Multi-Color FLUOROSPOT Counting Using ImmunoSpot(®) Fluoro-X™ Suite

Current and Emerging Assays for Measuring Human T-Cell Responses Against Beta-Cell Antigens in Type 1 Diabetes

Type 1 diabetes (T1D) is an autoimmune disease caused by T-cell mediated destruction of the pancreatic insulin-producing beta cells. Currently, the development of autoantibodies is the only measure of beta-cell autoimmunity used in the clinic. Despite T-cells' well-accepted role in the autoimmune pathogenesis of human T1D, autoimmune T-cell responses against beta cells remain very difficult to measure. An assay capable of measuring beta-cell antigen-specific T-cell responses has been a long-sought goal. Such an assay would facilitate the direct monitoring of T1D-associated T-cell responses facilitating, earlier diagnosis and rapid evaluation of candidate immune therapies in clinical trials. In addition, a simple and robust assay for beta-cell antigen-specific T-cell responses would be a powerful tool for dissecting the autoimmune pathogenesis of human T1D. Here, we review the challenges associated with measuring beta-cell antigen-specific T-cell responses, the current assays which are used to achieve this and, finally, we discuss BASTA, a promising emerging assay for measuring human beta-cell antigen-specific CD4+ T-cell responses.

Reagent Tracker™ Platform Verifies and Provides Audit Trails for the Error-Free Implementation of T-Cell ImmunoSpot® Assays

ELISPOT and FluoroSpot assays, collectively called ImmunoSpot assays, permit to reliable detection of rare antigen-specific T cells in freshly isolated cell material, such as peripheral blood mononuclear cells (PBMC). Establishing their frequency within all PBMC permits to assess the magnitude of antigen-specific T-cell immunity; the simultaneous measurement of their cytokine signatures reveals these T-cells' lineage and effector functions, that is, the quality of T-cell-mediated immunity. Because of their unparalleled sensitivity, ease of implementation, robustness, and frugality in PBMC utilization, T-cell ImmunoSpot assays are increasingly becoming part of the standard immune monitoring repertoire. For regulated workflows, stringent audit trails of the data generated are a requirement. While this has been fully accomplished for the analysis of T-cell ImmunoSpot assay results, such are missing for the wet laboratory implementation of the actual test performed. Here we introduce a solution for enhancing and verifying the error-free implementation of T-cell ImmunoSpot assays.

Artificial Intelligence-Based Counting Algorithm Enables Accurate and Detailed Analysis of the Broad Spectrum of Spot Morphologies Observed in Antigen-Specific B-Cell ELISPOT and FluoroSpot Assays

Antigen-specific B-cell ELISPOT and multicolor FluoroSpot assays, in which the membrane-bound antigen itself serves as the capture reagent for the antibodies that B cells secrete, inherently result in a broad range of spot sizes and intensities. The diversity of secretory footprint morphologies reflects the polyclonal nature of the antigen-specific B cell repertoire, with individual antibody-secreting B cells in the test sample differing in their affinity for the antigen, fine epitope specificity, and activation/secretion kinetics. To account for these heterogeneous spot morphologies, and to eliminate the need for setting up subjective counting parameters well-by-well, CTL introduces here its cutting-edge deep learning-based IntelliCount™ algorithm within the ImmunoSpot® Studio Software Suite, which integrates CTL's proprietary deep neural network. Here, we report detailed analyses of spots with a broad range of morphologies that were challenging to analyze using standard parameter-based counting approaches. IntelliCount™, especially in conjunction with high dynamic range (HDR) imaging, permits the extraction of accurate, high-content information of such spots, as required for assessing the affinity distribution of an antigen-specific memory B-cell repertoire ex vivo. IntelliCount™ also extends the range in which the number of antibody-secreting B cells plated and spots detected follow a linear function; that is, in which the frequencies of antigen-specific B cells can be accurately established. Introducing high-content analysis of secretory footprints in B-cell ELISPOT/FluoroSpot assays, therefore, fundamentally enhances the depth in which an antigen-specific B-cell repertoire can be studied using freshly isolated or cryopreserved primary cell material, such as peripheral blood mononuclear cells.

Current approaches to evaluate the function of cytotoxic T-cells in non-human primates

Cytotoxic T-lymphocytes (CTL) are a subset of T-cells that play a critical role in protecting against intracellular infections and cancer, and have the ability to identify and kill infected or transformed cells expressing non-self peptides associated with major histocompatibility (MHC) Class I molecules. Conversely, aberrant CTL activity can contribute to immune-related pathology under conditions of overwhelming infection or autoimmunity. Disease-modifying therapeutics can have unintended effects on CTL, and a growing number of therapeutics are intended to either suppress or enhance CTL or their functions. The susceptibility of CTL to unintended effects from common therapeutic modalities underscores the need for a better understanding of the impact that such therapies have on CTL function and the associated safety implications. While there are reliable ways of quantifying CTL, notably via flow cytometric analysis of specific CTL markers, it has been a greater challenge to implement fit-for-purpose methods measuring CTL function in the context of safety studies of therapeutics. This review focuses on methods for measuring CTL responses in the context of drug safety and pharmacology testing, with the goals of informing the reader about current approaches, evaluating their pros and cons, and providing perspectives on the utility of these approaches for safety evaluation.

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.

Unbiased, High-Throughput Identification of T Cell Epitopes by ELISPOT

Recent systematic immune monitoring efforts suggest that, in humans, epitope recognition by T cells is far more complex than has been assumed based on minimalistic murine models. The increased complexity is due to the higher number of HLA loci in humans, the typical heterozygosity for these loci in the outbred population, and the high number of peptides that each HLA restriction element can bind with an affinity that suffices for antigen presentation. The sizable array of potential epitopes on any given antigen is due to each individual's unique HLA allele makeup. Of this individualized potential epitope space, chance events occurring in the course of the T cell response determine which epitopes induce dominant T cell expansions. Establishing the actually-engaged T cell repertoire in each human subject, including the individualized peptides targeted, therefore requires the systematic testing of all peptides that constitute the potential epitope space in that person. The goal of comprehensive, high-throughput epitope mapping can be readily established by the methods described in this chapter.

Affinity Tag Coating Enables Reliable Detection of Antigen-Specific B Cells in Immunospot Assays

Assessment of humoral immunity to SARS-CoV-2 and other infectious agents is typically restricted to detecting antigen-specific antibodies in the serum. Rarely does immune monitoring entail assessment of the memory B-cell compartment itself, although it is these cells that engage in secondary antibody responses capable of mediating immune protection when pre-existing antibodies fail to prevent re-infection. There are few techniques that are capable of detecting rare antigen-specific B cells while also providing information regarding their relative abundance, class/subclass usage and functional affinity. In theory, the ELISPOT/FluoroSpot (collectively ImmunoSpot) assay platform is ideally suited for antigen-specific B-cell assessments since it provides this information at single-cell resolution for individual antibody-secreting cells (ASC). Here, we tested the hypothesis that antigen-coating efficiency could be universally improved across a diverse set of viral antigens if the standard direct (non-specific, low affinity) antigen absorption to the membrane was substituted by high-affinity capture. Specifically, we report an enhancement in assay sensitivity and a reduction in required protein concentrations through the capture of recombinant proteins via their encoded hexahistidine (6XHis) affinity tag. Affinity tag antigen coating enabled detection of SARS-CoV-2 Spike receptor binding domain (RBD)-reactive ASC, and also significantly improved assay performance using additional control antigens. Collectively, establishment of a universal antigen-coating approach streamlines characterization of the memory B-cell compartment after SARS-CoV-2 infection or COVID-19 vaccinations, and facilitates high-throughput immune-monitoring efforts of large donor cohorts in general.

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.

Detecting all Immunoglobulin Classes and Subclasses in a Multiplex 7 Color ImmunoSpot® Assay

Antibody molecules in peripheral blood have a relatively short half-life of roughly 20 days, and therefore their persistence in the serum depends on continuous replenishment by plasma cells. Serum antibody titers are thus indirect and unreliable indicators of immunological memory. In contrast, memory B cells persist in peripheral blood for decades, and enumerating these cells provides direct evidence of having developed an immune response to a given antigen. ELISPOT is an ideal research tool for enumerating antigen-specific memory B cells. Traditionally, B cell ELISPOT assays have been performed for detecting a single class of immunoglobulin (Ig), using a single colorimetric substrate. For comprehensive monitoring of B cell memory, however, all immunoglobulin classes and subclasses need to be assessed. Thus, seven single color assays would need to be performed to measure the numbers of antigen-specific B cells producing IgM, IgA, IgE, IgG₁, IgG₂, IgG₃, and IgG₄. We report here the development of a multiplex seven color B cell ImmunoSpot^® assay in which the number of antigen-specific B cells can be established simultaneously for all major antibody classes and subclasses, requiring the PBMC, antigen, and labor corresponding to a single color assay.

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.

Four Color ImmunoSpot® Assays for Identification of Effector T-Cell Lineages

Single color IFN-γ ELISPOT assays have evolved as a highly sensitive T cell immune monitoring platform. By detecting individual T cells that secrete IFN-γ in response to antigen exposure, these assays permit the measurement of the frequency of antigen-specific T cells among white blood cells. These assays therefore are well suited to assess clonal expansions, that is, whether a (Th1) T cell response has been induced to an antigen in a test subject. Single color IFN-γ ELISPOT assays are not suited, however, to provide information on the Th2/Th17 quality of the T cell response, nor do they provide insights into the differentiation state of CD8 cells. Recently it has been established that co-expression profiles of IL-2, TNF-α, and granzyme B along with IFN-γ permit to identify CD8 cell subpopulations. Naïve CD8 cells, central CD8 memory cells, CD8 terminal effector cells, polyfunctional CD8 cells, stem-cell like CD8 memory cells, dysfunctional- and senescent CD8 cells all differ in the extent they produce these molecules upon antigen re-encounter. We therefore have developed, and introduce here, a four color T cell ELISPOT assay in which the co-expression levels of IFN-γ, IL-2, TNF-α, and granzyme B can be established for individual antigen-specific CD8 cells, thereby identifying the activation/differentiation state of these cells.