Chronic stress disrupts the gut microbiota in patients with cancer; however, how stress-induced microbiota perturbations impact anti-tumor immunity remains unclear. Here, we show that the gut microbiota is required for chronic stress-induced glucocorticoid production, which impairs antigen-specific germinal center B cell responses. In mouse models of colorectal cancer or melanoma, chronic stress promotes translocation of a gut pathobiont, Enterococcus gallinarum (Eg), to tumors. Within tumors, Eg phage DNA induces glucocorticoid production by cancer-associated fibroblasts (CAFs) via TLR9, which suppresses anti-tumor B cell responses through the glucocorticoid receptor. Targeting intratumoral TLR9 or Eg significantly lowers intratumor glucocorticoid levels and reverses the tumor-promoting effects of chronic stress. Extending these findings to human cancer, we identify lytic phages in a Klebsiella pneumoniae isolate from human colorectal tumors that promote tumor growth and detect phage DNA in human brain tumors. Together, our study reveals a chronic stress-induced intratumor phage-CAF-B cell circuit that weakens anti-tumor immunity.

The epitope that monoclonal CR3022 binds to represents a promising target for broad protection against a wide range of human and zoonotic coronaviruses. We develop a powerful model to evaluate antibody affinity maturation in vivo using immunoglobulin (Ig)-humanized mice that express the predicted germline heavy chain of antibody CR3022. Severe acute respiratory syndrome coronavirus (SARS-CoV)/SARS-CoV-2 sequential immunization leads to the convergent evolution of the germline CR3022 through somatic hypermutation (SHM), resembling the affinity-matured CR3022 from a human but now also adapting to key variants and divergent sarbecoviruses. While simple prime-boost strategies drive CR3022-epitope targeting, an intensive vaccination protocol elicits dominant responses to other epitopes. X-ray crystal structures reveal that SARS-CoV-2-neutralizing CR3022-like antibodies exhibit enhanced affinity by increasing polar and electrostatic interactions. Overall, these findings show that CR3022-like clones can be readily adapted through SHM to increase breadth and potency to sarbecoviruses by relatively minor shifts in affinity with appropriate vaccination strategies.

Long-term in vivo production of therapeutic proteins and development of vaccines that elicit protective levels of broadly neutralizing antibodies (bNAbs) against major pathogens face challenges. In this study, we report on an alternative gene editing approach using small numbers of hematopoietic stem and progenitor cells (HSPCs) to direct long-term, high-level expression of antibodies or cargo proteins. In mice, edited B lymphocytes derived from transplanted HSPCs were activated by cognate antigen, underwent clonal expansion, and developed into specific antibody-synthesizing or cargo protein-synthesizing plasma cells. These cells produced long-lasting, therapeutic levels of serum antibody against HIV-1, malaria, or an anti-influenza virus bNAb that mediated universal protection from heterologous lethal challenge. Our data provide a paradigm for cell therapy approaches to prevent or treat disease using self-amplifying B cell protein factories.

Immune imprinting1 or original antigenic sin2 is a phenomenon whereby the immune system preferentially recalls its initial response to a related, often evolving pathogen after subsequent exposure. Despite its important implications for vaccine development, the causes of imprinting remain unclear. Here, to understand the basis and impact of imprinting by influenza A viruses, we characterized the B cell responses of young children after consecutive first infections with divergent H1N1 and H3N2 strains of influenza. Children had a primary but otherwise similar B cell response to that of adults. Adult B cells commonly cross-reacted with past strains using more stereotyped and mutated immunoglobulin genes, indicating substantial homosubtypic imprinting. In children, after consecutive heterosubtypic primary infections, up to 6% of memory B cells are H1/H3 cross-reactive and bind to the highly conserved central stalk epitope-a lead target for broadly protective vaccine candidates. Over 90% of these B cells had a higher affinity for the imprinting H3N2 strain, resulting in reduced breadth and neutralization potency against H1N1 strains. Mechanistically, the imprinting H3 strains and affected H1 strains shared a residue change in the stalk epitope (D46N) that was central to the nearly universal shift in reactivity, despite differing by only a single atomic group. In conclusion, imprinting by influenza viruses can cause a deleterious shift of nearly the entire memory recall response against key, conserved epitopes.

Viral entry glycoproteins are often shielded from immune recognition by dense N-linked glycans that limit antibody access to protein epitopes. While glycan-reactive antibodies with unusual architectures have been described, how canonical Y-shaped antibodies engage these glycan-rich surfaces remains poorly defined. Here, we characterize two human antibodies, VRC35 and VRC36, isolated from an HIV-1-infected donor, that recognize diverse glycosylated viral glycoproteins. Cryo-electron microscopy structural analyses of these antibodies in complex with viral entry glycoproteins, including HIV-1 envelope, influenza hemagglutinin, SARS-CoV-2 spike, and the Lassa virus glycoprotein complex, reveal adaptive Fab stoichiometries ranging from single-Fab binding to dimeric and higher-order assemblies are mediated by intra- and inter-IgG interactions that depend on local glycan organization. Dense glycan clustering on HIV-1 and influenza glycoproteins supports multivalent Fab assemblies and correlates with neutralization activity, whereas sparse glycan environments on SARS-CoV-2 and Lassa virus favor weak or heterogeneous engagement without neutralization. Structural and mutational analyses further demonstrate that homotypic Fab-Fab interactions stabilize multivalent engagement and contribute to neutralizing activity. Together, these findings define a structural framework in which viral glycan organization constrains antibody valency and engagement, while somatic hypermutation contributes to the acquisition of homotypic Fab-Fab interactions that facilitate multivalent recognition of viral glycan shields.

Background Numerous broadly reactive human monoclonal antibodies (mAbs) against the haemagglutinin (HA) of influenza A viruses have recognised conserved epitopes across HA subtypes or within subtypes. Most heterosubtypic mAbs target the HA stem, the receptor-binding site (RBS), or the trimeric interface. Although at least three H3-specific mAbs recognise epitopes outside these regions, the overall landscape of conserved H3-specific epitopes remains incompletely understood. This study aimed to identify and characterise conserved epitopes on H3-HA to inform the development of vaccines resilient to antigenic change. Methods We screened a panel of previously reported H3-HA-reactive human mAbs to identify mAbs recognising conserved epitopes. The candidate clone, 034-10040 4F02 (4F02), was evaluated for neutralising, haemagglutination inhibiting, and HA-mediated fusion-inhibitory, Fc receptor-mediated effector functions in vitro, and for protective efficacy in a lethal mouse challenge model. Cryo-electron microscopy was used to define the structural basis of 4F02 binding. Human sera were screened for antibodies targeting similar epitopes. Findings Clone 4F02 recognised the HA of human influenza A (H3N2) viruses that circulated across multiple decades. It neutralised multiple H3N2 viruses, exhibited weak haemagglutination inhibition, blocked HA-mediated fusion activity, activated Fc receptor-mediated signalling, and protected mice against lethal challenge. Cryo-electron microscopy revealed that 4F02 targets the base of the HA head at a head-stem interface spanning antigenic sites C, D, and E. Antibodies targeting similar epitopes were detected, albeit at a low level, in human sera. Interpretation Characterisation of the 4F02 epitope reveals a previously underappreciated site of vulnerability at the H3-HA head-stem interface. This finding expands our understanding of conserved epitopes and provides a target for the development of influenza vaccines resilient to antigenic change. Funding This work was supported by the Japan Agency for Medical Research and Development, JSPS KAKENHI, the National Institutes of Allergy and Infectious Diseases.

Influenza virus undergoes frequent changes in its main surface glycoprotein, hemagglutinin (HA), evading pre-existing immunity acquired by a previous infection or vaccination. To overcome this challenge, we developed a novel vaccination strategy based on recombinant mosaic HAs (mHAs) that are stabilized without the use of an exogenous trimerization domain (foldon). These stabilized mHAs maintained high trimeric HA content and demonstrated enhanced stability at elevated temperatures and low pH. In mice, sequential immunization with stabilized mHAs redirected the antibody response toward conserved HA regions, resulting in broad protection against diverse influenza virus strains. Compared with foldon-containing constructs, stabilized mHAs improved epitope exposure while avoiding unwanted anti-foldon immune responses. We further compared the immune responses elicited by stabilized mHAs with those induced by conventional seasonal influenza vaccines. Notably, stabilized mHA vaccines conferred protection in the absence of hemagglutination inhibition antibodies, unlike seasonal influenza vaccines. This protection was mediated by a combination of serum neutralization and Fc effector functions predominantly targeting the HA stalk domain. Stabilized mHAs also provided broad cross-protection against homologous (pH1N1), heterologous (SwH1N2), and cross-subtype (H5N1) virus challenges in the mouse model. Overall, stabilized mHAs represent a promising alternative for the development of next-generation universal influenza virus vaccines.

The S2 subunit of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is highly conserved across coronavirus strains and therefore is a potential pan-coronavirus vaccine target. However, antibodies targeting this region are typically non-neutralizing. We report herein that S2-targeting antibodies from patients who recovered from SARS-CoV-2 infection bound only closely related sarbecovirus subgenus strains and, like most known S2 antibodies, none of these were neutralizing. In contrast, first-exposure, severe acutely infected COVID-19 patients predominantly induced back-boosted antibody-secreting cells imprinted against past common cold coronavirus strain OC43 that were cross-reactive to as many as five subgenera of betacoronavirus strains and gave rise to antibodies that were neutralizing and protective. The antibodies targeted two different sites: one defined by competition with stem helix antibodies, and the second to an underdescribed epitope at the apex of S2. These findings suggest that S2-targeted vaccines could strategically exploit controlled OC43 priming followed by SARS-CoV-2 boosting to enhance the breadth and quality of protective antibody responses.

The efficacy of antibody responses is inherently linked to paratope diversity, as generated through V(D)J recombination and somatic hypermutation. Despite this, it is unclear how genetic diversification mechanisms evolved alongside codon optimality and affect antibody expression. Here, we analyze germline immunoglobulin (IG) genes, natural V(D)J repertoires, serum IgG, and monoclonal antibody (mAb) expression through the lens of codon optimality. Germline variable genes (IGVs) exhibit diverse optimality that is inversely related to mutability. Hypermutation deoptimizes heavy-chain (IGH) VDJ repertoires within human tonsils, bone marrow, lymph nodes (including SARS-CoV-2-specific clones), blood (HIV-1-specific clones), mice, and zebrafish. Analyses of mutation-affected codons show that targeting to complementarity-determining regions constrains deoptimization. Germline IGHV optimality correlates with serum variable fragment (VH) usage after influenza vaccination, while synonymous deoptimization attenuated mAb yield. These findings provide unanticipated insights into an antagonistic relationship between diversification mechanisms and codon optimality. Ultimately, the need for diversity takes precedence over that for the most optimal codon usage.

H1N1 influenza viruses are responsible for both seasonal and pandemic influenza. The continual antigenic shift and drift of these viruses highlight the urgent need for a universal influenza vaccine to elicit broadly neutralizing antibodies (bnAbs). Identification and characterization of bnAbs elicited in natural infection and immunization to influenza virus hemagglutinin (HA) can provide insights for development of a universal influenza vaccine. Here, we structurally and biophysically characterize four antibodies that bind to a conserved region on the HA membrane-proximal region known as the anchor epitope. Despite some diversity in their VH and VK genes, the antibodies interact with the HA through germline-encoded residues in HCDR2 and LCDR3. Somatic mutations on HCDR3 also contribute hydrophobic interactions with the conserved HA epitope. This convergent binding mode provides extensive neutralization breadth against H1N1 viruses and suggests possible countermeasures against H1N1 viruses. Structurally convergent antibodies targeting the conserved influenza HA anchor epitope have provided a template for next-generation vaccine development. The authors identified four anchor antibodies encoded by diverse germline genes with broad neutralizing activity against influenza H1N1 viruses.

First described as original antigenic sin (OAS), which is deleterious, or now immune imprinting, which also accounts for beneficial effects, it is clear that immune responses to viruses tend to be biased by previous exposure to similar strains1,2. Various non-exclusive models for the basis of imprinting include that it results from unique features of childhood immunity3,4; it is driven by pre-existing serum antibodies via epitope masking5; or it occurs as a byproduct of residual memory following viral antigenic evolution5. To understand the basis and impact of imprinting from influenza, we characterized the B cell responses of young children upon consecutive first infections with divergent H1N1 and H3N2 influenza viruses. Here, we show that beyond being a primary response, there are no major phenotypic differences in the B cell response of children compared to that of adults. The distinct immunoglobulin variable (IgV) gene repertoire of influenza virus hemagglutinin (HA)-reactive B cells in children, along with increased cross-reactivity to past strains in adults, suggests significant homosubtypic imprinting in adults. As most B cells induced after consecutive infections with antigenically distant H1N1 and H3N2 are strain-specific, heterosubtypic imprinting is rare. However, these successive infections resulted in up to 6% of H1/H3 cross-reactive B cells, targeting the highly conserved central stalk epitope. These B cells express antibodies that are dominantly affected by imprinting with reduced affinity, neutralization potency, and breadth of activity. Mechanistically, H3 to H1 imprinting was caused by a single amino acid change (D46N), differing by just a carboxyl versus an amide atomic group on the central stalk epitope, resulting in a detrimental shift in the specificity of most H1/H3 cross-neutralizing B cells from seven children. We conclude that imprinting by influenza is most evident at the individual epitope level, where minor molecular differences can have a significant impact and need to be accounted for in epitope-targeting vaccine designs.

The continuing emergence of immune evasive SARS-CoV-2 variants and the previous SARS-CoV-1 outbreak collectively underscore the need for broadly protective sarbecovirus vaccines. Targeting the conserved S2 subunit of SARS-CoV-2 is a particularly promising approach to elicit broad protection. Here, we describe a nanoparticle vaccine displaying multiple copies of the SARS-CoV-1 S2 subunit. This vaccine alone, or as a cocktail with a SARS-CoV-2 S2 subunit vaccine, protects female transgenic K18-hACE2 mice from challenges with Omicron subvariant XBB as well as several sarbecoviruses identified as having pandemic potential including the bat sarbecovirus WIV1, BANAL-236, and a pangolin sarbecovirus. Challenge studies in female Fc-γ receptor knockout mice reveal that antibody-based cellular effector mechanisms play a role in protection elicited by these vaccines. These results demonstrate that our S2-based vaccines provide broad protection against clade 1 sarbecoviruses and offer insight into the mechanistic basis for protection. Understanding the induced and cross reactive immunity to sarbecoviruses is an important step in rationale and widely applicable vaccine design. Here the authors use a multivalent S2 subunit vaccine and demonstrate protection in female mice against SARS-CoV-2-like and SARS-CoV-1-like coronaviruses.

Clinical trials show that strategies to elicit the production of broadly neutralizing antibodies have a promising start

In a phase 1 clinical trial, a chimeric hemagglutinin (cHA) immunogen induced antibody responses against the conserved hemagglutinin (HA) stalk domain as designed. Here, we determined the specificity, function, and subsets of B cells induced by cHA vaccination by pairing single-cell RNA sequencing and B cell receptor repertoire sequencing. We have shown that the cHA-inactivated vaccine with a squalene-based adjuvant induced a robust activated B cell and memory B cell (MBC) phenotype against two broadly neutralizing epitopes in the stalk domain. The overall specificities of the acute plasmablast (PB) and MBC responses clonally overlapped, suggesting B cell convergence to these broadly protective epitopes. At 1 year post immunization, we identified that cHA vaccination reshaped the HA-specific MBC pool to enrich for stalk-binding B cells. Altogether, these data indicate the cHA vaccine induced robust and durable B cell responses against broadly protective epitopes of the HA stalk domain, in line with serological data.

The studies reported here focus on the impact of pre-existing CD4 T cell immunity on the first encounter with SARS-CoV-2. They leverage PBMC samples from plasma donors collected after a first SARS-CoV-2 infection, prior to vaccine availability and compared to samples collected prior to the emergence of SARS-CoV-2. Analysis of CD4 T cell specificity across the entire SARS-CoV-2 proteome revealed that the recognition of SARS-CoV-2-derived epitopes by CD4 memory cells prior to the pandemic are enriched for reactivity toward non-structural proteins conserved across endemic CoV strains. However, CD4 T cells after primary infection with SARS-CoV-2 focus on epitopes from structural proteins. We observed little evidence for preferential recall to epitopes conserved between SARS-CoV-2 and seasonal CoV, a finding confirmed through use of selectively curated conserved and SARS-unique peptides. Our data suggest that SARS-CoV-2 CD4 T cells elicited by the first infection are primarily established from the naive CD4 T cell pool.

Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NPRBD) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NPRBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NPRBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.

Integrating machine learning (ML) models into clinical practice presents a challenge of maintaining their efficacy over time. While existing literature offers valuable strategies for detecting declining model performance, there is a need to document the broader challenges and solutions associated with the real-world development and integration of model monitoring solutions. This work details the development and use of a platform for monitoring the performance of a production-level ML model operating in Mayo Clinic. In this paper, we aimed to provide a series of considerations and guidelines necessary for integrating such a platform into a team’s technical infrastructure and workflow. We have documented our experiences with this integration process, discussed the broader challenges encountered with real-world implementation and maintenance, and included the source code for the platform. Our monitoring platform was built as an R shiny application, developed and implemented over the course of 6 months. The platform has been used and maintained for 2 years and is still in use as of July 2023. The considerations necessary for the implementation of the monitoring platform center around 4 pillars: feasibility (what resources can be used for platform development?); design (through what statistics or models will the model be monitored, and how will these results be efficiently displayed to the end user?); implementation (how will this platform be built, and where will it exist within the IT ecosystem?); and policy (based on monitoring feedback, when and what actions will be taken to fix problems, and how will these problems be translated to clinical staff?). While much of the literature surrounding ML performance monitoring emphasizes methodological approaches for capturing changes in performance, there remains a battery of other challenges and considerations that must be addressed for successful real-world implementation.

BACKGROUND:Studies have reported that repeated annual vaccination may influence influenza vaccination effectiveness in the current season. METHODS:We established a 5-year randomized placebo-controlled trial of repeated influenza vaccination (Flublok; Sanofi Pasteur) in adults 18-45 years of age. In the first 2 years, participants were randomized to receive vaccine or saline placebo as follows: placebo-placebo (P-P), placebo-vaccine (P-V), or vaccine-vaccine (V-V). Serum samples were collected each year just before vaccination and after 30 and 182 days. A subset of serum samples collected at 5 time points from 95 participants were tested for antibodies against vaccine strains. RESULTS:From 23 October 2020 through 11 March 2021 we enrolled and randomized 447 adults. Among vaccinated individuals, antibody titers increased between days 0 and 30 against each of the vaccine strains, with smaller increases for repeat vaccinees who on average had higher prevaccination titers in year 2. There were statistically significant differences in the proportions of participants achieving ≥4-fold rises in antibody titer for the repeat vaccinees for influenza A(H1N1), B/Victoria, and B/Yamagata, but not for A(H3N2). Among participants who received vaccination in year 2, there were no significant differences between the P-V and V-V groups in geometric mean titers at day 30 or the proportions of participants with antibody titers ≥40 at day 30 for any of the vaccine strains. CONCLUSIONS:In the first 2 years, during which influenza did not circulate, repeat and first-time vaccinees had similar postvaccination geometric mean titers to all 4 vaccine strains, indicative of similar levels of clinical protection. Clinical Trials Registration. NCT04576377.

Antibodies are powerful modulators of ongoing and future B cell responses. While the concept of antibody feedback has been appreciated for over a century, the topic has seen a surge in interest due to the evidence that the broadening of antibody responses to SARS-CoV-2 after a third mRNA vaccination is a consequence of antibody feedback. Moreover, the discovery that slow antigen delivery can lead to more robust humoral immunity has put a spotlight on the capacity for early antibodies to augment B cell responses. Here, we review the mechanisms whereby antibody feedback shapes B cell responses, integrating findings in humans and in mouse models. We consider the major influence of epitope masking and the diverse actions of complement and Fc receptors and provide a framework for conceptualizing the ways antigen-specific antibodies may influence B cell responses to any form of antigen, in conditions as diverse as infectious disease, autoimmunity, and cancer.

Cell hashing, a nucleotide barcode-based method that allows users to pool multiple samples and demultiplex in downstream analysis, has gained widespread popularity in single-cell sequencing due to its compatibility, simplicity, and cost-effectiveness. Despite these advantages, the performance of this method remains unsatisfactory under certain circumstances, especially in experiments that have imbalanced sample sizes or use many hashtag antibodies. Here, we introduce a hybrid demultiplexing strategy that increases accuracy and cell recovery in multi-sample single-cell experiments. This approach correlates the results of cell hashing and genetic variant clustering, enabling precise and efficient cell identity determination without additional experimental costs or efforts. In addition, we developed HTOreader, a demultiplexing tool for cell hashing that improves the accuracy of cut-off calling by avoiding the dominance of negative signals in experiments with many hashtags or imbalanced sample sizes. When compared to existing methods using real-world datasets, this hybrid approach and HTOreader consistently generate reliable results with increased accuracy and cell recovery.