitivity to benchmark v{beta}8-blocking antibodies. Inhibition studies showed potent dose-dependent blockade by an anti-v{beta}8 antibody. In contrast, pan-TGF-{beta} neutralizing antibody displayed markedly weaker apparent potency, suggesting that targeting localized v{beta}8-mediated activation is more effective than neutralizing released TGF-{beta} in this assay context. The assay also enabled screening and ranking of anti-v{beta}8 antibodies, identifying several high-potency clones, and detected v{beta}8-mediated activation of a non-cleavable latent TGF-{beta}1 mutant. This platform provides a sensitive, internally normalized, and scalable approach for mechanistic studies and therapeutic discovery targeting the v{beta}8-TGF-{beta} axis.

immunology↗

bioRxiv2026

Ultrasensitive voltage imaging reveals distinct electrical microdomains in neurons

For the brain to compute, electrical signals must propagate over the membranes of individual neurons, connecting synaptic inputs to synaptic outputs1. Complex neuronal morphologies coupled with the spatial organization of synaptic inputs and outputs enable diverse voltage transformations that underlie cell-type specific computations2,3. However, measuring these transformations in vivo has remained challenging, leaving a crucial gap in our mechanistic understanding of single neuron computation. Here, we develop ASAP7y, a genetically encoded voltage indicator with unprecedented subthreshold sensitivity and expanded excitation compatibility in both mice and flies. We leveraged ASAP7y combined with two-photon random-access microscopy to record sensory stimulus-evoked voltage dynamics with millisecond, subcellular, and subthreshold resolution along the neurites of individual neurons in Drosophila. We found remarkable heterogeneity in voltage propagation across cell-types, delineating a fundamental axis of electrical diversity. Leveraging a nanoscale EM reconstruction of the visual system4, we modeled the electrotonic properties of single neurons spanning 717 cell types, revealing how morphology shapes voltage transformations. Finally, we demonstrate that confined voltage propagation creates substrates for local computation, producing subcellular domains with distinct feature selectivity across multiple cell types. These results provide mechanistic insight into how critical single neuron computations arise and reveal parallel processing in single neurons.

neuroscience↗

bioRxiv2026

Phage terminase recognition by the bacterial immune sensors Avs2 and Upx

Prokaryotes employ diverse defense strategies to detect and halt the progression of phage infection. Multiple defense systems sense phage proteins through direct binding, including antiviral STAND NTPases (Avs), which oligomerize upon target recognition to induce programmed cell death. The widespread Avs2 family was previously shown to detect the large terminase subunit of tailed phages, but the mechanism of terminase sensing was unknown. Here, we determine the structural basis of terminase recognition by Avs2 from Escherichia coli (EcAvs2). A cryo-EM structure at 2.3 [A] resolution reveals that EcAvs2 forms a flat, C4-symmetric tetramer in which each protomer is bound to a single terminase monomer. Terminase recognition is mediated by a large, shape complementary binding pocket in the EcAvs2 sensor domain, including specific contacts with an unexpected ATP molecule at the interface of EcAvs2 and terminase. Furthermore, we demonstrate that the defense protein Upx also recognizes diverse phage terminases, despite lacking sequence and structural homology to Avs. AlphaFold 3 models indicate that Upx binds an unfolded state of the core terminase ATPase domain, mediated by {beta}-augmentation. These findings highlight the distinct modes of terminase recognition across structurally diverse defense proteins.

molecular biology↗

bioRxiv2026

Computational Study of Antibody Binding to SARS-CoV-2 Variants

Background/ObjectivesThe unprecedented structural and binding data for antibodies to the SARS-COV2 virus taken together with the mutations for the spike protein allows for a broad simulation study of antibody-spike protein binding. This provides an understanding of the co-evolution of human immunity and viral immunity escape. MethodsWe utilized the YASARA molecular dynamics program to generate initial antibody-spike structures and simulate to equilibration for six SARS-COV2 variants and 10 different antibodies sampling two different binding regions to the receptor binding domain of the spike (especially for the Class I antibodies in the same part of the spike which attaches to the ACE2 receptor protein) and one to the N-terminal of the spike. Starting structures for antibody binding to variant spike proteins are perturbatively achieved through point mutations and insertions/deletions in the YASARA program. We employed YASARA to measure interfacial hydrogen bound counts between antibodies and variant spike proteins, and the HawkDock MMGBSA program to characterize trends in binding energies with mutation for four of the antibodies. We utilized the VMD program to analyze the time course of hydrogen bond populations. ResultsAs seen in previous studies, interfacial hydrogen bond counts serve as an excellent proxy for binding energies without the large systematic error inherent in the latter. We find that there is generally a decline in antibody binding strength, as measured by interfacial hydrogen bond counts, with viral evolution, but that a modest re-entrance of binding strength is present for most antibodies studied. Generically, the antibody heavy chain binds more strongly to the spike protein, through for approximately half the antibodies the light chain binding strength converges to the heavy chain strength with viral evolution. ConclusionsThe key conclusion is that the identified re-entrant immunity, speculatively arising from a balancing of maintenance of ACE2-spike binding while escaping antibodies through mutation, allows for some maintenance and even strengthening of immunity for later viral strains from early infection or vaccination.

biophysics↗

bioRxiv2026

Diverse bacterial pattern recognition receptors sense the conserved phage proteome

Recognition of foreign molecules inside cells is critical for immunity across all domains of life. Proteins of the STAND NTPase superfamily1,2, including eukaryotic NOD-like receptors (NLRs), play a central role in this process3,4. In bacteria and archaea, although several STAND families sense phage proteins5-9, their functional diversity remains largely unexplored. We conducted a systematic phylogenetic analysis of prokaryotic STAND NTPases and identified at least 90 structurally distinct families associated with antiviral defense. We first show that the uncharacterized Avs7 family recognizes the major capsid protein (MCP) of tailed phages. Three cryo-EM structures of Salmonella enterica Avs7 reveal an asymmetric, butterfly-shaped tetramer that assembles stepwise via large, MCP-induced conformational changes, incorporating bacterial elongation factor Tu (EF-Tu) as a structural component that enhances defense. Using genetic screens with a library of 687 phage genes, we further show that 13 additional STAND families sense 13 conserved phage proteins, encompassing most of the core structural and replicative components of tailed phages. These include two distinct MCP-sensing families--Avs8 (PD-{lambda}-4) and Avs10 (Erebus/Hypnos/bNACHT64)--and 11 others (Avs11-21) recognizing the portal, portal adaptor, tail nozzle, head-tail connector, tail terminator, tail tube protein, tail assembly chaperone, tape measure protein, DNA polymerase, helicase/RecA-type ATPase, and single-stranded DNA annealing protein, respectively. Together, our findings highlight structurebased pattern recognition and host factor repurposing as fundamental strategies of bacterial immunity.

molecular biology↗

bioRxiv2025

Temporal Dynamics of Antigen-Specific T Cell Expansion in Primary SARS-CoV-2 Infection

Quantifying T cell response during primary infection in humans is crucial for understanding adaptive immunity. Leveraging a controlled human challenge to SARS-CoV-2, we characterized antigen-specific T cell response within and across individuals. Notably, individual clones reached similar maximum frequencies despite differences in the timing of their peak expansion. Mathematical modeling showed that this observation is consistent with precursor frequency, but not TCR signal strength, as the source of inter-clonal variability. Single-cell profiling revealed distinct temporal programs for CD4+ and CD8+ T cells, with CD4+ cells expanding earlier but contracting to a lower frequency. Clones with similar receptors, likely recognizing the same antigen, expanded at similar times. Together, these findings highlight how clone-intrinsic properties such as precursor frequency and lineage shape T cell clonal kinetics. These insights provide a quantitative framework for understanding T cell response in humans, with implications for vaccine design.

biophysics↗

bioRxiv2025

CMDdemux: an efficient single cell demultiplexing method

Multiplexing technologies label cells with molecular tags, allowing cells from different donors to be pooled together for sequencing. Although this approach enhances cell throughput, eliminates batch effects, and enables doublet detection, limitations of hashtag-based labelling can still lead to low-quality data. Existing demultiplexing methods can accurately assign donor identities in high-quality datasets, but they often fail on low-quality data. To address this, we developed CMDdemux, a method comprising three key steps: within-cell centered log-ratio (CLR) normalization of hashtag count data, K-medoids clustering, and classification of cells based on Mahalanobis distance. By integrating both hashing and mRNA data, CMDdemux achieves high accuracy in distinguishing singlets, doublets, and negatives. It also provides visualization tools to help users inspect potentially misclassified droplets. We benchmarked CMDdemux against existing methods using a range of high- and low-quality datasets. Results show that CMDdemux consistently outperforms other approaches, demonstrating robust performance on both high- and low-quality data where other methods fail. CMDdemux is particularly effective in handling diverse types of low-quality multiplexing data across different multiplexing technologies.

bioinformatics↗

bioRxiv2025

Rational design of oxidation-resistant antibodies through local electrostatic modulation

Oxidation is a significant degradation pathway in proteins, particularly therapeutic antibodies, that can impair function, efficacy, and stability. Understanding the sequence and structural factors that drive oxidation susceptibility is critical for incorporating chemical stability into early-stage antibody design. Here, we present a machine learning classifier trained on expert-guided structural features to assess tryptophan (Trp) oxidation risks in the complementarity-determining regions (CDR) of 187 antibodies produced internally at Genentech. The model reveals a strong correlation between local negative electrostatic potential and Trp oxidation susceptibility. A simplified two-parameter model derived from these insights achieves 79% accuracy in classifying oxidation risk, compared to 84% accuracy with the full-feature classifier. Beyond our internal dataset, the two-parameter model successfully predicted oxidation risk for all CDR Trp sites in a blind subset of eight clinical-stage antibodies. In addition, we show that modulating the electrostatic potential around the Trp side-chains through distant charge-altering mutations can significantly reduce oxidation rates. In four out of five re-engineered antibodies, oxidation rates decreased by approximately 50%, while half of these maintained binding affinity. Finally, we demonstrate that this approach can guide multi-property optimization by balancing oxidation resistance and affinity in an anti-CD33 antibody. These results establish a strong link between local electrostatic environments and Trp oxidation susceptibility, and provide a practical framework for designing oxidation resistant biotherapeutics.

biochemistry↗

bioRxiv2024

Proinsulin C-peptide is a major source of HLA-DQ8 restricted HIPs recognized by human Islet-Infiltrating CD4+ T cells

Type 1 diabetes (T1D) is an autoimmune disease that develops when T cells destroy the pancreatic insulin-producing beta cells that reside in the pancreatic islets. Immune cells, including T cells infiltrate the islets and gradually destroy the beta cells. Human islet-infiltrating CD4+ T cells recognize peptide epitopes derived from proinsulin, particularly C-peptide. Hybrid Insulin peptides (HIPs) are neoepitopes formed by the fusion of two peptides derived from beta-cell granule proteins and are known to be the targets of pathogenic CD4+ T cells in the NOD mouse and human islet-infiltrating CD4+ T cells. Proinsulin is widely recognized as a central antigen in T1D, but its role in forming HIPs is unclear. We developed a method to functionally screen TCRs derived from human islet-infiltrating CD4+ T cells and applied this to the identification of new proinsulin-derived HIPs. We generated a library of 4,488 candidate HIPs formed by fusion of proinsulin fragments and predicted to bind to HLA-DQ8. This library was screened against 109 islet-infiltrating CD4+ T-cell TCRs isolated from four organ donors who had T1D. We identified 13 unique HIPs recognized by 9 different TCRs from two organ donors. HIP specific T-cell avatars responded specifically to a peptide extract from human islets. These new HIPs predominantly stimulated CD4+ T-cell proliferation in PBMCs from people with T1D in contrast to HLA-matched controls. This is the first unbiased functional, islet-infiltrating T-cell based, screen to identify proinsulin derived HIPs. It has revealed many new HIPs and a central role of proinsulin C-peptide in their formation. SUMMARYType 1 diabetes is an autoimmune disease caused by T cells destroying the pancreatic insulin-producing beta cells. The antigens/epitopes seen by disease promoting CD4+ T cells are poorly understood. Hybrid insulin peptides (HIPs) are a new class of CD4+ antigen recognized by pathogenic NOD mouse CD4+ T cells. In humans very few HIPs recognized by human islet-infiltrating CD4+ T cells are known. We show that proinsulin HIPs are recognized by human islet-infiltrating CD4+ T cells from T1D donors and describe 13 new HIPs formed by fusion of proinsulin peptides. This work shows that proinsulin, particularly C-peptide, is a major contributor to the pool HIPs recognized by human islet-infiltrating CD4+ T cells and are therefore central to autoimmunity in T1D.

immunology↗

bioRxiv2024

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

Troides aeacus, the golden birdwing (Lepidoptera, Papilionidae) is a large swallowtail butterfly widely distributed in Asia. Despite its occurrence, T. aeacus has been assigned as a major protective species in many places given the loss of their native habitats under urbanisation and anthropogenic activities. Nevertheless, the lack of its genomic resources hinders our understanding of their biology, diversity, as well as carrying out conservation measures based on genetic information or markers. Here, we report the first chromosomal-level genome assembly of T. aeacus using a combination of PacBio SMRT and Omni-C scaffolding technologies. The assembled genome (351 Mb) contains 98.94% of the sequences anchored to 30 pseudo-molecules. The genome assembly also has high sequence continuity with scaffold length N50 = 12.2 Mb. A total of 28,749 protein-coding genes were predicted, and high BUSCO score completeness (98.9% of BUSCO metazoa_odb10 genes) was also revealed. This high-quality genome offers a new and significant resource for understanding the swallowtail butterfly biology, as well as carrying out conservation measures of this ecologically important lepidopteran species.

genomics↗

bioRxiv2023

Development and validation of a respiratory syncytial virus multiplex immunoassay

Respiratory syncytial virus (RSV) is one of the leading causes of severe respiratory disease in infants and adults. RSV exists as two subtypes A and B, which co-circulate throughout the season, although one will usually become dominant. While vaccines and monoclonal therapeutic antibodies either are or will shortly become available, correlates of protection remain unclear. For this purpose, we developed an RSV multiplex immunoassay that analyses antibody titers towards the post-F, Nucleoprotein, and a diverse mix of G proteins. Technical and clinical validation showed outstanding performance, while methodological developments enabled identification of the subtype of previous infections through use of the diverse G proteins for approximately 50% of samples. As a proof of concept to show the suitability of the assay in serosurveillance studies, we then evaluated titer decay and age- dependent antibody responses within population cohorts. Overall, the developed assay shows robust performance, is scalable, provides additional information on infection subtype, and is therefore ideally suited to be used in future population cohort studies. ImportanceAlthough respiratory syncytial virus (RSV) is endemic and re-infections are common and harmless to the majority of the population, it is a leading cause of hospitalization in young children, the elderly, or immunocompromised individuals. A better characterization of RSV immunology and spreading dynamics is thus critical for preparedness, especially when interventions aiming to mitigate other diseases (e.g., COVID-19) disturb its endemic cycles. This requires high-throughput information-dense assays. We therefore developed a bead-based multiplex immunoassay that allows measurements of antibodies against multiple RSV antigens simultaneously. We identified antibodies which were strong indicators of previous infection, while others allowed identification of the subtype of the previous infection. The assay itself was shown to be robust and scalable, making it ideal for to keep track of the temporal variation RSV immunity profiles within the population.

immunology↗

bioRxiv2023

The chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans

SET-26, HCF-1, and HDA-1 are highly conserved chromatin factors with key roles in development and aging. Here we present mechanistic insights into how these factors regulate gene expression and modulate longevity in C. elegans. We show that SET-26 and HCF-1 cooperate to regulate a common set of genes, and both antagonize the histone deacetylase HDA-1 to limit longevity. We propose a model in which SET-26 recruits HCF-1 to chromatin in somatic cells, where they stabilize each other at the promoters of a subset of genes, particularly mitochondrial function genes, and regulate their expression. HDA-1 opposes SET-26 and HCF-1 on the regulation of a subset of their common target genes and in longevity. Our findings suggest that SET-26, HCF-1, and HDA-1 comprise a mechanism to fine-tune gene expression and longevity and likely have important implications for the mechanistic understanding of how these factors function in diverse organisms, particularly in aging biology.

genomics↗

bioRxiv2022

Single-cell genome-wide association reveals a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus

Diversity in the human genome is one factor that confers resistance and susceptibility to infectious diseases. This is observed most dramatically during pandemics, where individuals exhibit large differences in risk and clinical outcomes against a pathogen infecting large portions of the worlds populations. Here, we developed scHi-HOST (single cell High-throughput Human in vitrO Susceptibility Testing), a method for rapidly identifying genetic variants that confer resistance and susceptibility to pathogens. scHi-HOST leverages scRNA-seq (single-cell RNA-sequencing) to simultaneously assign genetic identity to individual cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral entry and replication, and identify expression quantitative trait loci (eQTLs). Applying scHi-HOST to influenza A virus (IAV), we identified eQTLs at baseline and in genes that are induced by IAV infection. Integration of scHi-HOST with a human IAV challenge study (Prometheus) revealed that a missense variant in ERAP1 (Endoplasmic reticulum aminopeptidase 1; rs27895) was associated with IAV burden in cells and human volunteers. Functional studies using RNA interference, ERAP1 inhibitor, and overexpression of alternative alleles demonstrated that ERAP1 is exploited by IAV to promote infection. Specifically, the nonsynonymous substitution, which results in a glycine to aspartate substitution at ERAP1 residue 348, would disrupt the substrate binding pocket of ERAP1, likely resulting in a significantly altered preference for substrates, poorer catalytic efficiency, or both. Finally, rs27895 exhibits substantial population differentiation, with the higher frequency of the minor T allele in two African populations likely contributing to the greater permissivity of cells from these populations to IAV infection. scHi-HOST is an important resource for understanding susceptibility to influenza and is a broadly applicable method for decoding human genetics of infectious disease.

genetics↗

bioRxiv2021

Pandemic, epidemic, endemic: B cell repertoire analysis reveals unique anti-viral responses to SARS-CoV-2, Ebola and Respiratory Syncytial Virus

Immunoglobulin gene heterogeneity reflects the diversity and focus of the humoral immune response towards different infections, enabling inference of B cell development processes. Detailed compositional and lineage analysis of long read IGH repertoire sequencing, combining examples of pandemic, epidemic and endemic viral infections with control and vaccination samples, demonstrates general responses including increased use of IGHV4-39 in both EBOV and COVID-19 infection cohorts. We also show unique characteristics absent in RSV infection or yellow fever vaccine samples: EBOV survivors show unprecedented high levels of class switching events while COVID-19 repertoires from acute disease appear underdeveloped. Despite the high levels of clonal expansion in COVID-19 IgG1 repertoires there is a striking lack of evidence of germinal centre mutation and selection. Given the differences in COVID-19 morbidity and mortality with age, it is also pertinent that we find significant differences in repertoire characteristics between young and old patients. Our data supports the hypothesis that a primary viral challenge can result in a strong but immature humoral response where failures in selection of the repertoire risks off-target effects.

immunology↗

bioRxiv2021

An intranasal ASO therapeutic targeting SARS-CoV-2

The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity1. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic2. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identified an LNA ASO binding to the 5 leader sequence of SARS-CoV-2 ORF1a/b that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the K18-hACE2 humanized COVID-19 mouse model potently (98-99%) suppressed viral replication in the lungs of infected mice, revealing strong prophylactic and treatment effects. We found that the LNA ASO also represses viral infection in golden Syrian hamsters, and is highly efficacious in countering all SARS-CoV-2 "variants of concern" tested in vitro and in vivo, including B.1.427, B.1.1.7, and B.1.351 variants3. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce transmission of variants partially resistant to vaccines and monoclonal antibodies, and could be deployed intranasally for prophylaxis or via lung delivery by nebulizer to decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences4, and they may have particular impact in areas where vaccine distribution is a challenge, and could be stockpiled for future coronavirus pandemics.

microbiology↗