Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

Resident memory CD4+ T lymphocytes mobilize from bone marrow to contribute to a systemic secondary immune reaction

Resident memory T lymphocytes (T_RM ) of epithelial tissues and the bone marrow protect their host tissue. To what extent these cells are mobilized and contribute to systemic immune reactions is less clear. Here we show that in secondary immune reactions to the measles-mumps-rubella (MMR) vaccine, CD4⁺ T_RM are mobilized into the blood within 16 to 48 hours after immunization in humans. This mobilization of T_RM is cognate: T_RM recognizing other antigens are not mobilized, unless they cross-react with the vaccine. We also demonstrate through methylome analyses that T_RM are mobilized from the bone marrow. These mobilized cells make significant contribution to the systemic immune reaction, as evidenced by their T-cell receptor Vβ clonotypes represented among the newly generated circulating memory T-cells, 14 days after vaccination. Thus, T_RM of the bone marrow confer not only local, but also systemic immune memory. This article is protected by copyright. All rights reserved.

Protocol for generating human immune system mice and hydrodynamic injection to analyze human hematopoiesis in vivo

Human immune system (HIS) mice provide a valuable platform to investigate and modulate human hematopoiesis development in vivo. Here, we describe detailed protocols for the construction of HIS mice, modulation of human hematopoiesis in vivo using hydrodynamic injection of plasmids encoding cytokines of interest, and flow cytometry analysis of humanization levels and human immune subsets. This approach can be easily applied to screen or verify factors that regulate human hematopoiesis and immune system.

For complete details on the use and execution of this protocol, please refer to Cardoso et al. (2021) and Li et al. (2017).

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The protocol for construction of human immune system mice

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Detailed procedure for hydrodynamic injection

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Characterization of human immune subpopulations by flow cytometry

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In vivo modulation of human hematopoiesis

Guidelines for standardizing T-cell cytometry assays to link biomarkers, mechanisms, and disease outcomes in type 1 diabetes

Cytometric immunophenotyping is a powerful tool to discover and implement T-cell biomarkers of type 1 diabetes (T1D) progression and response to clinical therapy. Although many discovery-based T-cell biomarkers have been described, to date, no such markers have been widely adopted in standard practice. The heterogeneous nature of T1D and lack of standardized assays and experimental design across studies is a major barrier to the broader adoption of T-cell immunophenotyping assays. There is an unmet need to harmonize the design of immunophenotyping assays, including those that measure antigen-agnostic cell populations, such that data collected from different clinical trial sites and T1D cohorts are comparable, yet account for cohort-specific features and different drug mechanisms of action. In these Guidelines, we aim to provide expert advice on how to unify aspects of study design and practice. We provide recommendations for defining cohorts, method implementation, as well as tools for data analysis and reporting by highlighting and building on selected successes. Harmonization of cytometry-based T-cell assays will allow researchers to better integrate findings across trials, ultimately enabling the identification and validation of biomarkers of disease progression and treatment response in T1D.

Specificity of mouse and human Fcgamma receptors and their polymorphic variants for IgG subclasses of different species

Immunoglobulin G (IgG) is the predominant antibody class generated during infections and used for the generation of therapeutic antibodies. Antibodies are mainly characterized in or generated from animal models that support particular infections, respond to particular antigens or allow the generation of hybridomas. Due to the availability of numerous transgenic mouse models and the ease of performing bioassays with human blood cells in vitro, most antibodies from species other than mice and humans are tested in vitro using human cells and/or in vivo using mice. In this process, it is expected, but not yet systematically documented, that IgG from these species interact with human or mouse IgG receptors (FcγRs). In this study, we undertook a systematic assessment of binding specificities of IgG from various species to the families of mouse and human FcγRs, including their polymorphic variants. Our results document the specific binding patterns for each of these IgG (sub)classes, reveal possible caveats of antibody-based immunoassays, and will be a useful reference for the transition from one animal model to preclinical mouse models or human cell-based bioassays. This article is protected by copyright. All rights reserved.

Global koff -rates of polyclonal T cell populations merge subclonal avidities and predict functionality

The avidity of T cell receptors (TCRs) for peptide-major histocompatibility complexes (pMHCs) is a governing factor in how T cells respond to antigen. TCR avidity is generally linked to T cell functionality and there is growing evidence for distinct roles of low and high avidity T cells in different phases of immune responses. While physiological immune responses and many therapeutic T cell products targeting infections or cancers consist of polyclonal T cell populations with a wide range of individual avidities, the role of T cell avidity is usually investigated only in monoclonal experimental settings. In this report, we induced polyclonal T cell responses with a wide range of avidities towards a model epitope by altered peptide ligands (APL), and benchmarked global avidity of physiological polyclonal populations by investigation of TCR-pMHC k_off -rates. We then investigated how varying sizes and avidities of monoclonal subpopulations translate into global k_off -rates. Global k_off -rates integrate subclonal avidities in a predictably weighted manner and robustly correlate with the functionality of murine polyclonal T cell populations in vitro and in vivo. Surveying the full avidity spectrum is essential to accurately assess polyclonal immune responses and inform the design of polyclonal T cell therapeutics. This article is protected by copyright. All rights reserved.

Innate lymphoid cell characterization in the rat and their correlation to gut commensal microbes

Innate lymphoid cells (ILCs) are important for tissue immune homeostasis, and are thoroughly characterized in mice and humans. Here, we have performed in-depth characterization of rat ILCs. Rat ILCs were identified based on differential expression of transcription factors and lack of lineage markers. ILC3s represented the major ILC population of the small intestine, while ILC2s were infrequent but most prominent in liver. Two major subsets of group 1 ILCs were defined. Lineage^- T-bet⁺ Eomes⁺ cells were identified as conventional NK cells, while lineage^- T-bet⁺ Eomes^- cells were identified as the probable rat counterpart of ILC1s based on their selective expression of the ILC marker CD200R. Rat ILC1s were particularly abundant in liver and intestinal tissues, and were functionally similar to NK cells. Single cell transcriptomics of spleen and liver cells confirmed the main division of NK cells and ILC1-like cells, and demonstrated Granzyme A as additional ILC1 marker. We further report differential distributions of NK cells and ILCs along the small and large intestines, and the association of certain bacterial taxa to frequencies of ILCs. In conclusion, we provide a framework for future studies of ILCs in diverse rat experimental models, and novel data on the potential interplay between commensals and intestinal ILCs. This article is protected by copyright. All rights reserved.

SARS-CoV-2 infection activates dendritic cells via cytosolic receptors rather than extracellular TLRs

Severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) causes coronavirus disease 2019 (COVID‐19), an infectious disease characterized by strong induction of inflammatory cytokines, progressive lung inflammation, and potentially multiorgan dysfunction. It remains unclear how SARS‐CoV‐2 infection leads to immune activation. The Spike (S) protein of SARS‐CoV‐2 has been suggested to trigger TLR4 and thereby activate immunity. Here, we have investigated the role of TLR4 in SARS‐CoV‐2 infection and immunity. Neither exposure of isolated S protein, SARS‐CoV‐2 pseudovirus nor primary SARS‐CoV‐2 isolate induced TLR4 activation in a TLR4‐expressing cell line. Human monocyte‐derived DCs express TLR4 but not angiotensin converting enzyme 2 (ACE2), and DCs were not infected by SARS‐CoV‐2. Notably, neither S protein nor SARS‐CoV‐2 induced DC maturation or cytokines, indicating that both S protein and SARS‐CoV‐2 virus particles do not trigger extracellular TLRs including TLR4. Ectopic expression of ACE2 in DCs led to efficient infection by SARS‐CoV‐2 and, strikingly, efficient type I IFN and cytokine responses. These data strongly suggest that not extracellular TLRs but intracellular viral sensors are key players in sensing SARS‐CoV‐2. These data imply that SARS‐CoV‐2 escapes direct sensing by TLRs, which might underlie the lack of efficient immunity to SARS‐CoV‐2 early during infection.

Initial properdin binding contributes to alternative pathway activation at the surface of viable and necrotic cells

Properdin, the only known positive regulator of the complement system, stabilizes the C3 convertase, thereby increasing its half‐life. In contrast to most other complement factors, properdin is mainly produced extrahepatically by myeloid cells. Recent data suggest a role for properdin as a pattern recognition molecule. Here, we confirmed previous findings of properdin binding to different necrotic cells including Jurkat T cells. Binding can occur independent of C3, as demonstrated by HAP‐1 C3 KO cells, excluding a role for endogenous C3. In view of the cellular source of properdin, interaction with myeloid cells was examined. Properdin bound to the surface of viable monocyte‐derived pro‐ and anti‐inflammatory macrophages, but not to DCs. Binding was demonstrated for purified properdin as well as fractionated P2, P3, and P4 properdin oligomers. Binding contributed to local complement activation as determined by C3 and C5b‐9 deposition on the cell surfaces and seems a prerequisite for alternative pathway activation. Interaction of properdin with cell surfaces could be inhibited with the tick protein Salp20 and by different polysaccharides, depending on sulfation and chain length. These data identify properdin as a factor interacting with different cell surfaces, being either dead or alive, contributing to the local stimulation of complement activation.

B cell modulation with anti-CD79bantibodies ameliorates experimental autoimmune encephalitis in mice

B cells play a major role in the pathogenesis of many autoimmune diseases like multiple sclerosis, rheumatoid arthritis or systemic lupus erythematosus. Depletion of B cells with anti-CD20 antibodies is an established therapy for multiple sclerosis. However, total B cell depletion will also affect regulatory B cells that are known to suppress autoimmune responses. In our studies we describe an alternative approach based on targeting of CD79b that induces only partial B cell depletion and achieves therapeutic effects by B cell modulation. Prophylactic and therapeutic treatment with an antibody against CD79b and also a deglycosylated variant of this antibody, lacking effector function like antibody-dependent cellular cytotoxicity or complement activation, significantly reduced the development and progression of experimental autoimmune encephalitis (EAE) in mice. Our data show that modulation of B cells via CD79b is equally effective as almost complete B cell depletion with anti-CD20 antibodies and may constitute an alternative approach to treat multiple sclerosis. This article is protected by copyright. All rights reserved.

Glutamine promotes the generation of B10+ cells via the mTOR/GSK3 pathway

Alterations in cell metabolism can shift the differentiation of immune cells towards a regulatory or inflammatory phenotype, thus opening up new therapeutic opportunities for immune-related diseases. Indeed, growing knowledge on T cell metabolism has revealed differences in the metabolic programs of suppressive regulatory T cells (Tregs) as compared to inflammatory Th1 and Th17 cells. In addition to Tregs, IL-10-producing regulatory B cells are crucial for maintaining tolerance, inhibiting inflammation and autoimmunity. Yet, the metabolic networks regulating diverse B lymphocyte responses are not well known. Here, we show that glutaminase blockade decreased downstream mTOR activation and attenuated IL-10 secretion. Direct suppression of mTOR activity by rapamycin selectively impaired IL-10 production by B cells whereas secretion was restored upon GSK3 inhibition. Mechanistically, we found mTORC1 activation leads to GSK3 inhibition, identifying a key signalling pathway regulating IL-10 secretion by B lymphocytes. Thus, our results identify glutaminolysis and the mTOR/GSK3 signalling axis, as critical regulators of the generation of IL-10 producing B cells with regulatory functions. This article is protected by copyright. All rights reserved.