Fluorescently labeled dengue viruses as probes to identify antigen-specific memory B cells by multiparametric flow cytometry

Modeling human immune responses to vaccination in vitro

The human immune system is a complex network of coordinated components that are crucial for health and disease. Animal models, commonly used to study immunomodulatory agents, are limited by species-specific differences, low throughput, and ethical concerns. In contrast, in vitro modeling of human immune responses can enable species- and population-specific mechanistic studies and translational development within the same study participant. Translational accuracy of in vitro models is enhanced by accounting for genetic, epigenetic, and demographic features such as age, sex, and comorbidity. This review explores various human in vitro immune models, considers evidence that they may resemble human in vivo responses, and assesses their potential to accelerate and de-risk vaccine discovery and development.

The phenotype of HLA-binding B cells from sensitized kidney transplant recipients correlates with clinically prognostic patterns of interferon-γ production against purified HLA proteins

B cells play crucial roles in cell-mediated alloimmune responses. In vitro, B cells can support or regulate indirect T-cell alloreactivity in response to donor antigens on ELISpot and these patterns associate with clinical outcome. Previous reports of associations between B-cell phenotype and function have examined global phenotypes and responses to polyclonal stimuli. We hypothesized that studying antigen-specific B cells, using samples from sensitized patients, would inform further study to identify novel targets for intervention. Using biotinylated HLA proteins, which bind HLA-specific B cells via the B-cell receptor in a dose-dependent fashion, we report the specific phenotype of HLA-binding B cells and define how they associated with patterns of anti-HLA response in interferon-γ ELISpot. HLA-binding class-switched and IgM+CD27+ memory cells associated strongly with B-dependent interferon-γ production and appeared not suppressible by endogenous Tregs. When the predominant HLA-binding phenotype was naïve B cells, the associated functional ELISpot phenotype was determined by other cells present. High numbers of non-HLA-binding transitional cells associated with B-suppressed interferon-γ production, especially if Tregs were present. However, high frequencies of HLA-binding marginal-zone precursors associated with B-dependent interferon-γ production that appeared suppressible by Tregs. Finally, non-HLA-binding marginal zone precursors may also suppress interferon-γ production, though this association only emerged when Tregs were absent from the ELISpot. Thus, our novel data provide a foundation on which to further define the complexities of interactions between HLA-specific T and B cells and identify new targets for intervention in new therapies for chronic rejection.

Memory B cell and antibody responses to flavivirus infection and vaccination

Flaviviruses are a group of mosquito- or tick-borne single-stranded RNA viruses that can cause a wide range of clinical manifestations in humans and animals, including asymptomatic, flu-like febrile illness, hemorrhagic fever, encephalitis, birth defects, and death. Many of them have no licensed vaccines available for human use. Memory B cell development and induction of neutralizing antibody responses, which are important for the control of flavivirus infection and dissemination, have been used as biomarkers for vaccine efficacy. In this review, we will discuss recent findings on memory B cells and antibody responses from studies in clinical specimen and animal models of flavivirus infection and vaccination with a focus on several clinically important flaviviruses, including dengue, West Nile, yellow fever, and Zika viruses.

Dysregulation of humoral immunity in chronic infection

Chronic viral infections disrupt the ability of the humoral immune response to produce neutralizing antibody or form effective immune memory, preventing viral clearance and making vaccine design difficult. Multiple components of the B-cell response are affected by pathogens that are not cleared from the host. Changes in the microenvironment shift production of B cells to short-lived plasma cells early in the response. Polyclonal B cells are recruited into both the plasma cell and germinal center compartments, inhibiting the formation of a targeted, high-affinity response. Finally, memory B cells shift toward an "atypical" phenotype, which may in turn result in changes to the functional properties of this population. While similar properties of B-cell dysregulation have been described across different types of persistent infections, key questions about the underlying mechanisms remain. This review will discuss the recent advances in this field, as well as highlight the critical questions about the interplay between viral load, microenvironment, the polyclonal response and atypical memory B cells that are yet to be answered. Design of new preventative treatments will rely on identifying the extrinsic and intrinsic modulators that push B cells toward an ineffective response, and thus identify new ways to guide them back onto the best path for clearance of virus and formation of effective immune memory.

Exploiting B Cell Receptor Analyses to Inform on HIV-1 Vaccination Strategies

The human antibody repertoire is generated by the recombination of different gene segments as well as by processes of somatic mutation. Together these mechanisms result in a tremendous diversity of antibodies that are able to combat various pathogens including viruses and bacteria, or malignant cells. In this review, we summarize the opportunities and challenges that are associated with the analyses of the B cell receptor repertoire and the antigen-specific B cell response. We will discuss how recent advances have increased our understanding of the antibody response and how repertoire analyses can be exploited to inform on vaccine strategies, particularly against HIV-1.

Broadly neutralizing human antibodies against dengue virus identified by single B cell transcriptomics

Eliciting broadly neutralizing antibodies (bNAbs) against the four dengue virus serotypes (DENV1-4) that are spreading into new territories is an important goal of vaccine design. To define bNAb targets, we characterized 28 antibodies belonging to expanded and hypermutated clonal families identified by transcriptomic analysis of single plasmablasts from DENV-infected individuals. Among these, we identified J9 and J8, two somatically related bNAbs that potently neutralized DENV1-4. Mutagenesis studies showed that the major recognition determinants of these bNAbs are in E protein domain I, distinct from the only known class of human bNAbs against DENV with a well-defined epitope. B cell repertoire analysis from acute-phase peripheral blood suggested that J9 and J8 followed divergent somatic hypermutation pathways, and that a limited number of mutations was sufficient for neutralizing activity. Our study suggests multiple B cell evolutionary pathways leading to DENV bNAbs targeting a new epitope that can be exploited for vaccine design.

Approaches to Interrogating the Human Memory B-Cell and Memory-Derived Antibody Repertoire Following Dengue Virus Infection

Memory B-cells (MBCs) are potential antibody secreting immune cells that differentiate and mature following host exposure to a pathogen. Following differentiation, MBCs remain in peripheral circulation after recovery and are poised to secrete antigen-specific antibodies if and when they are re-exposed to their cognate antigen. Consequently, MBCs form the founder population and provide one of the first lines of pathogen-specific defense against reinfection. The role MBCs play is complicated for viruses that are heterologous, such as dengue virus (DENV), which exist as antigenically different serotypes. On second infection with a different serotype, MBCs from initial dengue infection rapidly proliferate and secrete antibodies: many of these MBC derived antibodies will be cross-reactive and weakly neutralizing, while some antibodies may recognize epitopes conserved across serotypes and have the capacity to broadly neutralize 2 or more serotypes. It is also possible that a new population of MBCs and antibodies specific for the second virus serotype need to arise for long-term broader immunity to develop. Methods to interrogate and track memory B cell responses are important for evaluating both natural immunity and vaccine response. However, the low abundance of MBCs for any specific pathogen makes it challenging to interrogate frequency, specificity, and breadth for the pathogen of interest. This review discusses current approaches that have been used to interrogate the memory B cell immune response against viral pathogens in general and DENV specifically. Including strengths, limitations, and future directions. Single-cell approaches could help uncover the DENV specific MBC antibody repertoire, and improved methods for isolating DENV specific monoclonal antibodies from human peripheral blood cells would allow for a functional analysis of the anti-DENV repertoire.

Multiplexed FluoroSpot for the Analysis of Dengue Virus- and Zika Virus-Specific and Cross-Reactive Memory B Cells

Dengue virus (DENV) and Zika virus (ZIKV) are mosquito-borne pathogens that have a significant impact on human health. Immune sera, mAbs, and memory B cells (MBCs) isolated from patients infected with one DENV type can be cross-reactive with the other three DENV serotypes and even more distantly related flaviviruses such as ZIKV. Conventional ELISPOTs effectively measure Ab-secreting B cells but because they are limited to the assessment of a single Ag at a time, it is challenging to distinguish serotype-specific and cross-reactive MBCs in the same well. We developed a novel multifunction FluoroSpot assay using fluorescently labeled DENV and ZIKV (FLVs) that measures the cross-reactivity of Abs secreted by single B cells. Conjugation efficiency and recognition of FLVs by virus-specific Abs were confirmed by flow cytometry. Using a panel of DENV immune, ZIKV immune, and naive PBMC, FLVs were able to simultaneously detect DENV serotype-specific, ZIKV-specific, DENV serotype cross-reactive, and DENV/ZIKV cross-reactive Abs secreted by individual MBCs. Our findings indicate that the FLVs are sensitive and specific tools to detect specific and cross-reactive MBCs. These reagents will allow the assessment of the breadth as well as the durability of DENV/ZIKV B cell responses following vaccination or natural infection. This novel approach using FLVs in a FluoroSpot assay can be applied to other diseases such as influenza in which prior immunity with homosubtype- or heterosubtype-specific MBCs may influence subsequent infections.

Detection, phenotyping and quantification of dengue virus-specific B cells using fluorescent probes

Dengue viruses are some of the most important mosquito-borne pathogens worldwide. They cause illness in 50-100 million individuals per year and have a significant global health impact in low- and middle-income countries. It is important to improve our understanding of the humoral response to dengue virus, as antibodies (Abs) are associated with protection from or susceptibility to severe dengue disease. In recent years, significant advances have been made toward identifying Ab targets and evaluating the functional properties of Abs. However, much less is known about the cellular source of Abs, B cells, in part because the reagents to phenotype and characterize antigen-specific B cells have been challenging to develop. Here, we discuss our recent experience with developing and using fluorescent viruses to probe the B cell response to dengue virus. We present the strengths and weaknesses of flow cytometric analysis of antigen-specific B cells and discuss the use of these probes to phenotype and characterize specific B cells during and after natural infection and in ongoing dengue vaccine trials.

Enhanced sensitivity in detection of antiviral antibody responses using biotinylation of foot-and-mouth disease virus (FMDV) capsids

Analysis of the immune response to infection of livestock by foot-and-mouth disease virus (FMDV) is most often reported as the serum antibody response to the virus. While measurement of neutralizing antibody has been sensitive and specific, measurements of the quality of the antibody response are less robust. Determining the immunoglobulin (Ig) isotype of the serum antibody response provides a deeper understanding of the biology of the response and more sensitive methods for these assays will facilitate analyses of B cell mediated immunity. We tested the hypothesis that using the virus as the molecular probe could be achieved by adding tags to the surface of the FMDV capsid, and that would enhance sensitivity in assays for anti-FMDV antibody responses. The use of a FLAG-tagged virus in these assays failed to yield improvement whereas chemically biotinylating the virus capsid resulted in significant enhancement of the signal. Here we describe methods using biotinylated virus for measuring anti-viral antibody in serum and antibody secreting cells (ASCs) in blood that are sensitive and specific. Finally, we describe using the biotinylated virus in flow cytometry where such assays should greatly enhance the analysis of anti-virus antibody producing B cells, allowing the investigator to focus on only the FMDV specific B cells when analyzing the development of the B cell response to either infection or vaccination.

Evaluation and optimization of SYBR Green real-time reverse transcription polymerase chain reaction as a tool for diagnosis of the Flavivirus genus in Brazil

INTRODUCTION

The genus Flavivirus includes several pathogenic species that cause severe illness in humans. Therefore, a rapid and accurate molecular method for diagnosis and surveillance of these viruses would be of great importance. Here, we evaluate and optimize a quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) method for the diagnosis of the Flavivirus genus.

METHODS

We evaluated different commercial kits that use the SYBR Green system for real-time RT-PCR with a primer set that amplifies a fragment of the NS5 flavivirus gene. The specificity and sensitivity of the assay were tested using twelve flaviviruses and ribonucleic acid (RNA) transcribed from the yellow fever virus. Additionally, this assay was evaluated using the sera of 410 patients from different regions of Brazil with acute febrile illness and a negative diagnosis for the dengue virus.

RESULTS

The real-time RT-PCR amplified all flaviviruses tested at a melting temperature of 79.92 to 83.49°C. A detection limit of 100 copies per ml was determined for this assay. Surprisingly, we detected dengue virus in 4.1% (17/410) of samples from patients with febrile illness and a supposedly negative dengue infection diagnosis. The viral load in patients ranged from 2.1×107to 3.4×103copies per ml.

CONCLUSIONS

The real-time RT-PCR method may be very useful for preliminary diagnoses in screenings, outbreaks, and other surveillance studies. Moreover, this assay can be easily applied to monitor viral activity and to measure viral load in pathogenesis studies.

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

B cells reactive with a specific antigen usually occur at a frequency of <0.05% of lymphocytes. For decades researchers have sought methods to isolate and enrich these rare cells for studies of their phenotype and biology. Approaches are inevitably based on the principle that B cells recognize native antigen by virtue of cell surface receptors that are representative in specificity of antibodies that will eventually be secreted by their differentiated daughters. Perhaps the most obvious approach to the problem involves use of fluorochrome-conjugated antigens in conjunction with fluorescence-activated cell sorting (FACS). However, the utility of these methods is limited by cell frequency and the achievable rate of analysis and isolation by electronic sorting. A novel method to enrich rare antigen-specific B cells using magnetic nanoparticles that results in high yield enrichment of antigen-reactive B cells from large starting cell populations is described. This method enables improved monitoring of the phenotype and biology of antigen reactive cells before and following in vivo antigen encounter, such as after immunization or during development of autoimmunity.

Antibody responses to de novo identified citrullinated fibrinogen peptides in rheumatoid arthritis and visualization of the corresponding B cells

BACKGROUND

Antibodies against citrullinated proteins (ACPA) are common in patients with rheumatoid arthritis (RA). ACPA can appear before disease onset and target many self-antigens. Citrullinated fibrin/fibrinogen represents a classical ACPA target antigen, and mass spectrometry of RA synovial fluid reveals elevated citrullinated (cit) fibrinogen (Fib) peptides compared to non-RA controls. We investigated the extent to which these less-studied peptides represent autoantibody targets and sought to visualize the corresponding cit-Fib-reactive B cells in RA patients.

METHODS

An in-house ELISA was established against four cit-Fib α-subunit peptides (cit-Fib α-35; cit-Fib α-216,218; cit-Fib α-263,271 and cit-Fib α-425,426) and serum from patients with established RA (n = 347) and disease controls with psoriatic arthritis (PsA) or ankylosing spondylitis (AS) (n = 236) were analyzed. RA patients were genotyped for HLA-DR alleles, PTPN22 R620W and screened for anti-CCP2 and cit-Fib protein antibodies. The cit-Fib peptides were also used to assemble antigen tetramers to identify cit-Fib-reactive B cells in peripheral blood by flow cytometry.

RESULTS

The frequencies of autoantibodies against different cit-Fib epitopes in RA patients compared to PsA/AS patients were: cit-Fib α-35 (RA 20%, vs PsA/AS 1%); cit-Fib α-216,218 (13% vs 0.5%); cit-Fib α-263,271 (21% vs 0.5%) and cit-Fib α-425,426 (17% vs 1%). The presence of autoantibodies against these peptides was associated with presence of anti-CCP2 and anti-cit-Fib protein antibodies. No association was found between HLA-DR shared epitope and antibodies to the different cit-Fib peptides. However, association was observed between the PTPN22 risk allele and positivity to cit-Fib α-35 and cit-Fib α-263,271. B cells carrying surface Ig reactive to these cit-Fib peptides were found in RA peripheral blood and these tend to be more common in PTPN22 risk allele carriers.

CONCLUSIONS

Our data show that several cit-Fib peptides are targeted by autoantibodies in RA, but not in PsA/AS, implicating that these are not due to arthritis but more specific for RA etiology. The RA-associated anti-cit protein response is broad with many parallel immune responses. The association between cit-Fib autoantibodies and the PTPN22 R620W risk allele supports the hypothesis of altered B cell regulation, such as autoreactive B cells evading tolerance checkpoints.

Dynamics of Dengue Virus (DENV)-Specific B Cells in the Response to DENV Serotype 1 Infections, Using Flow Cytometry With Labeled Virions

BACKGROUND

The development of reagents to identify and characterize antigen-specific B cells has been challenging.

METHODS

We recently developed Alexa Fluor-labeled dengue viruses (AF DENVs) to characterize antigen-specific B cells in the peripheral blood of DENV-immune individuals.

RESULTS

In this study, we used AF DENV serotype 1 (AF DENV-1) together with AF DENV-2 on peripheral blood mononuclear cells (PBMCs) from children in Thailand with acute primary or secondary DENV-1 infections to analyze the phenotypes of antigen-specific B cells that reflected their exposure or clinical diagnosis. DENV serotype-specific and cross-reactive B cells were identified in PBMCs from all subjects. Frequencies of AF DENV(+) class-switched memory B cells (IgD(-)CD27(+) CD19(+) cells) reached up to 8% during acute infection and early convalescence. AF DENV-labeled B cells expressed high levels of CD27 and CD38 during acute infection, characteristic of plasmablasts, and transitioned into memory B cells (CD38(-)CD27(+)) at the early convalescent time point. There was higher activation of memory B cells early during acute secondary infection, suggesting reactivation from a previous DENV infection.

CONCLUSIONS

AF DENVs reveal changes in the phenotype of DENV serotype-specific and cross-reactive B cells during and after natural DENV infection and could be useful in analysis of the response to DENV vaccination.