T-bet+ Memory B Cells Link to Local Cross-Reactive IgG upon Human Rhinovirus Infection

Emerging insights into atypical B cells in pediatric chronic infectious diseases and immune system disorders: T(o)-bet on control of B-cell immune activation

Repetitive or persistent cellular stimulation in vivo has been associated with the development of a heterogeneous B-cell population that exhibits a distinctive phenotype and, in addition to classical B-cell markers, often expresses the transcription factor T-bet and myeloid marker CD11c. Research suggests that this atypical population consists of B cells with distinct B-cell receptor specificities capable of binding the antigens responsible for their development. The expansion of this population occurs in the presence of chronic inflammatory conditions and autoimmune diseases where different nomenclatures have been used to describe them. However, as a result of the diverse contexts in which they have been investigated, these cells have remained largely enigmatic, with much ambiguity remaining regarding their phenotype and function in humoral immune response as well as their role in autoimmunity. Atypical B cells have garnered considerable interest because of their ability to produce specific antibodies and/or autoantibodies and because of their association with key disease manifestations. Although they have been widely described in the context of adults, little information is present for children. Therefore, the aim of this narrative review is to describe the characteristics of this population, suggest their function in pediatric immune-related diseases and chronic infections, and explore their potential therapeutic avenues.

Age-associated B cells are long-lasting effectors that impede latent γHV68 reactivation

Age-associated B cells (ABCs; CD19⁺CD11c⁺T-bet⁺) are a unique population that are increased in an array of viral infections, though their role during latent infection is largely unexplored. Here, we use murine gammaherpesvirus 68 (γHV68) to demonstrate that ABCs remain elevated long-term during latent infection and express IFNγ and TNF. Using a recombinant γHV68 that is cleared following acute infection, we show that ABCs persist in the absence of latent virus, though their expression of IFNγ and TNF is decreased. With a fluorescent reporter gene-expressing γHV68 we demonstrate that ABCs are infected with γHV68 at similar rates to other previously activated B cells. We find that mice without ABCs display defects in anti-viral IgG2a/c antibodies and are more susceptible to reactivation of γHV68 following virus challenges that typically do not break latency. Together, these results indicate that ABCs are a persistent effector subset during latent viral infection that impedes γHV68 reactivation.

Age-associated B cells are long-lasting effectors that impede latent γHV68 reactivation

Age-associated B cells (ABCs; CD19⁺CD11c⁺T-bet⁺) are a unique population that are increased in an array of viral infections, though their role during latent infection is largely unexplored. Here, we use murine gammaherpesvirus 68 (γHV68) to demonstrate that ABCs remain elevated long-term during latent infection and express IFNγ and TNF. Using a recombinant γHV68 that is cleared following acute infection, we show that ABCs persist in the absence of latent virus, though their expression of IFNγ and TNF is decreased. With a fluorescent reporter gene-expressing γHV68 we demonstrate that ABCs are infected with γHV68 at similar rates to other previously activated B cells. We find that mice without ABCs display defects in anti-viral IgG2a/c antibodies and are more susceptible to reactivation of γHV68 following virus challenges that typically do not break latency. Together, these results indicate that ABCs are a persistent effector subset during latent viral infection that impedes γHV68 reactivation.

Gammaherpesvirus infection drives age-associated B cells toward pathogenicity in EAE and MS

While age-associated B cells (ABCs) are known to expand and persist following viral infection and during autoimmunity, their interactions are yet to be studied together in these contexts. Here, we directly compared CD11c⁺T-bet⁺ ABCs using models of Epstein-Barr virus (EBV), gammaherpesvirus 68 (γHV68), multiple sclerosis (MS), and experimental autoimmune encephalomyelitis (EAE), and found that each drives the ABC population to opposing phenotypes. EBV infection has long been implicated in MS, and we have previously shown that latent γHV68 infection exacerbates EAE. Here, we demonstrate that ABCs are required for γHV68-enhanced disease. We then show that the circulating ABC population is expanded and phenotypically altered in people with relapsing MS. In this study, we show that viral infection and autoimmunity differentially affect the phenotype of ABCs in humans and mice, and we identify ABCs as functional mediators of viral-enhanced autoimmunity.

Age-associated B cells in autoimmune diseases

Age-associated B cells (ABCs) are a transcriptionally and functionally unique B cell population. In addition to arising with age and following infection, ABCs are expanded during autoimmune disease, including those with systemic lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. The exact nature of how ABCs impact disease remains unclear. Here, we review what is known regarding ABC development and distribution during diseases including systemic lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. We discuss possible mechanisms by which ABCs could contribute to disease, including the production of cytokines and autoantibodies or stimulation of T cells. Finally, we speculate on how ABCs might act as mediators between sex, infection, and autoimmune disease, and discuss avenues for further research.

Age-associated B cells in viral infection

Age-associated B cells (ABCs) are a recently identified, unique B cell population that displays both protective and pathogenic characteristics, depending on the context. A major role of ABCs is to protect from viral infection. ABCs expand during an array of viral infections and display various functional capacities, including secretion of antibodies and activation of T cells. Following resolution of infection, ABCs appear to persist and play a crucial role in memory and recall responses. Here, we review the currently understanding of ABCs in the antiviral response in both humans and mice. We discuss avenues for future research, including the impact of sex on the ABC population and heterogeneity of ABCs between contexts.

Antibody structure prediction using interpretable deep learning

Therapeutic antibodies make up a rapidly growing segment of the biologics market. However, rational design of antibodies is hindered by reliance on experimental methods for determining antibody structures. Here, we present DeepAb, a deep learning method for predicting accurate antibody F_V structures from sequence. We evaluate DeepAb on a set of structurally diverse, therapeutically relevant antibodies and find that our method consistently outperforms the leading alternatives. Previous deep learning methods have operated as “black boxes” and offered few insights into their predictions. By introducing a directly interpretable attention mechanism, we show our network attends to physically important residue pairs (e.g., proximal aromatics and key hydrogen bonding interactions). Finally, we present a novel mutant scoring metric derived from network confidence and show that for a particular antibody, all eight of the top-ranked mutations improve binding affinity. This model will be useful for a broad range of antibody prediction and design tasks.

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DeepAb, a deep learning method for antibody structure, is presented

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Structures from DeepAb are more accurate than alternatives

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Outputs of DeepAb provide interpretable insights into structure predictions

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DeepAb predictions should facilitate design of novel antibody therapeutics

Accurate structure models are critical for understanding the properties of potential therapeutic antibodies. Conventional methods for protein structure determination require significant investments of time and resources and may fail. Although greatly improved, methods for general protein structure prediction still cannot consistently provide the accuracy necessary to understand or design antibodies. We present a deep learning method for antibody structure prediction and demonstrate improvement over alternatives on diverse, therapeutically relevant benchmarks. In addition to its improved accuracy, our method reveals interpretable outputs about specific amino acids and residue interactions that should facilitate design of novel therapeutic antibodies.

B cell class switching in intestinal immunity in health and disease

The gastrointestinal tract is colonized by trillions of commensal microorganisms that collectively form the microbiome and make essential contributions to organism homeostasis. The intestinal immune system must tolerate these beneficial commensals, whilst preventing pathogenic organisms from systemic spread. Humoral immunity plays a key role in this process, with large quantities of immunoglobulin (Ig)A secreted into the lumen on a daily basis, regulating the microbiome and preventing bacteria from encroaching on the epithelium. However, there is an increasing appreciation of the role of IgG antibodies in intestinal immunity, including beneficial effects in neonatal immune development, pathogen and tumour resistance, but also of pathological effects in driving chronic inflammation in inflammatory bowel disease (IBD). These antibody isotypes differ in effector function, with IgG exhibiting more proinflammatory capabilities compared with IgA. Therefore, the process that leads to the generation of different antibody isotypes, class-switch recombination (CSR), requires careful regulation and is orchestrated by the immunological cues generated by the prevalent local challenge. In general, an initiating signal such as CD40 ligation on B cells leads to the induction of activation-induced cytidine deaminase (AID), but a second cytokine-mediated signal determines which Ig heavy chain is expressed. Whilst the cytokines driving intestinal IgA responses are well-studied, there is less clarity on how IgG responses are generated in the intestine, and how these cues might become dysfunctional in IBD. Here, we review the key mechanisms regulating class switching to IgA vs IgG in the intestine, processes that could be therapeutically manipulated in infection and IBD.

Experimental rhinovirus infection induces an antiviral response in circulating B cells which is dysregulated in patients with asthma

BACKGROUND

Rhinoviruses are the predominant cause of respiratory viral infections and are strongly associated with asthma exacerbations. While humoral immunity plays an important role during virus infections, cellular aspects of this response are less well understood. Here, we investigated the antiviral response of circulating B cells upon experimental rhinovirus infection in healthy individuals and asthma patients.

METHODS

We purified B cells from experimentally infected healthy individuals and patients with asthma and subjected them to total RNA-sequencing. Rhinovirus-derived RNA was measured in isolated B cells using a highly sensitive PCR. B cells were stimulated with rhinovirus in vitro to further study gene expression, expression of antiviral proteins and B-cell differentiation in response rhinovirus stimulation. Protein expression of pro-inflammatory cytokines in response to rhinovirus was assessed using a proximity extension assay.

RESULTS

B cells isolated from experimentally infected subjects exhibited an antiviral gene profile linked to IFN-alpha, carried viral RNA in vivo and were transiently infected by rhinovirus in vitro. B cells rapidly differentiated into plasmablasts upon rhinovirus stimulation. While B cells lacked expression of interferons in response to rhinovirus exposure, co-stimulation with rhinovirus and IFN-alpha upregulated pro-inflammatory cytokine expression suggesting a potential new function of B cells during virus infections. Asthma patients showed extensive upregulation and dysregulation of antiviral gene expression.

CONCLUSION

These findings add to the understanding of systemic effects of rhinovirus infections on B-cell responses in the periphery, show potential dysregulation in patients with asthma and might also have implications during infection with other respiratory viruses.

Analyzing high-dimensional cytometry data using FlowSOM

The dimensionality of cytometry data has strongly increased in the last decade, and in many situations the traditional manual downstream analysis becomes insufficient. The field is therefore slowly moving toward more automated approaches, and in this paper we describe the protocol for analyzing high-dimensional cytometry data using FlowSOM, a clustering and visualization algorithm based on a self-organizing map. FlowSOM is used to distinguish cell populations from cytometry data in an unsupervised way and can help to gain deeper insights in fields such as immunology and oncology. Since the original FlowSOM publication (2015), we have validated the tool on a wide variety of datasets, and to write this protocol, we made use of this experience to improve the user-friendliness of the package (e.g., comprehensive functions replacing commonly required scripts). Where the original paper focused mainly on the algorithm description, this protocol offers user guidelines on how to implement the procedure, detailed parameter descriptions and troubleshooting recommendations. The protocol provides clearly annotated R code, and is therefore relevant for all scientists interested in computational high-dimensional analyses without requiring a strong bioinformatics background. We demonstrate the complete workflow, starting from data preparation (such as compensation, transformation and quality control), including detailed discussion of the different FlowSOM parameters and visualization options, and concluding with how the results can be further used to answer biological questions, such as statistical comparison between groups of interest. An average FlowSOM analysis takes 1-3 h to complete, though quality issues can increase this time considerably.

Behavioral strategies to prevent and mitigate COVID-19 infection

The single stranded RNA virus SARS-CoV-2 has caused a massive addition to the already leading global cause of mortality, viral respiratory tract infections. Characterized by and associated with early and deleteriously enhanced production of pro-inflammatory cytokines by respiratory epithelial cells, severe COVID-19 illness has the potential to inflict acute respiratory distress syndrome and even death. Due to the fast spreading nature of COVID-19 and the current lack of a vaccine or specific pharmaceutical treatments, understanding of viral pathogenesis, behavioral prophylaxis, and mitigation tactics are of great public health concern. This review article outlines the immune response to viral pathogens, and due to the novelty of COVID-19 and the large body of evidence suggesting the respiratory and immune benefits from regular moderate intensity exercise, provides observational and mechanistic evidence from research on other viral infections that suggests strategically planned exercise regimens may help reduce susceptibility to infection, while also mitigating severe immune responses to infection commonly associated with poor COVID-19 prognosis. We propose that regular moderate intensity exercise should be considered as part of a combinatorial approach including widespread hygiene initiatives, properly planned and well-executed social distancing policies, and use of efficacious facial coverings like N95 respirators. Studies discerning COVID-19 pathogenesis mechanisms, transfer dynamics, and individual responses to pharmaceutical and adjunct treatments are needed to reduce viral transmission and bring an end to the COVID-19 pandemic.

Human TH1 and TH2 cells targeting rhinovirus and allergen coordinately promote allergic asthma

BACKGROUND

Allergic asthmatic subjects are uniquely susceptible to acute wheezing episodes provoked by rhinovirus. However, the underlying immune mechanisms and interaction between rhinovirus and allergy remain enigmatic, and current paradigms are controversial.

OBJECTIVE

We sought to perform a comprehensive analysis of type 1 and type 2 innate and adaptive responses in allergic asthmatic subjects infected with rhinovirus.

METHODS

Circulating virus-specific T_H1 cells and allergen-specific T_H2 cells were precisely monitored before and after rhinovirus challenge in allergic asthmatic subjects (total IgE, 133-4692 IU/mL; n = 28) and healthy nonallergic controls (n = 12) using peptide/MHCII tetramers. T cells were sampled for up to 11 weeks to capture steady-state and postinfection phases. T-cell responses were analyzed in parallel with 18 cytokines in the nose, upper and lower airway symptoms, and lung function. The influence of in vivo IgE blockade was also examined.

RESULTS

In uninfected asthmatic subjects, higher numbers of circulating virus-specific PD-1⁺ T_H1 cells, but not allergen-specific T_H2 cells, were linked to worse lung function. Rhinovirus infection induced an amplified antiviral T_H1 response in asthmatic subjects versus controls, with synchronized allergen-specific T_H2 expansion, and production of type 1 and 2 cytokines in the nose. In contrast, T_H2 responses were absent in infected asthmatic subjects who had normal lung function, and in those receiving anti-IgE. Across all subjects, early induction of a minimal set of nasal cytokines that discriminated high responders (G-CSF, IFN-γ, TNF-α) correlated with both egress of circulating virus-specific T_H1 cells and worse symptoms.

CONCLUSIONS

Rhinovirus induces robust T_H1 responses in allergic asthmatic subjects that may promote disease, even after the infection resolves.

Understanding the Heterogeneous Population of Age-Associated B Cells and Their Contributions to Autoimmunity and Immune Response to Pathogens

In humans and mice, susceptibility to infections and autoimmunity increases with age due to age-associated changes in innate and adaptive immune responses. Aged innate cells are also less active, leading to decreased naive T- and B-cell responses. Aging innate cells contribute to an overall heightened inflammatory environment. Naive T and B cells undergo cell-intrinsic age-related changes that result in reduced effector and memory responses. However, previously established B- and T-cell memory responses persist with age. One dramatic change is the appearance of a newly recognized population of age-associated B cells (ABCs) that has a unique cluster of differentiation (CD)21-CD23- phenotype. Here, we discuss the discovery and origins of the naive phenotype immunoglobulin (Ig)D+ versus activated CD11c+T-bet+ ABCs, with a focus on protective and pathogenic properties. In humans and mice, antigen-experienced CD11c+T-bet+ ABCs increase with autoimmunity and appear in response to bacterial and viral infections. However, our analyses indicate that CD21-CD23- ABCs include a resting, naive, progenitor ABC population that expresses IgD. Similar to generation of CD11c+T-bet+ ABCs, naive ABC response to pathogens depends on toll-like receptor stimulation, making this a key feature of ABC activation. Here, we put forward a potential developmental map of distinct subsets from putative naive ABCs. We suggest that defining signals that can harness the naive ABC response may contribute to protection against pathogens in the elderly. CD11c+T-bet+ ABCs may be useful targets for therapeutic strategies to counter autoimmunity.