Do more with Less: Improving High Parameter Cytometry Through Overnight Staining

A Workflow to Achieve Saturation of Fluorophore-Conjugated Monoclonal Antibodies for Robust Comparison of Biomarker Expression

Antibody titration is an important step in every cytometric workflow, with the goal being to determine antibody concentrations that ensure highly reproducible results. When aiming to compare antigen expression between samples using mean or median fluorescence intensity (MFI), reagents should be used at a saturating concentration so that unavoidable variations in staining conditions do not affect the fluorescence signal. The recommended concentrations of commercially available fluorophore-labeled monoclonal antibodies (mAbs) may not achieve plateau staining, and their saturating concentration may be too high to be experimentally useful. To address these common concerns, we present a novel method to achieve saturation of fluorophore-conjugated mAbs, by 'spiking-in' unlabelled antibody of the same clone. Here, we demonstrate the application of this workflow to human anti-CD3 (clone OKT3, mouse IgG2a) and anti-TCRαβ (clone IP26, mouse IgG1), two mAbs that do not achieve saturation at 2-fold above their commercially recommended concentrations. First, the saturating concentration of unlabelled (purified) OKT3 and IP26 was determined by detection with a fluorophore-labeled anti-mouse IgG (H + L) secondary antibody. Titration curves of unlabelled and labeled mAbs were compared for each clone to determine whether labeling had resulted in any loss in binding activity. Unlabelled antibody was then 'spiked' into the labeled antibody at varying ratios, and those that achieved saturation while maintaining an adequate fluorescence signal were identified. We demonstrate that antibody saturation can be achieved with an optimized mixture of labeled and unlabelled antibody, while maintaining a clear signal from the fluorophore. While this workflow has only been applied to OKT3 and IP26, it has potential applicability for any antibody clone for which both labeled and unlabelled preparations are available. This method has significance for robust comparison of biomarker expression when fluorophore labeled reagents do not reach saturation under standard staining conditions.

Diving Deep: Profiling Exhausted T Cells in the Tumor Microenvironment Using Spectral Flow Cytometry

Fresh tumor cytometric profiling is essential for interrogating the tumor microenvironment (TME) and identifying potential therapeutic targets to enhance antitumor immunity. Challenges arise due to the limited number of cells in clinical biopsies and inter-patient variability. To maximize data derived from a single biopsy, spectral cytometry was leveraged, enabling extensive profiling with significantly fewer cells than mass cytometry. Furthermore, the utilization of multiple markers within one tube can potentially reveal novel and extensive dynamic immune characteristics in cancer, thereby aiding treatment strategies and enhancing patient outcomes. Here, we introduce a customized 39-color panel for in-depth phenotyping of exhausted T cells (TEX), which are dysfunctional T-cell subsets that arise during cancer progression. This study aims to investigate profiles of CD4 T, CD8 T, regulatory T (Treg), and γδ2 cells while exploring the heterogeneity of CD8+ TEX subsets. Given the rarity and heterogeneity of tumor biopsies, we evaluated the effects of tissue dissociation enzymes on staining protocols using cryopreserved peripheral blood mononuclear cells (PBMCs). This is vital for the development of high-dimensional cytometry panels, especially since collagenases may cleave markers in dissociated tumor cells (DTCs). Our protocol also optimizes intracellular marker staining, enhancing insights into TEX function and biology, ultimately identifying potential therapeutic targets.

Maternal obesity associates with altered humoral immunity in blood and colostrum

Maternal obesity is a condition with increasing prevalence worldwide, that correlates with negative infant outcomes. Here we performed an observational cross-sectional study, where peripheral blood and colostrum samples from 37 mothers with BMI between 18.5-25 or > 30 kg/m2 (21 and 16 mothers, respectively) were collected 24-48 h postpartum. B lymphocyte subpopulations were investigated using flow cytometry. IgG, IgA, and IgM concentrations, and antibody production from colostrum-resident B cells were quantified. Overall, naïve B lymphocytes were the most abundant subtype in peripheral blood, while CD27-IgD- double-negative B cells were the most frequent in colostrum. The colostrum from mothers with BMI > 30 kg/m2 contained significantly more IgG-secreting colostrum-resident B cells, more total IgG, and less total IgA. Mothers with BMI > 30 kg/m2 who had been vaccinated with the Pfizer BioNTech bivalent vaccine during the third trimester of pregnancy (n = 8) did not show higher IgA or IgG antibody responses against SARS-CoV-2 RBD in either tissue types compared to unvaccinated mothers, contrasting with mother of BMI between 18.5-25 kg/m2 (n = 7). This is the first characterization of B lymphocyte subpopulations and antibodies in the colostrum of mothers with obesity. This work uncovers maternal obesity as a possible modifier of humoral immune components in colostrum.

Directed disruption of IL2 aggregation and receptor binding sites produces designer biologics with enhanced specificity and improved production capacity

The pleotropic nature of interleukin-2 (IL2) has allowed it to be used as both a pro-inflammatory and anti-inflammatory therapeutic agent, through promotion of regulatory T cell (Treg) responses via the trimeric IL2RABG receptor or promotion of CD8 T cell responses via the dimeric IL2RBG receptor, respectively. However, the utility of IL2 as a treatment is limited by this same pleiotropy, and protein engineering to bias specificity towards either Treg or CD8 T cell lineage often requires a trade-off in protein production or total bioactivity. Here we use SolubiS and dTANGO, computational algorithm-based methods, to predict mutations within the IL2 structure to improve protein production yield in muteins with altered cellular selectivity, to generate combined muteins with elevated therapeutic potential. The design and testing process identified the V106R (murine) / V91R (human) mutation as a Treg-enhancing mutein, creating a cation repulsion to inhibit primary binding to IL2RB, with a post-IL2RA confirmational shift enabling secondary IL2RB binding, and hence allowing the trimeric receptor complex to form. In human IL2, additional N90R T131R aggregation-protecting mutations could improve protein yield of the V91R mutation. The approach also generated novel CD8 T cell-promoting mutations. Y59K created a cation-cation repulsion with IL2RA, while Q30W enhanced CD8 T cell activity through potential π-stacking enhancing binding to IL2RB, with the combination highly stimulatory for CD8 T cells. For human IL2, Y45K (homolog to murine Y59K) coupled with E62K prevented IL2RA binding, however it required the aggregation-protecting mutations of N90R T131R to rescue production. These muteins, designed with both cellular specificity and protein production features, have potential as both biological tools and therapeutics.

Mass Cytometry Immunophenotyping of Graft-Conditioned Cells Following Major Histocompatibility Complex Mismatched Murine Allograft

Allogeneic hematopoietic cell transplantation (allo-HCT) is a potentially curative therapy for a variety of blood disorders but primarily reserved for blood cancer patients due to the life-threatening risk of acute graft-versus-host disease (aGVHD). Development of aGVHD is driven by alloreactive T cells that recognize the recipient's tissues as foreign and initiate a robust immune response causing severe tissue damage of the skin, liver, and gut. While methods to reduce aGVHD incidence and severity exist including posttransplant cyclophosphamide, relapse rates and transplantation-related mortality remain. We previously published a study using graft conditioning with glucocorticoids as a strategy to modify the immune repertoire in the donor grafts prior to transplantation to reduce aGVHD. Here, we describe a protocol to characterize the T-cell response in recipient mice given transplantation of graft-conditioned allogeneic donor cells via mass cytometry. Mass cytometry is a technology that uses heavy metal tags in place of fluorochromes to allow high-dimensional flow cytometric analysis. In this protocol, we include an antibody panel of 39 different antibodies conjugated to 41 different heavy metal tags that have been validated and titrated for barcoding and immunophenotyping by lineage markers, activation markers, cytokine secretion, and transcription factors. This chapter details the graft conditioning, transplantation, processing, barcoding, staining, and mass cytometric analysis of immune cells following murine allo-HCT.

A novel murine syngeneic CD8 peripheral T-cell lymphoma model with preclinical applications

Peripheral T-cell Lymphoma (PTCL) represents a heterogenous group of aggressive non-Hodgkin Lymphomas with poor prognostic outcomes and limited treatment options. The development and refinement of therapeutic strategies for PTCL are impeded by a paucity of reliable preclinical models that accurately mimic the disease's pathophysiology. There is a dire need for more physiologically relevant models for PTCL. Here we describe a spontaneousCD8+ peripheral T-cell lymphoma cell line (LM-23) derived from a 12-week-old female Balb/cJ mouse. Both intravenous and subcutaneous administration of this cell line to syngeneic Balb/cJ mice resulted in rapid establishment of tumor growth. CHOP and anti-PD1 treatment both displayed no benefit to mice in regulating tumor growth. Such results along with its phenotypic characteristics, rapid growth, and metastatic behavior in syngeneic mice highlight its value in studying the elusive disease and discovery of novel therapeutics.

Coronavirus disease 2019-related myocardial injury is associated with immune dysregulation in symptomatic patients with cardiac magnetic resonance imaging abnormalities

AIMS

While acute cardiovascular complications of coronavirus disease 2019 (COVID-19) are well described, less is known about longer-term cardiac sequelae. For many individuals with cardiac signs or symptoms arising after COVID-19 infection, the aetiology remains unclear. We examined immune profiles associated with magnetic resonance imaging (MRI) abnormalities in patients with unexplained cardiac injury after COVID-19.

METHODS AND RESULTS

Twenty-one participants {mean age 47 [standard deviation (SD) 13] years, 71% female} with long COVID-19 (n = 17), raised troponin (n = 2), or unexplained new-onset heart failure (n = 2), who did not have pre-existing heart conditions or recent steroid/immunosuppression treatment, were enrolled a mean 346 (SD 191) days after COVID-19 infection in a prospective observational study. Cardiac MRI and blood sampling for deep immunophenotyping using mass cytometry by time of flight and measurement of proteomic inflammatory markers were performed. Nine of the 21 (43%) participants had MRI abnormalities (MRI(+)), including non-ischaemic patterns of late gadolinium enhancement and/or visually overt myocardial oedema in 8 people. One patient had mildly impaired biventricular function without fibrosis or oedema, and two had severe left ventricular (LV) impairment. MRI(+) individuals had higher blood CCL3, CCL7, FGF-23, and CD4 Th2 cells, and lower CD8 T effector memory (TEM) cells, than MRI(-). Cluster analysis revealed lower expression of inhibitory receptors PD1 and TIM3 in CD8 TEM cells from MRI(+) patients than MRI(-) patients, and functional studies of CD8 T αβ cells showed higher proportions of cytotoxic granzyme B+(GZB+)-secreting cells upon stimulation. CD8 TEM cells and CCL7 were the strongest predictors of MRI abnormalities in a least absolute shrinkage and selection operator regression model (composite area under the curve 0.96, 95% confidence interval 0.88-1.0). CCL7 was correlated with diffuse myocardial fibrosis/oedema detected by quantitative T1 mapping (r = 0.47, P = 0.04).

CONCLUSION

COVID-19-related cardiac injury in symptomatic patients with non-ischaemic myocarditis-like MRI abnormalities is associated with immune dysregulation, including decreased peripheral CD8 TEM cells and increased CCL7, persisting long after the initial infection.

Maternal thirdhand exposure to e-cigarette vapor alters lung and bone marrow immune cell responses in offspring in the absence or presence of influenza infection

There is increasing evidence that thirdhand exposure to e-cigarette vapor (e-vapor) can have detrimental effects on the lungs. However, whether maternal exposure during pregnancy results in harmful changes to the offspring is unknown. Using two different e-cigarette settings (low vs. high power), BALB/c mice were subjected to thirdhand e-vapor (e-vapor deposited onto towels, towels changed daily) in the absence or presence of nicotine, before, during, and after pregnancy. Male adult offspring were then infected with mouse-adapted influenza A virus (A/PR/8/34 H1N1; Flu) and lung and bone marrow immune cell responses were assessed 7 days postinfection. Maternal thirdhand exposure to low-power (MLP) or high-power (MHP) e-vapor with nicotine (MLP + NIC and MHP + NIC, respectively) increased the percentage of lung immune cells and neutrophils in the bone marrow. Interestingly, Flu-infected offspring from MLP + NIC and MHP + NIC groups had lower percentages of lung alveolar macrophages and more pronounced increases in neutrophils in the bone marrow, when compared with offspring from MSham Flu controls. Flu infection also decreased the percentage of lung CD4+ T cells and increased the percentage of lung CD8+ T cells, irrespective of maternal exposure (MLP -/+ NIC and MHP -/+ NIC). Significantly, both MLP + NIC and MHP + NIC resulted in blunted activation of lung CD4+ T cells, but only MLP + NIC caused blunted activation of lung CD8+ T cells. Together, we show for the first time that maternal thirdhand exposure to e-vapor results in significant, long-lived effects on lung and bone marrow immune cell responses in offspring at baseline and response to Flu infection.NEW & NOTEWORTHY Maternal exposure to environmental residues of e-cigarette use has significant effects on immune cell responses in the lungs and bone marrow of offspring at both baseline and in response to influenza A virus (Flu) infection.

The Power of Reagent Titration in Flow Cytometry

Flow cytometry facilitates the detection of multiple cell parameters simultaneously with a high level of resolution and throughput, enabling in-depth immunological evaluations. High data resolution in flow cytometry depends on multiple factors, including the concentration of reagents used in the staining protocol, and reagent validation and titration should be the first step in any assay optimization. Titration is the process of finding the concentration of the reagent that best resolves a positive signal from the background, with the saturation of all binding sites, and minimal antibody excess. The titration process involves the evaluation of serial reagent dilutions in cells expressing the antigen target for the tested antibody. The concentration of antibody that provides the highest signal to noise ratio is calculated by plotting the percentage of positive cells and the intensity of the fluorescence of the stained cells with respect to the negative events, in a concentration-response curve. The determination of the optimal antibody concentration is necessary to ensure reliable and reproducible results and is required for each sample type, reagent clone and lot, as well as the methods used for cell collection, staining, and storage conditions. If the antibody dilution is too low, the signal will be too weak to be accurately determined, leading to suboptimal data resolution, high variability across measurements, and the underestimation of the frequency of cells expressing a specific marker. The use of excess antibodies could lead to non-specific binding, reagent misuse, and detector overloading with the signal off scale and higher spillover spreading. In this publication, we summarized the titration fundamentals and best practices, and evaluated the impact of using a different instrument, sample, staining, acquisition, and analysis conditions in the selection of the optimal titer and population resolution.

Protocol for the collection and analysis of the different immune cell subsets in the murine intestinal lamina propria

The intestinal lamina propria (LP) is a leukocyte-rich cornerstone of the immune system owing to its vital role in immune surveillance and barrier defense against external pathogens. Here, we present a protocol for isolating and analyzing immune cell subsets from the mouse intestinal LP for further downstream applications. Starting from tissue collection and cleaning, epithelium removal, and enzymatic digestion to collection of single cells, we explain each step in detail to maximize the yield of immune cells from the intestinal LP.

Evaluation of anti-vector immune responses to adenovirus-mediated lung gene therapy and modulation by αCD20

Although the last decade has seen tremendous progress in drugs that treat cystic fibrosis (CF) due to mutations that lead to protein misfolding, there are approximately 8%-10% of subjects with mutations that result in no significant CFTR protein expression demonstrating the need for gene editing or gene replacement with inhaled mRNA or vector-based approaches. A limitation for vector-based approaches is the formation of neutralizing humoral responses. Given that αCD20 has been used to manage post-transplant lymphoproliferative disease in CF subjects with lung transplants, we studied the ability of αCD20 to module both T and B cell responses in the lung to one of the most immunogenic vectors, E1-deleted adenovirus serotype 5. We found that αCD20 significantly blocked luminal antibody responses and efficiently permitted re-dosing. αCD20 had more limited impact on the T cell compartment, but reduced tissue resident memory T cell responses in bronchoalveolar lavage fluid. Taken together, these pre-clinical studies suggest that αCD20 could be re-purposed for lung gene therapy protocols to permit re-dosing.

Shedding Light on Intracellular Proteins using Flow Cytometry

Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.

IFNγ Production by Functionally Reprogrammed Tregs Promotes Antitumor Efficacy of OX40/CD137 Bispecific Agonist Therapy

Regulatory T cells (Treg) are highly enriched within many tumors and suppress immune responses to cancer. There is intense interest in reprogramming Tregs to contribute to antitumor immunity. OX40 and CD137 are expressed highly on Tregs, activated and memory T cells, and NK cells. In this study, using a novel bispecific antibody targeting mouse OX40 and CD137 (FS120m), we show that OX40/CD137 bispecific agonism induces potent antitumor immunity partially dependent upon IFNγ production by functionally reprogrammed Tregs. Treatment of tumor-bearing animals with OX40/CD137 bispecific agonists reprograms Tregs into both fragile Foxp3+ IFNγ+ Tregs with decreased suppressive function and lineage-instable Foxp3- IFNγ+ ex-Tregs. Treg fragility is partially driven by IFNγ signaling, whereas Treg instability is associated with reduced IL2 responsiveness upon treatment with OX40/CD137 bispecific agonists. Importantly, conditional deletion of Ifng in Foxp3+ Tregs and their progeny partially reverses the antitumor efficacy of OX40/CD137 bispecific agonist therapy, revealing that reprogramming of Tregs into IFNγ-producing cells contributes to the anti-tumor efficacy of OX40/CD137 bispecific agonists. These findings provide insights into mechanisms by which bispecific agonist therapies targeting costimulatory receptors highly expressed by Tregs potentiate antitumor immunity in mouse models.

SIGNIFICANCE

The bispecific antibody FS120, an immunotherapy currently being tested in the clinic, partially functions by inducing anti-tumor activity of Tregs, which results in tumor rejection.

The tissue-resident regulatory T cell pool is shaped by transient multi-tissue migration and a conserved residency program

The tissues are the site of many important immunological reactions, yet how the immune system is controlled at these sites remains opaque. Recent studies have identified Foxp3+ regulatory T (Treg) cells in non-lymphoid tissues with unique characteristics compared with lymphoid Treg cells. However, tissue Treg cells have not been considered holistically across tissues. Here, we performed a systematic analysis of the Treg cell population residing in non-lymphoid organs throughout the body, revealing shared phenotypes, transient residency, and common molecular dependencies. Tissue Treg cells from different non-lymphoid organs shared T cell receptor (TCR) sequences, with functional capacity to drive multi-tissue Treg cell entry and were tissue-agnostic on tissue homing. Together, these results demonstrate that the tissue-resident Treg cell pool in most non-lymphoid organs, other than the gut, is largely constituted by broadly self-reactive Treg cells, characterized by transient multi-tissue migration. This work suggests common regulatory mechanisms may allow pan-tissue Treg cells to safeguard homeostasis across the body.

Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation

The role of T cell receptor (TCR) diversity in infectious disease susceptibility is not well understood. We use a systems immunology approach on three cohorts of herpes zoster (HZ) patients and controls to investigate whether TCR diversity against varicella-zoster virus (VZV) influences the risk of HZ. We show that CD4+ T cell TCR diversity against VZV glycoprotein E (gE) and immediate early 63 protein (IE63) after 1-week culture is more restricted in HZ patients. Single-cell RNA and TCR sequencing of VZV-specific T cells shows that T cell activation pathways are significantly decreased after stimulation with VZV peptides in convalescent HZ patients. TCR clustering indicates that TCRs from HZ patients co-cluster more often together than TCRs from controls. Collectively, our results suggest that not only lower VZV-specific TCR diversity but also reduced functional TCR affinity for VZV-specific proteins in HZ patients leads to lower T cell activation and consequently affects the susceptibility for viral reactivation.

Development of a customizable mouse backbone spectral flow cytometry panel to delineate immune cell populations in normal and tumor tissues

Introduction

In vivo studies of cancer biology and assessment of therapeutic efficacy are critical to advancing cancer research and ultimately improving patient outcomes. Murine cancer models have proven to be an invaluable tool in pre-clinical studies. In this context, multi-parameter flow cytometry is a powerful method for elucidating the profile of immune cells within the tumor microenvironment and/or play a role in hematological diseases. However, designing an appropriate multi-parameter panel to comprehensively profile the increasing diversity of immune cells across different murine tissues can be extremely challenging.

Methods

To address this issue, we designed a panel with 13 fixed markers that define the major immune populations -referred to as the backbone panel- that can be profiled in different tissues but with the option to incorporate up to seven additional fluorochromes, including any marker specific to the study in question.

Results

This backbone panel maintains its resolution across different spectral flow cytometers and organs, both hematopoietic and non-hematopoietic, as well as tumors with complex immune microenvironments.

Discussion

Having a robust backbone that can be easily customized with pre-validated drop-in fluorochromes saves time and resources and brings consistency and standardization, making it a versatile solution for immuno-oncology researchers. In addition, the approach presented here can serve as a guide to develop similar types of customizable backbone panels for different research questions requiring high-parameter flow cytometry panels.

OT-I TCR Transgenic Mice to Study the Role of PTPN22 in Anti-cancer Immunity

Phosphotyrosine phosphatase non-receptor type 22 (PTPN22) is a key regulator of immune cell activation and responses. Genetic polymorphisms of PTPN22 have been strongly linked with an increased risk of developing autoimmune diseases, while analysis of PTPN22-deficient mouse strains has determined that PTPN22 serves as a negative regulator of T cell antigen receptor signaling. As well as these key roles in maintaining immune tolerance, PTPN22 acts as an intracellular checkpoint for T cell responses to cancer, suggesting that PTPN22 might be a useful target to improve T cell immunotherapies. To assess the potential for targeting PTPN22, we have crossed Ptpn22-deficient mice to an OT-I TCR transgenic background and used adoptive T cell transfer approaches in mouse cancer models. We provide basic methods for the in vitro expansion of effector OT-I cytotoxic T lymphocytes, in vitro phenotypic analysis, and in vivo adoptive T cell transfer models to assess the role of PTPN22 in anti-cancer immunity.

Protocol for isolation and spectral flow cytometry analysis of immune cells from the murine exocrine and endocrine pancreas

Diabetes mellitus is a disease of the hormone-secreting endocrine pancreas. However, increasing evidence suggests that the exocrine pancreas is also involved in the pathogenesis of diabetes. In this protocol, we describe how to harvest both isolated islets and exocrine tissue from one mouse pancreas, followed by a detailed explanation of how to isolate and analyze immune cells using full-spectrum flow cytometry.

Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain

Cognitive decline is a common pathological outcome during aging, with an ill-defined molecular and cellular basis. In recent years, the concept of inflammaging, defined as a low-grade inflammation increasing with age, has emerged. Infiltrating T cells accumulate in the brain with age and may contribute to the amplification of inflammatory cascades and disruptions to the neurogenic niche observed with age. Recently, a small resident population of regulatory T cells has been identified in the brain, and the capacity of IL2-mediated expansion of this population to counter neuroinflammatory disease has been demonstrated. Here, we test a brain-specific IL2 delivery system for the prevention of neurological decline in aging mice. We identify the molecular hallmarks of aging in the brain glial compartments and identify partial restoration of this signature through IL2 treatment. At a behavioral level, brain IL2 delivery prevented the age-induced defect in spatial learning, without improving the general decline in motor skill or arousal. These results identify immune modulation as a potential path to preserving cognitive function for healthy aging.

Green Labs: a guide to developing sustainable science in your organization

Scientific research plays a vital role for society, but carries a significant environmental footprint, involving intensive use of energy and resources. Scientists are well placed to understand the unfolding climate and ecological crises, but may not appreciate how heavily their research, and other work-related activities, contribute to emissions and pollution. With the consequences of climate change and ecological breakdown playing out in real time, scientists now have an important, urgent role to play in catalyzing solutions. Here, we explore how research organizations can reduce their environmental impact, share useful resources and encourage the global community to engage in making science more sustainable.