An antigen-specific, four-color, B-cell FluoroSpot assay utilizing tagged antigens for detection

Antigen-specificity measurements are the key to understanding T cell responses

Antigen-specific T cells play a central role in the adaptive immune response and come in a wide range of phenotypes. T cell receptors (TCRs) mediate the antigen-specificities found in T cells. Importantly, high-throughput TCR sequencing provides a fingerprint which allows tracking of specific T cells and their clonal expansion in response to particular antigens. As a result, many studies have leveraged TCR sequencing in an attempt to elucidate the role of antigen-specific T cells in various contexts. Here, we discuss the published approaches to studying antigen-specific T cells and their specific TCR repertoire. Further, we discuss how these methods have been applied to study the TCR repertoire in various diseases in order to characterize the antigen-specific T cells involved in the immune control of disease.

A FluoroSpot B assay for the detection of IgA and IgG SARS-CoV-2 spike-specific memory B cells: Optimization and qualification for use in COVID-19 vaccine trials

BACKGROUND

The generation of antigen-specific memory B cells is crucial to the long-term effectiveness of vaccines. When the protective antibodies circulating in the blood wane, memory B cells (MBC) can be rapidly reactivated and differentiated into antibody-secreting cells during a new infection. Such MBC responses are considered to be key in providing long-term protection after infection or vaccination. Here, we describe the optimization and qualification of a FluoroSpot assay to measure MBCs directed against the SARS-CoV-2 spike protein in the peripheral blood, for use in COVID-19 vaccine trials.

METHODS

We developed a FluoroSpot assay enabling simultaneous enumeration of B cells secreting IgA or IgG spike-specific antibodies after polyclonal stimulation of peripheral blood mononuclear cells (PBMCs) with interleukin-2 and the toll-like receptor agonist R848 for 5 days. The antigen coating was optimized using a capture antibody directed against the spike subunit-2 glycoprotein of SARS-CoV-2 to immobilize recombinant trimeric spike protein onto the membrane.

RESULTS

Compared to a direct spike protein coating, the addition of a capture antibody increased the number and the quality of detected spots for both spike-specific IgA and IgG secreting cells in PBMCs from COVID-19 convalescents. The qualification showed good sensitivity of the dual-color IgA-IgG FluoroSpot assay, with lower limits of quantitation of 18 background-subtracted (BS) antibody-secreting cells (ASCs)/well for spike-specific IgA and IgG responses. Linearity was demonstrated at values ranging from 18 to 73 and from 18 to 607 BS ASCs/well for spike-specific IgA and IgG, respectively, as was precision, with intermediate precision (percentage geometric coefficients of variation) of 12% and 26% for the proportion of spike-specific IgA and IgG MBCs (ratio specific/total IgA or Ig). The assay was specific, since no spike-specific MBCs were detected in PBMCs from pre-pandemic samples; the results were below the limit of detection of 17 BS ASCs/well.

CONCLUSIONS

These results show that the dual-color IgA-IgG FluoroSpot provides a sensitive, specific, linear, and precise tool to detect spike-specific MBC responses. This MBC FluoroSpot assay is a method of choice for monitoring spike-specific IgA and IgG MBC responses induced by COVID-19 candidate vaccines in clinical trials.

Release Assays and Potency Assays for CAR T-Cell Interventions

Chimeric antigen receptor (CAR) T-cells are considered "living drugs" and offer a compelling alternative to conventional anticancer therapies. Briefly, T-cells are redirected, using gene engineering technology, toward a specific cancer cell surface target antigen via a synthetic chimeric antigen receptor (CAR) protein. CARs have a modular design comprising four main structures: an antigen-binding domain, a hinge region, a transmembrane domain, and one or more intracellular signaling domains for T-cell activation. A major challenge in the CAR T-cell manufacturing field is balancing product quality with scalability and cost-effectiveness, especially when transitioning from an academic clinical trial into a marketed product, to be implemented across many collection, manufacturing, and treatment sites. Achieving product consistency while circumnavigating the intrinsic variability associated with autologous products is an additional barrier. To overcome these limitations, a robust understanding of the product and its biological actions is crucial to establish a target product profile with a defined list of critical quality attributes to be assessed for each batch prior to product certification. Additional challenges arise as the field progresses, such as new safety considerations associated with the use of allogenic T-cells and genome editing tools. In this chapter, we will discuss the release and potency assays required for CAR T-cell manufacturing, covering their relevance, current challenges, and future perspectives.

Cellular assays to evaluate B-cell function

Inborn errors of immunity (IEI) that present with recurrent infections are largely due to antibody (Ab) deficiencies. Therefore, assessment of the B-cell and Ab compartment is a major part of immunologic evaluation. Here we provide an overview about cellular assays used to study B-cell function and focus on lymphocyte proliferation assay (LPA), opsonophagocytic assay (OPA), and the Enzyme-linked Immunosorbent Spot Assay (ELISPOT) including clinical applications and limitations of these techniques. LPAs assess ex-vivo cell proliferation in response to various stimuli. Clinically available LPAs utilize peripheral blood mononuclear cells and mostly assess T-cell proliferation with pokeweed mitogen considered the most B-cell specific stimulus. In the research setting, isolating B cells or using more B-cell specific stimuli such as CD40L with IL-4/IL-21 or the TLR9 ligand CpG can more specifically capture the proliferative ability of B cells. OPAs are functional in-vitro killing assays used to evaluate the ability of IgG Ab to induce phagocytosis applied when assessing the potency of vaccine candidates or along with avidity assays to evaluate the quality of secreted IgG. The B-cell ELISPOT assesses Ab production at a cellular level and can characterize the Ab response of particular B-cell subtypes. It can be used in patients on IgG therapy by capturing specific Abs produced by individual B cells, which is not affected by exogenous IgG from plasma donors, and when assessing the vaccine response in patients on immunomodulatory drugs that can affect memory B-cell function. Emerging approaches that are only available in research settings are also briefly introduced.

Analysis of allelic cross-reactivity of monoclonal IgG antibodies by a multiplexed reverse FluoroSpot assay

The issue of antibody cross-reactivity is of central importance in immunology, and not least in protective immunity to Plasmodium falciparum malaria, where key antigens show substantial allelic variation (polymorphism). However, serological analysis often does not allow the distinction between true cross-reactivity (one antibody recognizing multiple antigen variants) and apparent cross-reactivity (presence of multiple variant-specific antibodies), as it requires analysis at the single B-cell/monoclonal antibody level. ELISpot is an assay that enables that, and a recently developed multiplexed variant of ELISpot (FluoroSpot) facilitates simultaneous assessment of B-cell/antibody reactivity to several different antigens. In this study, we present a further enhancement of this assay that makes direct analysis of monoclonal antibody-level cross-reactivity with allelic variants feasible. Using VAR2CSA-type PfEMP1-a notoriously polymorphic antigen involved in the pathogenesis of placental malaria-as a model, we demonstrate the robustness of the assay and its applicability to analysis of true cross-reactivity of monoclonal VAR2CSA-specific antibodies in naturally exposed individuals. The assay is adaptable to the analysis of other polymorphic antigens, rendering it a powerful tool in studies of immunity to malaria and many other diseases.

Plasmodium falciparum-Specific Memory B-Cell and Antibody Responses Are Associated With Immunity in Children Living in an Endemic Area of Kenya

Identifying the mechanism of naturally acquired immunity against Plasmodium falciparum malaria could contribute to the design of effective malaria vaccines. Using a recently developed multiplexed FluoroSpot assay, we assessed cross-sectional pre-existing memory B-cells (MBCs) and antibody responses against six well known P. falciparum antigens (MSP-119, MSP-2 (3D7), MSP-2 (FC27), MSP-3, AMA-1 and CSP) and measured their associations with previous infections and time to clinical malaria in the ensuing malaria season in Kenyan children. These children were under active weekly surveillance for malaria as part of a long-term longitudinal malaria immunology cohort study, where they are recruited from birth. After performing Cox regression analysis, we found that children with a breadth of three or more antigen-specific MBC or antibody responses at the baseline had a reduced risk for malaria in the ensuing P. falciparum transmission season. Specifically, MBC responses against AMA-1, MSP-2 (3D7) and MSP-3, as well as antibody responses to MSP-2 (3D7) and MSP-3 were prospectively associated with a reduced risk for malaria. The magnitude or breadth of MBC responses were however not correlated with the cumulative number of malaria episodes since birth. We conclude that increased breadth for merozoite antigen-specific MBC and antibody responses is associated with protection against malaria.

Detection and Enumeration of Cytokine-Secreting Cells by FluoroSpot

The FluoroSpot assay is a development of the highly sensitive enzyme-linked immunospot (ELISpot) assay which enables functional measurement of immunity at the single-cell level. Both assays are performed in a 96-well format and measures the frequency of analyte-secreting cells, in ELISpot usually limited to one analyte per well due to the use of enzymes and precipitating substrates for detection. FluoroSpot, performed in a similar way as ELISpot, overcomes this limitation by detecting each analyte with an assigned fluorophore instead of an enzyme. By using readers equipped with fluorophore-specific filters, cells producing single or multiple cytokines can be identified simultaneously in the same well. This greatly facilitates the analysis of functionally distinct subpopulations in heterogenous cell samples, for example, the frequency of polyfunctional T cells, suggested to be of importance in various disease states. FluoroSpot maintains the simplicity and sensitivity of the ELISpot while taking the assay a step further towards a multiplex analysis and an in-depth understanding of the quality of an immune response. We describe here a 96-well plate method to analyze cells that have secreted up to four different cytokines simultaneously (Four-color Fluorospot).

Miniaturized single-cell technologies for monoclonal antibody discovery

Antibodies (Abs) are among the most important class of biologicals, showcasing a high therapeutic and diagnostic value. In the global therapeutic Ab market, fully-human monoclonal Abs (FH-mAbs) are flourishing thanks to their low immunogenicity and high specificity. The rapidly emerging field of single-cell technologies has paved the way to efficiently discover mAbs by facilitating a fast screening of the antigen (Ag)-specificity and functionality of Abs expressed by B cells. This review summarizes the principles and challenges of the four key concepts to discover mAbs using these technologies, being confinement of single cells using either droplet microfluidics or microstructure arrays, identification of the cells of interest, retrieval of those cells and single-cell sequence determination required for mAb production. This review reveals the enormous potential for mix-and-matching of the above-mentioned strategies, which is illustrated by the plethora of established, highly integrated devices. Lastly, an outlook is given on the many opportunities and challenges that still lie ahead to fully exploit miniaturized single-cell technologies for mAb discovery.

Managing the Impact of Immunogenicity in an Era of Immunotherapy: From Bench to Bedside

Biotherapeutics have revolutionized our ability to treat life-threatening diseases. Despite clinical success, the use of biotherapeutics has sometimes been limited by the immune response mounted against them in the form of anti-drug antibodies (ADAs). The multifactorial nature of immunogenicity has prevented a standardized approach for assessing this and each of the assessment methods developed so far does not exhibit high enough reliability to be used alone, due to limited predictiveness. This prompted the Roche Pharma Research and Early Development (pRED) Immunogenicity Working Group to establish an internal preclinical immunogenicity toolbox of in vitro/in vivo approaches and accompanying guidelines for a harmonized assessment and management of immunogenicity in early development. In this article, the complex factors influencing immunogenicity and their associated clinical ramifications are discussed to highlight the importance of an end-to-end approach conducted from lead optimization to clinical candidate selection. We then examine the impact of the resulting lead candidate categorization on the design and implementation of a multi-tiered ADA/immunogenicity assay strategy prior to phase I (entry into human) through early clinical development. Ultimately, the Immunogenicity Toolbox ensures that Roche pRED teams are equipped to address immunogenicity in a standardized manner, paving the way for lifesaving products with improved safety and efficacy.

Measuring single-cell protein secretion in immunology: Technologies, advances, and applications

The dynamics, nature, strength, and ultimately protective capabilities of an active immune response are determined by the extracellular constitution and concentration of various soluble factors. Generated effector cells secrete such mediators, including antibodies, chemo‐ and cytokines to achieve functionality. These secreted factors organize the individual immune cells into functional tissues, initiate, orchestrate, and regulate the immune response. Therefore, a single‐cell resolved analysis of protein secretion is a valuable tool for studying the heterogeneity and functionality of immune cells. This review aims to provide a comparative overview of various methods to characterize immune reactions by measuring single‐cell protein secretion. Spot‐based and cytometry‐based assays, such as ELISpot and flow cytometry, respectively, are well‐established methods applied in basic research and clinical settings. Emerging novel technologies, such as microfluidic platforms, offer new ways to measure and exploit protein secretion in immune reactions. Further technological advances will allow the deciphering of protein secretion in immunological responses with unprecedented detail, linking secretion to functionality. Here, we summarize the development and recent advances of tools that allow the analysis of protein secretion at the single‐cell level, and discuss and contrast their applications within immunology.

Memory B-Cell Responses Against Merozoite Antigens After Acute Plasmodium falciparum Malaria, Assessed Over One Year Using a Novel Multiplexed FluoroSpot Assay

Memory B cells (MBCs) are believed to be important for the maintenance of immunity to malaria, and these cells need to be explored in the context of different parasite antigens and their breadth and kinetics after natural infections. However, frequencies of antigen-specific MBCs are low in peripheral blood, limiting the number of antigens that can be studied, especially when small blood volumes are available. Here, we developed a multiplexed reversed B-cell FluoroSpot assay capable of simultaneously detecting MBCs specific for the four Plasmodium falciparum blood-stage antigens, MSP-1₁₉, MSP-2, MSP-3 and AMA-1. We used the assay to study the kinetics of the MBC response after an acute episode of malaria and up to one year following treatment in travelers returning to Sweden from sub-Saharan Africa. We show that the FluoroSpot assay can detect MBCs to all four merozoite antigens in the same well, and that the breadth and kinetics varied between individuals. We further found that individuals experiencing a primary infection could mount and maintain parasite-specific MBCs to a similar extent as previously exposed adults, already after a single infection. We conclude that the multiplexed B-cell FluoroSpot is a powerful tool for assessing antigen-specific MBC responses to several antigens simultaneously, and that the kinetics of MBC responses against merozoite surface antigens differ over the course of one year. These findings contribute to the understanding of acquisition and maintenance of immune responses to malaria.

SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery

Since the publication of the Society for Immunotherapy of Cancer's (SITC) original cancer immunotherapy biomarkers resource document, there have been remarkable breakthroughs in cancer immunotherapy, in particular the development and approval of immune checkpoint inhibitors, engineered cellular therapies, and tumor vaccines to unleash antitumor immune activity. The most notable feature of these breakthroughs is the achievement of durable clinical responses in some patients, enabling long-term survival. These durable responses have been noted in tumor types that were not previously considered immunotherapy-sensitive, suggesting that all patients with cancer may have the potential to benefit from immunotherapy. However, a persistent challenge in the field is the fact that only a minority of patients respond to immunotherapy, especially those therapies that rely on endogenous immune activation such as checkpoint inhibitors and vaccination due to the complex and heterogeneous immune escape mechanisms which can develop in each patient. Therefore, the development of robust biomarkers for each immunotherapy strategy, enabling rational patient selection and the design of precise combination therapies, is key for the continued success and improvement of immunotherapy. In this document, we summarize and update established biomarkers, guidelines, and regulatory considerations for clinical immune biomarker development, discuss well-known and novel technologies for biomarker discovery and validation, and provide tools and resources that can be used by the biomarker research community to facilitate the continued development of immuno-oncology and aid in the goal of durable responses in all patients.

Multiplex analysis of antigen-specific memory B cells in humans using reversed B-cell FluoroSpot

Analysis of B-cell specificities at the single cell level provides important information on how the B-cell compartment responds when challenged by infection or vaccination. We recently developed a reversed B-cell FluoroSpot assay and showed that it could be used to detect B cells specific for different antigens simultaneously in a mouse model. The aim of this study was to further develop the method to detect and quantify antigen-specific memory B cells (MBCs) in humans where circulating antigen-specific cells are less frequent. We show that MBCs specific for three antigens, tetanus toxoid, hepatitis B surface antigen and cytomegalovirus pp65, could be detected simultaneously in one well. In addition to enumerating antigen-specific MBCs, we also assessed the spot volume to estimate the intensity of the response in individual cells and found this to be a new and sensitive approach to study MBC responses after vaccination. This unique B-cell FluoroSpot approach provides a simple and sensitive multiplex analysis of MBCs and can be adapted to most antigens and host species.

Detection of Cross-Reactive B Cells Using the FluoroSpot Assay

B cell ELISpot enables a sensitive analysis of antigen-specific B cells at the single cell level but is limited to the analysis of reactivity with a single antigen. By reversing the B cell ELISpot and using anti-IgG capture antibodies instead of coated antigen, the specificity of antibodies secreted by B cells can be defined using soluble tagged antigen for detection. When combining this approach with fluorescent detection of the antigen in a B cell FluoroSpot assay, reactivity with multiple antigens can be defined. In the protocol described herein, splenocytes from a mouse immunized with an antigen were analyzed for their reactivity with the antigen used for immunization and for cross-reactivity with a different but structurally related antigen. Using this assay, we found that at least 15% of the B cells displayed detectable cross-reactivity. B cell FluoroSpot utilizing multiple antigens provides a tool for a single-cell analysis of B cell cross-reactivity, for example, with variable and polymorphic antigens found in various pathogens; or analysis of other types of immune responses where analysis of cross-reactivity is of interest. It is also possible to simultaneously analyze B cell reactivity to completely different antigens.

A multicolour HLA-specific B-cell FluoroSpot assay to functionally track circulating HLA-specific memory B cells

Emerging evidence suggests that donor-reactive memory B cells (mBC) play a key role inducing antibody-mediated rejection (ABMR) after solid organ transplantation and show a broader antigen repertoire than plasma cells thus, being potentially present even in absence of donor-specific antibodies. Therefore, the development of novel immune assays capable of quantifying circulating donor-reactive mBC in organ transplantation is highly warranted. We developed a novel HLA-specific B-cell FluoroSpot assay capable of enumerating multiple HLA-specific Antibody Secreting Cells (ASC) originated from circulating mBC after in-vitro polyclonal activation. We performed a thorough characterization of distinct selective in-vitro mBC activation methods based on either the TLR7,8 agonist R848 plus Interleukin-2 or an anti-CD40 agonist monoclonal antibody, assessed optimal activation culture conditions, cell sources, activation time-frame as well as the advantage of measuring HLA-specific IgG-ASC as compared to HLA-IgG Ab detected in supernatants of in-vitro stimulated B-cell to characterize anti-HLA alloreactivity. Notably, using fluorescently-labeled multimerized HLA molecules as detection matrix, we show the ability of this assay to precisely quantify multiple anti-HLA mBC specificities. In conclusion, evaluating circulating donor-reactive mBC using new technology may provide novel insight of the pathogenesis of humoral rejection and may help identifying transplant recipients at high risk of allograft rejection.

Multiplex ImmunoSpot® Assays for the Study of Functional B Cell Subpopulations

B cells mediate humoral immunity by producing antibody molecules, but they also participate in innate and acquired immune functions via the secretion of effector molecules such as cytokines, chemokines, and granzyme. B cell subpopulations releasing such effector molecules have been implicated in immunobiology and a number of diseases.Unlike antigen-specific T cells that can be identified by multimer staining, and then counter-stained to define T cell subpopulations, antigen-specific B cells cannot be detected by flow cytometry. Staining antigen-specific B cells with labeled antigen, in large, has been unsuccessful. Instead, antigen-specific B cells can be and are commonly studied by ELISPOT. In the ELISPOT approach, the B cell is identified via the antibody that it secretes being captured on a membrane by the antigen itself. Should it be feasible to measure simultaneously antibody production and the secretion of other secretory B cell products, it would then be possible to identify B cell subpopulations that co-express effector molecules. Here we introduce multiplex ELISPOT assays in which measurements of antibody secretion are combined with the detection of Granzyme B, IL-6, IL-10, IFN-γ, and TNF-α. Such multiplex assays will help define effector B cell subpopulations, as well as the understanding of their role in health and disease.

B Cells and B Cell Blasts Withstand Cryopreservation While Retaining Their Functionality for Producing Antibody

In individuals who have once developed humoral immunity to an infectious/foreign antigen, the antibodies present in their body can mediate instant protection when the antigen re-enters. Such antigen-specific antibodies can be readily detected in the serum. Long term humoral immunity is, however, also critically dependent on the ability of memory B cells to engage in a secondary antibody response upon re-exposure to the antigen. Antibody molecules in the body are short lived, having a half-life of weeks, while memory B cells have a life span of decades. Therefore, the presence of serum antibodies is not always a reliable indicator of B cell memory and comprehensive monitoring of humoral immunity requires that both serum antibodies and memory B cells be assessed. The prevailing view is that resting memory B cells and B cell blasts in peripheral blood mononuclear cells (PBMC) cannot be cryopreserved without losing their antibody secreting function, and regulated high throughput immune monitoring of B cell immunity is therefore confined to-and largely limited by-the need to test freshly isolated PBMC. Using optimized protocols for freezing and thawing of PBMC, and four color ImmunoSpot® analysis for the simultaneous detection of all immunoglobulin classes/subclasses we show here that both resting memory B cells and B cell blasts retain their ability to secrete antibody after thawing, and thus demonstrate the feasibility of B cell immune monitoring using cryopreserved PBMC.