Deep Profiling Human T Cell Heterogeneity by Mass Cytometry

Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders

Primary immunodeficiencies were initially identified on the basis of recurrent, severe or unusual infections. Subsequently, it was noted that these diseases can also manifest with autoimmunity, autoinflammation, allergy, lymphoproliferation and malignancy, hence a conceptual change and their renaming as inborn errors of immunity. Ongoing advances in flow cytometry provide the opportunity to expand or modify the utility and scope of existing laboratory tests in this field to mirror this conceptual change. Here we have used the B cell subset, variably known as CD21low B cells, age-associated B cells and T-bet+ B cells, as an example to demonstrate this possibility.

Evolving Approach to Clinical Cytometry for Immunodeficiencies and Other Immune Disorders

Primary immunodeficiencies were initially identified on the basis of recurrent, severe or unusual infections. Subsequently, it was noted that these diseases can also manifest with autoimmunity, autoinflammation, allergy, lymphoproliferation and malignancy, hence a conceptual change and their renaming as inborn errors of immunity. Ongoing advances in flow cytometry provide the opportunity to expand or modify the utility and scope of existing laboratory tests in this field to mirror this conceptual change. Here we have used the B cell subset, variably known as CD21low B cells, age-associated B cells and T-bet+ B cells, as an example to demonstrate this possibility.

Novel Techniques and Future Perspective for Investigating Critical-Size Bone Defects

A critical-size bone defect is a challenging clinical problem in which a gap between bone ends will not heal and will become a nonunion. The current treatment is to harvest and transplant an autologous bone graft to facilitate bone bridging. To develop less invasive but equally effective treatment options, one needs to first have a comprehensive understanding of the bone healing process. Therefore, it is imperative to leverage the most advanced technologies to elucidate the fundamental concepts of the bone healing process and develop innovative therapeutic strategies to bridge the nonunion gap. In this review, we first discuss the current animal models to study critical-size bone defects. Then, we focus on four novel analytic techniques and discuss their strengths and limitations. These four technologies are mass cytometry (CyTOF) for enhanced cellular analysis, imaging mass cytometry (IMC) for enhanced tissue special imaging, single-cell RNA sequencing (scRNA-seq) for detailed transcriptome analysis, and Luminex assays for comprehensive protein secretome analysis. With this new understanding of the healing of critical-size bone defects, novel methods of diagnosis and treatment will emerge.

Memory CD8+ T cell heterogeneity is primarily driven by pathogen-specific cues and additionally shaped by the tissue environment

Factors that govern the complex formation of memory T cells are not completely understood. A better understanding of the development of memory T cell heterogeneity is however required to enhance vaccination and immunotherapy approaches. Here we examined the impact of pathogen- and tissue-specific cues on memory CD8⁺ T cell heterogeneity using high-dimensional single-cell mass cytometry and a tailored bioinformatics pipeline. We identified distinct populations of pathogen-specific CD8⁺ T cells that uniquely connected to a specific pathogen or associated to multiple types of acute and persistent infections. In addition, the tissue environment shaped the memory CD8⁺ T cell heterogeneity, albeit to a lesser extent than infection. The programming of memory CD8⁺ T cell differentiation during acute infection is eventually superseded by persistent infection. Thus, the plethora of distinct memory CD8⁺ T cell subsets that arise upon infection is dominantly sculpted by the pathogen-specific cues and further shaped by the tissue environment.

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Heterogeneous subsets of both circulating and tissue-resident memory CD8⁺ T cells exist

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Memory CD8⁺ T cell heterogeneity is profoundly sculpted by pathogen-specific cues

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Memory CD8⁺ T cell heterogeneity is additionally shaped by the tissue environment

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Viral persistance supersedes memory CD8⁺ T cell differentiation after acute infection

IL-7 receptor alpha defines heterogeneity and signature of human effector memory CD8+ T cells in high dimensional analysis

The IL-7 receptor alpha chain (IL-7Rα or CD127) can be differentially expressed in memory CD8+ T cells. Here we investigated whether IL-7Rα could serve as a key molecule in defining a comprehensive landscape of heterogeneity in human effector memory (EM) CD8+ T cells using high-dimensional Cytometry by Time-Of-Flight (CyTOF) and single-cell RNA-seq (scRNA-seq). IL-7Rα had diverse, but organized, expressional relationship in EM CD8+ T cells with molecules related to cell function and gene regulation, which rendered an immune landscape defining heterogeneous cell subsets. The differential expression of these molecules likely has biological implications as we found in vivo signatures of transcription factors and homeostasis cytokine receptors, including T-bet and IL-7Rα. Our findings indicate the existence of heterogeneity in human EM CD8+ T cells as defined by distinct but organized expression patterns of multiple molecules in relationship to IL-7Rα and its possible biological significance in modulating downstream events.

α-Synuclein-specific T cell reactivity is associated with preclinical and early Parkinson's disease

A diagnosis of motor Parkinson’s disease (PD) is preceded by a prolonged premotor phase with accumulating neuronal damage. Here we examined the temporal relation between α-synuclein (α-syn) T cell reactivity and PD. A longitudinal case study revealed that elevated α-syn-specific T cell responses were detected prior to the diagnosis of motor PD, and declined after. The relationship between T cell reactivity and early PD in two independent cohorts showed that α-syn-specific T cell responses were highest shortly after diagnosis of motor PD and then decreased. Additional analysis revealed significant association of α-syn-specific T cell responses with age and lower levodopa equivalent dose. These results confirm the presence of α-syn-reactive T cells in PD and show that they are most abundant immediately after diagnosis of motor PD. These cells may be present years before the diagnosis of motor PD, suggesting avenues of investigation into PD pathogenesis and potential early diagnosis.

α-Synuclein-specific T cell reactivity is preferentially associated with Parkinson’s disease (PD) patients, but the temporal relation with diagnosis was previously unknown. This study reveals that α-syn-reactive T cells are highest before and shortly after diagnosis of motor PD, and then decrease.

Recent advances in single-cell analysis by mass spectrometry

Cells are the most basic structural units that play vital roles in the functioning of living organisms. Analysis of the chemical composition and content of a single cell plays a vital role in ensuring precise investigations of cellular metabolism, and is a crucial aspect of lipidomic and proteomic studies. In addition, structural knowledge provides a better understanding of cell behavior as well as the cellular and subcellular mechanisms. However, single-cell analysis can be very challenging due to the very small size of each cell as well as the large variety and extremely low concentrations of substances found in individual cells. On account of its high sensitivity and selectivity, mass spectrometry holds great promise as an effective technique for single-cell analysis. Numerous mass spectrometric techniques have been developed to elucidate the molecular profiles at the cellular level, including electrospray ionization mass spectrometry (ESI-MS), secondary ion mass spectrometry (SIMS), laser-based mass spectrometry and inductively coupled plasma mass spectrometry (ICP-MS). In this review, the recent advances in single-cell analysis by mass spectrometry are summarized. The strategies of different ionization modes to achieve single-cell analysis are classified and discussed in detail.

Expansion and activation of distinct central memory T lymphocyte subsets in complex regional pain syndrome

BACKGROUND

Complex regional pain syndrome (CRPS) is a debilitating condition where trauma to a limb results in devastating persistent pain that is disproportionate to the initial injury. The pathophysiology of CRPS remains unknown; however, accumulating evidence suggests it is an immunoneurological disorder, especially in light of evidence of auto-antibodies in ~ 30% of patients. Despite this, a systematic assessment of all circulating leukocyte populations in CRPS has never been performed.

METHODS

We characterised 14 participants as meeting the Budapest clinical criteria for CRPS and assessed their pain ratings and psychological state using a series of questionnaires. Next, we performed immunophenotyping on blood samples from the 14 CRPS participants as well as 14 healthy pain-free controls using mass cytometry. Using a panel of 38 phenotypic and activation markers, we characterised the numbers and intracellular activation status of all major leukocyte populations using manual gating strategies and unsupervised cluster analysis.

RESULTS

We have shown expansion and activation of several distinct populations of central memory T lymphocytes in CRPS. The number of central memory CD8+ T cells was increased 2.15-fold; furthermore, this cell group had increased phosphorylation of NFkB and STAT1 compared to controls. Regarding central memory CD4+ T lymphocytes, the number of Th1 and Treg cells was increased 4.98-fold and 2.18-fold respectively, with increased phosphorylation of NFkB in both populations. We also found decreased numbers of CD1c+ myeloid dendritic cells, although with increased p38 phosphorylation. These changes could indicate dendritic cell tissue trafficking, as well as their involvement in lymphocyte activation.

CONCLUSIONS

These findings represent the first mass cytometry immunophenotyping study in any chronic pain state and provide preliminary evidence of an antigen-mediated T lymphocyte response in CRPS. In particular, the presence of increased numbers of long-lived central memory CD4+ and CD8+ T lymphocytes with increased activation of pro-inflammatory signalling pathways may indicate ongoing inflammation and cellular damage in CRPS.

Exploiting Molecular Barcodes in High-Throughput Cellular Assays

Multiplexing strategies, which greatly increase the number of simultaneously measured parameters in single experiments, are now being widely implemented by both the pharmaceutical industry and academic researchers. Color has long been used to identify biological signals and, when combined with molecular barcodes, has substantially enhanced the depth of multiplexed sample characterization. Moreover, the recent advent of DNA barcodes has led to an explosion of innovative cell sequencing approaches. Novel barcoding strategies also show great promise for encoding spatial information in transcriptomic studies, and for precise assessment of molecular abundance. Both color- and DNA-based barcodes can be conveniently analyzed with either a microscope or a cytometer, or via DNA sequencing. Here we review the basic principles of several technologies used to create barcodes and detail the type of samples that can be identified with such tags.

Ultrasensitive Quantification of Cytokine Proteins in Single Lymphocytes From Human Blood Following ex-vivo Stimulation

In this study we demonstrate the feasibility of direct, quantitative measurement of cytokine proteins in single human CD8 lymphocytes from fresh peripheral blood of healthy donors following a brief ex vivo stimulation. Cytokine-secreting cells were identified using cell surface “catch” reagents and single cell data were obtained by sorting of individual cytokine-secreting cells into 96 well plates containing lysis buffer followed by analysis using ultrasensitive immunoassays for interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α). CD8 cells negative for cytokine production, as determined by the cell surface catch reagents were used as negative controls. Furthermore, studies were undertaken to compare the mean fluorescence intensity (MFI) values of cytokine staining by flow cytometry with the quantification of cytokines using the current method. This study demonstrates that it is feasible to quantify cytokines from individual primary cells. A shift from qualitative to quantitative determinations of cytokine protein levels in single cells will permit more precise and reproducible studies of heterogeneity in the immune system and can be accomplished with readily available instrumentation.

Neurotransmitter signalling via NMDA receptors leads to decreased T helper type 1-like and enhanced T helper type 2-like immune balance in humans

Given the pivotal roles that CD4⁺ T cell imbalance plays in human immune disorders, much interest centres on better understanding influences that regulate human helper T-cell subset dominance in vivo. Here, using primary CD4⁺ T cells and short-term T helper type 1 (Th1) and Th2-like lines, we investigated roles and mechanisms by which neurotransmitter receptors may influence human type 1 versus type 2 immunity. We hypothesized that N-methyl-d-aspartate receptors (NMDA-R), which play key roles in memory and learning, can also regulate human CD4⁺ T cell function through induction of excitotoxicity. Fresh primary CD4⁺ T cells from healthy donors express functional NMDA-R that are strongly up-regulated upon T cell receptor (TCR) mediated activation. Synthetic and physiological NMDA-R agonists elicited Ca²⁺ flux and led to marked inhibition of type 1 but not type 2 or interleukin-10 cytokine responses. Among CD4⁺ lines, NMDA and quinolinic acid preferentially reduced cytokine production, Ca²⁺ flux, proliferation and survival of Th1-like cells through increased induction of cell death whereas Th2-like cells were largely spared. Collectively, the findings demonstrate that (i) NMDA-R is rapidly up-regulated upon CD4⁺ T cell activation in humans and (ii) Th1 versus Th2 cell functions such as proliferation, cytokine production and cell survival are differentially affected by NMDA-R agonists. Differential cytokine production and proliferative capacity of Th1 versus Th2 cells is attributable in part to increased physiological cell death among fully committed Th1 versus Th2 cells, leading to increased Th2-like dominance. Hence, excitotoxicity, beyond its roles in neuronal plasticity, may contribute to ongoing modulation of human T cell responses.

Human T cell immune surveillance: Phenotypic, functional and migratory heterogeneity for tailored immune responses

The human immune system constantly provides a balance between pathogen clearance as well as tolerance for autoantigens and the commensal microbiota. This is achieved by immune responses, which are highly specialized and diversified in terms of their phenotype, function, regulation and location. Despite the complexity that is inherent to human immunity, our current knowledge is primarily shaped by very reductionist insights gained from peripheral blood T cells. Since only 2% of human T cells recirculate in the blood, the vast majority remains undetected by common sampling strategies and therefore unexplored. This review highlights and discusses recent developments in human T cell immune surveillance with a particular focus on functional and migratory T cell heterogeneity and provides a critical framework for new conceptual ideas, which could serve as a starting point in the quest for novel targeted therapies for chronic tissue restricted inflammatory diseases.

Applying Mass Cytometry to the Analysis of Lymphoid Populations in Transplantation

Single-cell flow cytometric techniques have been indispensable to improving our understanding of the phenotype and function of immune cell subsets that are important in both rejection and tolerance after transplant. Mass cytometry, or cytometry by time of flight, is a single-cell-based platform that utilizes antibodies conjugated to rare heavy metal ions for analysis of cellular proteins by a time-of-flight mass spectrometer. This new technology allows for the evaluation of >40 simultaneous cellular parameters in a single sample because the limitation of spectral overlap, seen in conventional flow cytometry, is eliminated. In this review, we discuss the current state of mass cytometry, describe the advantages and disadvantages compared with multiparameter flow cytometry, introduce novel methods of high-dimensional data analysis and visualization, and review some recent studies using mass cytometry to profile the immune systems of healthy people and transplant recipients.

Research Techniques Made Simple: Mass Cytometry Analysis Tools for Decrypting the Complexity of Biological Systems

Mass cytometry by time-of-flight experiments allow analysis of over 40 functional and phenotypic cellular markers simultaneously at the single-cell level. The data dimensionality escalation accentuates limitations, inherent to manual analysis, as being subjective, labor-intensive, slow, and often incapable of showing the detailed features of each unique cell within populations. The subsequent challenge of examining, visualizing, and presenting mass cytometry data has motivated continuous development of dimensionality reduction methods. As a result, an increasing recognition of the inherent diversity and complexity of cellular networks is emerging, with the discovery of unexpected cell subpopulations, hierarchies, and developmental pathways, such as those existing within the immune system. Here, we briefly review some frequently used and accessible mass cytometry data analysis tools, including principal component analysis (PCA); spanning-tree progression analysis of density-normalized events (SPADE); t-distributed stochastic neighbor embedding (t-SNE)-based visualization (viSNE); automatic classification of cellular expression by nonlinear stochastic embedding (ACCENSE); and cluster identification, characterization, and regression (CITRUS). Mass cytometry, used together with these innovative analytic tools, has the power to lead to key discoveries in investigative dermatology, including but not limited to identifying signaling phenotypes with predictive value for early diagnosis, prognosis, or relapse and a thorough characterization of intratumor heterogeneity and disease-resistant cell populations, that may ultimately unveil novel therapeutic approaches.