Variability of the IFN-γ ELISpot assay in the context of proficiency testing and bridging studies

Theoretical and practical considerations for validating antigen-specific B cell ImmunoSpot assays

Owing to their ability to reliably detect even very rare antigen-specific B cells in cellular isolates such as peripheral blood mononuclear cells (PBMC), and doing so robustly in a high throughput-compatible manner, B cell ELISPOT/FluoroSpot (collectively "B cell ImmunoSpot") tests have become increasingly attractive for immune monitoring in regulated settings. Presently, there are no guidelines for the qualification and validation of B cell ImmunoSpot assay results. Here, we propose such guidelines, building on the experience acquired from T cell ImmunoSpot testing in an environment adhering to the requirements of regulatory bodies yet taking the unique features of B cell assays into account. A streamlined protocol is proposed that permits the performance of all tests needed for the formal validation of an antigen-specific B cell ImmunoSpot assay in only three experiments, utilizing 2.2 × 107 PBMC per donor. Subsequently, utilizing only 1-2 × 106 PBMC per sample (obtainable from 1 to 2 mL of blood), a validated multiplexed assay enables accurate quantification of the frequency of antigen-specific memory B cell-derived blasts secreting IgM, IgG, IgA or IgE antibodies. Collectively, such multiplexed B cell ImmunoSpot assays offer immense value for B cell immune monitoring programs due to their ease of implementation, scalability, applicability to essentially any antigenic system, economy of PBMC utilization, and last but not least, the high content information gained.

Decreased variability in the site-specific results during participation in the External Quality Assurance Program Oversight Laboratory (EQAPOL) proficiency program for IFN-gamma enzyme-linked immunospot (IFN-γ ELISpot) assay

The NIAID DAIDS-sponsored External Quality Assurance Program Oversight Laboratory (EQAPOL) manages an interferon-gamma (IFN-γ) enzyme-linked immunospot (ELISpot) external proficiency program. The ELISpot program evaluates the accuracy and variability of results across laboratories. The variability in the program is quantified via the dispersion, which is the ratio of the variance over the mean of the background-corrected spot-forming cells (SFC) replicates obtained under stimulation with different peptide pools (CMV, CEF). This report includes the longitudinal analysis of the ELISpot program cohort composed of 22 laboratories from 2011 to 2022 to assess whether the within-lab variability has improved over time. Random intercept models of the dispersion over time showed a significant decrease in overall dispersion from an average of approximately 1.8 in 2011 to approximately 1.25 in 2022. Out of the 21 sites, 16 sites (4 being statistically significant) had a negative trend for dispersion over time. Our finding of a reduction of overall within-lab variability demonstrates the need for and benefit of proficiency testing programs.

Validation of the performance and suitability of a new class of FBS optimized for use in single-cell functional assays

The use of conventional serum for supplementation of media in cell-based and single-cell functional assays has been a major challenge for assay performance, standardization, optimization, and reproducibility. It has been identified as the leading cause of variability and suboptimal performance in large, international Elispot proficiency panels (Janetzki et al., 2008; Rountree et al., 2016). Extensive pretesting and optimization activities are one approach to overcome these challenges, but they are time-consuming and resource-intensive because suitable lots of serum are difficult to identify and secure in sufficient quantities to provide stability in long-term studies. Advancements in manufacturing methods have resulted in a new class of serum with the potential to solve these challenges. An IFNɣ Elispot study was designed by the External Quality Assurance Program Oversight Laboratory (EQAPOL) at Duke Human Vaccine Institute's (DHVI) Immunology and Virology Quality Assessment Center (IVQAC) to test this new class of serum against their in-house, validated control serum, which is regarded as a global standard in performance for high functionality, recovery, and viability. Commonly used serum-free media were also included in the study. The results of this study compellingly demonstrate that this new class of serum produces high responses and low background reactivity comparable to the included serum standard, with excellent recovery and viability of cells. A protocol for ongoing testing has been developed to continuously validate new batches of this serum with the goal to make available to the field a pretested and validated serum that can be used with confidence in functional cell-based assays.

Comparison of Rapid Cytokine Immunoassays for Functional Immune Phenotyping

Background

Cell-based functional immune-assays may allow for risk stratification of patients with complex, heterogeneous immune disorders such as sepsis. Given the heterogeneity of patient responses and the uncertain immune pathogenesis of sepsis, these assays must first be defined and calibrated in the healthy population.

Objective

Our objective was to compare the internal consistency and practicality of two immune assays that may provide data on surrogate markers of the innate and adaptive immune response. We hypothesized that a rapid turnaround, microfluidic-based immune assay (ELLA) would be comparable to a dual-color, enzyme-linked immunospot (ELISpot) assay in identifying tumor necrosis factor (TNF) and interferon (IFN)γ production following ex vivo whole blood stimulation.

Design

This was a prospective, observational cohort analysis. Whole blood samples from ten healthy, immune-competent volunteers were stimulated for either 4 hours or 18 hours with lipopolysaccharide, anti-CD3/anti-CD28 antibodies, or phorbol 12-myristate 13-acetate with ionomycin to interrogate innate and adaptive immune responses, respectively.

Measurements and Main Results

ELLA analysis produced more precise measurement of TNF and IFNγ concentrations as compared with ELISpot, as well as a four- to five-log₁₀ dynamic range for TNF and IFNγ concentrations, as compared with a two-log₁₀ dynamic range with ELISpot. Unsupervised clustering accurately predicted the ex vivo immune stimulant used for 90% of samples analyzed via ELLA, as compared with 72% of samples analyzed via ELISpot.

Conclusions

We describe, for the first time, a rapid and precise assay for functional interrogation of the innate and adaptive arms of the immune system in healthy volunteers. The advantages of the ELLA microfluidic platform may represent a step forward in generating a point-of-care test with clinical utility, for identifying deranged immune phenotypes in septic patients.

The immunologic dominance of an epitope within a rationally designed poly-epitope vaccine is influenced by multiple factors

INTRODUCTION

CD4⁺ T cells are essential for inducing optimal CD8⁺ T cell and antibody-producing B cell responses and maintaining their long-term immunological memory. Therefore, CD4⁺ T cells are a critical component in HIV vaccine development. Due to enormous viral gene variation and significant human host genetic diversity, HIV vaccines may need to be custom-made for different countries.

METHODS

Previously, we designed a CD4⁺ T cell vaccine based on Chinese HIV isolates and HLA-DR alleles using bioinformatics tools and predicted that 20 epitopes could cover 98.1% of the Chinese population. In vivo testing of the poly-epitope antigen in mice only activated specific T cells for some epitopes. To elucidate the mechanism of the observed differential immunogenicity, we examined poly-epitope antigen processing and presentation using in vitro and in vivo analytical methods.

RESULTS

Enzymatic digestion indicated that all 20 epitopes comprising the poly-epitope antigen could be liberated, but MHC II binding assays showed that neither binding affinity nor dissociation rate was associated with the magnitude of T cell immune responses elicited by each peptide epitope in vaccinated mice. Mass spectrometry analysis of MHC II-bound peptides suggested that the abundance of endogenously processed peptides bound to MHC II molecules was significantly associated with the relative immunodominance of these epitopes.

CONCLUSION

These results provide a new rationale for improving the design and testing of poly-epitope vaccines for HIV and other diseases.

Mastering the Computational Challenges of Elispot Plate Evaluation

Much has been written about Elispot and how to optimally run the assay for a wide variety of applications. But only a limited number of articles exist addressing the analysis step, the plate evaluation. Comparing that fact with the vast amount of analysis advise available for other single cell immune assay, for example, intracellular cytokine staining, the overall impression may be that Elispot evaluation is just simple enough to not require extensive elaboration and guidance. At first thought this appears reasonable because how difficult can it be counting colored spots on a white background. In addition, automated Elispot readers were already introduced more than 20 years ago (Herr et al., J Immunol Methods 203, 141-152, 1997), easing the strenuous load of manual counting and providing means to decrease the subjectivity in Elispot analysis. Just shortly thereafter however, the first report was published about the subjectivity and operator-dependency of plate evaluation even when using automated reader systems (Janetzki et al., J Immunol Methods 291, 175-183, 2004). Later, the plate evaluation was identified as a main factor causing variability in Elispot results, triggering the inclusion of recommendations on handling of artifacts and the audits of plate reading results in the Initial Elispot Harmonization guidelines (Janetzki et al., Cancer Immunol Immunother 57, 303-315, 2008; Britten et al., Cancer Immunol Immunother 57, 289-302, 2008). In follow-up, a large international study with 75 laboratories was conducted to address the current approaches taken to evaluate Elispot plates and to establish consensus guidelines for plate evaluation (Janetzki et al., Nat Protoc 10, 1098-1115, 2015). This article addresses the special challenges of plate evaluation, gives explanations for unusual observation, and provides overall recommendations on how to work through the labyrinth of available algorithms and reader settings to obtain reliable Elispot data.