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1.
Cell ; 184(17): 4447-4463.e20, 2021 08 19.
Article in English | MEDLINE | ID: mdl-34363755

ABSTRACT

TANK binding kinase 1 (TBK1) regulates IFN-I, NF-κB, and TNF-induced RIPK1-dependent cell death (RCD). In mice, biallelic loss of TBK1 is embryonically lethal. We discovered four humans, ages 32, 26, 7, and 8 from three unrelated consanguineous families with homozygous loss-of-function mutations in TBK1. All four patients suffer from chronic and systemic autoinflammation, but not severe viral infections. We demonstrate that TBK1 loss results in hypomorphic but sufficient IFN-I induction via RIG-I/MDA5, while the system retains near intact IL-6 induction through NF-κB. Autoinflammation is driven by TNF-induced RCD as patient-derived fibroblasts experienced higher rates of necroptosis in vitro, and CC3 was elevated in peripheral blood ex vivo. Treatment with anti-TNF dampened the baseline circulating inflammatory profile and ameliorated the clinical condition in vivo. These findings highlight the plasticity of the IFN-I response and underscore a cardinal role for TBK1 in the regulation of RCD.


Subject(s)
Inflammation/enzymology , Protein Serine-Threonine Kinases/deficiency , Tumor Necrosis Factor-alpha/pharmacology , A549 Cells , Adaptor Proteins, Signal Transducing/metabolism , Apoptosis , Autoimmunity/drug effects , Brain/diagnostic imaging , Cell Death/drug effects , Cytokines/metabolism , Deubiquitinating Enzyme CYLD/metabolism , Female , HEK293 Cells , Homozygote , Humans , I-kappa B Kinase/metabolism , Immunophenotyping , Inflammation/pathology , Interferon Type I/metabolism , Interferon-gamma/metabolism , Loss of Function Mutation/genetics , Male , Pedigree , Phosphorylation/drug effects , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Receptors, Pattern Recognition/metabolism , Toll-Like Receptor 3/metabolism , Transcriptome/genetics , Vesiculovirus/drug effects , Vesiculovirus/physiology
2.
Annu Rev Immunol ; 31: 635-674, 2013.
Article in English | MEDLINE | ID: mdl-23330956

ABSTRACT

To directly study complex human hemato-lymphoid system physiology and respective system-associated diseases in vivo, human-to-mouse xenotransplantation models for human blood and blood-forming cells and organs have been developed over the past three decades. We here review the fundamental requirements and the remarkable progress made over the past few years in improving these systems, the current major achievements reached by use of these models, and the future challenges to more closely model and study human health and disease and to achieve predictive preclinical testing of both prevention measures and potential new therapies.


Subject(s)
Hematopoiesis/immunology , Lymphoid Tissue/immunology , Lymphoid Tissue/transplantation , Models, Animal , Animals , Hematopoietic Stem Cell Transplantation/methods , Hematopoietic Stem Cell Transplantation/trends , Humans , Immunophenotyping , Lymphoid Tissue/pathology , Mice , Translational Research, Biomedical/methods , Translational Research, Biomedical/trends , Transplantation, Heterologous
3.
Annu Rev Immunol ; 31: 195-225, 2013.
Article in English | MEDLINE | ID: mdl-23298211

ABSTRACT

Severe combined immunodeficiency (SCID) comprises a group of disorders that are fatal owing to genetic defects that abrogate T cell development. Numerous related defects have recently been identified that allow T cell development but that compromise T cell function by affecting proximal or distal steps in intracellular signaling. These functional T cell immunodeficiencies are characterized by immune dysregulation and increased risk of malignancies, in addition to infections. The study of patients with these rare conditions, and of corresponding animal models, illustrates the importance of intracellular signaling to maintain T cell homeostasis.


Subject(s)
Severe Combined Immunodeficiency/immunology , Severe Combined Immunodeficiency/pathology , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/pathology , Animals , Disease Models, Animal , Homeostasis/genetics , Homeostasis/immunology , Humans , Immunophenotyping , Severe Combined Immunodeficiency/genetics , Signal Transduction/genetics , Signal Transduction/immunology , T-Lymphocyte Subsets/metabolism
4.
Nat Immunol ; 22(3): 322-335, 2021 03.
Article in English | MEDLINE | ID: mdl-33531712

ABSTRACT

Immune system dysfunction is paramount in coronavirus disease 2019 (COVID-19) severity and fatality rate. Mucosal-associated invariant T (MAIT) cells are innate-like T cells involved in mucosal immunity and protection against viral infections. Here, we studied the immune cell landscape, with emphasis on MAIT cells, in cohorts totaling 208 patients with various stages of disease. MAIT cell frequency is strongly reduced in blood. They display a strong activated and cytotoxic phenotype that is more pronounced in lungs. Blood MAIT cell alterations positively correlate with the activation of other innate cells, proinflammatory cytokines, notably interleukin (IL)-18, and with the severity and mortality of severe acute respiratory syndrome coronavirus 2 infection. We also identified a monocyte/macrophage interferon (IFN)-α-IL-18 cytokine shift and the ability of infected macrophages to induce the cytotoxicity of MAIT cells in an MR1-dependent manner. Together, our results suggest that altered MAIT cell functions due to IFN-α-IL-18 imbalance contribute to disease severity, and their therapeutic manipulation may prevent deleterious inflammation in COVID-19 aggravation.


Subject(s)
COVID-19/immunology , Interferon-alpha/immunology , Interleukin-18/immunology , Macrophages/immunology , Monocytes/immunology , Mucosal-Associated Invariant T Cells/immunology , Adult , Aged , Aged, 80 and over , Animals , Bronchoalveolar Lavage , Case-Control Studies , Chlorocebus aethiops , Cohort Studies , Female , France , Humans , Immunophenotyping , Interleukin-10/immunology , Interleukin-15/immunology , Interleukin-1beta/immunology , Interleukin-6/immunology , Interleukin-8/immunology , Male , Middle Aged , RNA-Seq , SARS-CoV-2 , Severity of Illness Index , Single-Cell Analysis , Vero Cells , Young Adult
5.
Cell ; 173(6): 1385-1397.e14, 2018 05 31.
Article in English | MEDLINE | ID: mdl-29706550

ABSTRACT

Post-translational modifications of histone proteins and exchanges of histone variants of chromatin are central to the regulation of nearly all DNA-templated biological processes. However, the degree and variability of chromatin modifications in specific human immune cells remain largely unknown. Here, we employ a highly multiplexed mass cytometry analysis to profile the global levels of a broad array of chromatin modifications in primary human immune cells at the single-cell level. Our data reveal markedly different cell-type- and hematopoietic-lineage-specific chromatin modification patterns. Differential analysis between younger and older adults shows that aging is associated with increased heterogeneity between individuals and elevated cell-to-cell variability in chromatin modifications. Analysis of a twin cohort unveils heritability of chromatin modifications and demonstrates that aging-related chromatin alterations are predominantly driven by non-heritable influences. Together, we present a powerful platform for chromatin and immunology research. Our discoveries highlight the profound impacts of aging on chromatin modifications.


Subject(s)
Aging , Chromatin/chemistry , Epigenesis, Genetic , Adolescent , Adult , Aged , Cell Lineage , Cell Separation , Diseases in Twins , Female , Flow Cytometry , Histones/metabolism , Humans , Immune System , Immunophenotyping , Leukocytes, Mononuclear/cytology , Male , Middle Aged , Monocytes/cytology , Principal Component Analysis , Protein Processing, Post-Translational , Registries , Young Adult
6.
Cell ; 175(4): 1141-1155.e16, 2018 11 01.
Article in English | MEDLINE | ID: mdl-30343902

ABSTRACT

CRISPR pools are being widely employed to identify gene functions. However, current technology, which utilizes DNA as barcodes, permits limited phenotyping and bulk-cell resolution. To enable novel screening capabilities, we developed a barcoding system operating at the protein level. We synthesized modules encoding triplet combinations of linear epitopes to generate >100 unique protein barcodes (Pro-Codes). Pro-Code-expressing vectors were introduced into cells and analyzed by CyTOF mass cytometry. Using just 14 antibodies, we detected 364 Pro-Code populations; establishing the largest set of protein-based reporters. By pairing each Pro-Code with a different CRISPR, we simultaneously analyzed multiple phenotypic markers, including phospho-signaling, on dozens of knockouts. Pro-Code/CRISPR screens found two interferon-stimulated genes, the immunoproteasome component Psmb8 and a chaperone Rtp4, are important for antigen-dependent immune editing of cancer cells and identified Socs1 as a negative regulator of Pd-l1. The Pro-Code technology enables simultaneous high-dimensional protein-level phenotyping of 100s of genes with single-cell resolution.


Subject(s)
CRISPR-Cas Systems , Flow Cytometry/methods , Genomics/methods , Mass Spectrometry/methods , Single-Cell Analysis/methods , Animals , Epitopes/chemistry , Epitopes/classification , Epitopes/genetics , HEK293 Cells , Humans , Immunophenotyping/methods , Jurkat Cells , Mice, Inbred BALB C , Proteome/chemistry , Proteome/classification , Proteome/genetics , THP-1 Cells
7.
Nat Immunol ; 21(12): 1506-1516, 2020 12.
Article in English | MEDLINE | ID: mdl-33028979

ABSTRACT

A wide spectrum of clinical manifestations has become a hallmark of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) COVID-19 pandemic, although the immunological underpinnings of diverse disease outcomes remain to be defined. We performed detailed characterization of B cell responses through high-dimensional flow cytometry to reveal substantial heterogeneity in both effector and immature populations. More notably, critically ill patients displayed hallmarks of extrafollicular B cell activation and shared B cell repertoire features previously described in autoimmune settings. Extrafollicular activation correlated strongly with large antibody-secreting cell expansion and early production of high concentrations of SARS-CoV-2-specific neutralizing antibodies. Yet, these patients had severe disease with elevated inflammatory biomarkers, multiorgan failure and death. Overall, these findings strongly suggest a pathogenic role for immune activation in subsets of patients with COVID-19. Our study provides further evidence that targeted immunomodulatory therapy may be beneficial in specific patient subpopulations and can be informed by careful immune profiling.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , B-Lymphocytes/immunology , COVID-19/immunology , SARS-CoV-2/immunology , Humans , Immunophenotyping
8.
Nat Immunol ; 21(1): 86-100, 2020 01.
Article in English | MEDLINE | ID: mdl-31844327

ABSTRACT

By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic 'hits', of which most had no previous immunologic association. Furthermore, hits were collectively enriched in genes for which humans show poor tolerance to loss of function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with each other and with specific physiologic traits. Such linkages limit freedom of movement for individual immune parameters, thereby imposing genetically regulated 'immunologic structures', the integrity of which was associated with immunocompetence. Hence, we provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.


Subject(s)
Enterobacteriaceae Infections/immunology , Genetic Variation/genetics , High-Throughput Screening Assays/methods , Immunophenotyping/methods , Salmonella Infections/immunology , Animals , Citrobacter/immunology , Enterobacteriaceae Infections/microbiology , Female , Humans , Male , Mice , Mice, Inbred C57BL , Mice, Knockout , Models, Animal , Salmonella/immunology , Salmonella Infections/microbiology
9.
Nat Immunol ; 21(11): 1384-1396, 2020 11.
Article in English | MEDLINE | ID: mdl-32989327

ABSTRACT

T follicular helper (TFH) cells are critical in adaptive immune responses to pathogens and vaccines; however, what drives the initiation of their developmental program remains unclear. Studies suggest that a T cell antigen receptor (TCR)-dependent mechanism may be responsible for the earliest TFH cell-fate decision, but a critical aspect of the TCR has been overlooked: tonic TCR signaling. We hypothesized that tonic signaling influences early TFH cell development. Here, two murine TCR-transgenic CD4+ T cells, LLO56 and LLO118, which recognize the same antigenic peptide presented on major histocompatibility complex molecules but experience disparate strengths of tonic signaling, revealed low tonic signaling promotes TFH cell differentiation. Polyclonal T cells paralleled these findings, with naive Nur77 expression distinguishing TFH cell potential. Two mouse lines were also generated to both increase and decrease tonic signaling strength, directly establishing an inverse relationship between tonic signaling strength and TFH cell development. Our findings elucidate a central role for tonic TCR signaling in early TFH cell-lineage decisions.


Subject(s)
Receptors, Antigen, T-Cell/metabolism , Signal Transduction , T Follicular Helper Cells/immunology , T Follicular Helper Cells/metabolism , Animals , Antigens/immunology , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/metabolism , Cell Differentiation/immunology , H-2 Antigens/immunology , Immunization , Immunophenotyping , Lymphocyte Activation/immunology , Mice , Mice, Knockout , Mice, Transgenic , Peptides/immunology
10.
Nat Immunol ; 21(12): 1563-1573, 2020 12.
Article in English | MEDLINE | ID: mdl-33106669

ABSTRACT

Chronic cytomegalovirus (CMV) infection leads to long-term maintenance of extraordinarily large CMV-specific T cell populations. The magnitude of this so-called 'memory inflation' is thought to mainly depend on antigenic stimulation during the chronic phase of infection. However, by mapping the long-term development of CD8+ T cell families derived from single naive precursors, we find that fate decisions made during the acute phase of murine CMV infection can alter the level of memory inflation by more than 1,000-fold. Counterintuitively, a T cell family's capacity for memory inflation is not determined by its initial expansion. Instead, those rare T cell families that dominate the chronic phase of infection show an early transcriptomic signature akin to that of established T central memory cells. Accordingly, a T cell family's long-term dominance is best predicted by its early content of T central memory precursors, which later serve as a stem-cell-like source for memory inflation.


Subject(s)
Clonal Evolution/immunology , Host-Pathogen Interactions/immunology , Immunologic Memory , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Virus Diseases/etiology , Virus Diseases/metabolism , Acute Disease , Animals , Biomarkers , Chronic Disease , Cytomegalovirus/immunology , Cytomegalovirus Infections/immunology , Cytomegalovirus Infections/virology , Gene Expression Profiling , Humans , Immunophenotyping , Mice , Muromegalovirus/immunology
11.
Nat Immunol ; 21(12): 1585-1596, 2020 12.
Article in English | MEDLINE | ID: mdl-33020659

ABSTRACT

Sepsis is a biphasic disease characterized by an acute inflammatory response, followed by a prolonged immunosuppressive phase. Therapies aimed at controlling inflammation help to reduce the time patients with sepsis spend in intensive care units, but they do not lead to a reduction in overall mortality. Recently, the focus has been on addressing the immunosuppressive phase, often caused by apoptosis of immune cells. However, molecular triggers of these events are not yet known. Using whole-genome CRISPR screening in mice, we identified a triggering receptor expressed on myeloid cells (TREM) family receptor, TREML4, as a key regulator of inflammation and immune cell death in sepsis. Genetic ablation of Treml4 in mice demonstrated that TREML4 regulates calcium homeostasis, the inflammatory cytokine response, myeloperoxidase activation, the endoplasmic reticulum stress response and apoptotic cell death in innate immune cells, leading to an overall increase in survival rate, both during the acute and chronic phases of polymicrobial sepsis.


Subject(s)
Disease Susceptibility , Immunity, Innate , Receptors, Immunologic/genetics , Receptors, Immunologic/metabolism , Sepsis/etiology , Animals , Biomarkers , Cell Death , Clustered Regularly Interspaced Short Palindromic Repeats , Cytokines/metabolism , Disease Models, Animal , Disease Susceptibility/immunology , Gene Editing , Gene Knockdown Techniques , Gene Targeting , Genomics/methods , Immunophenotyping , Inflammation/etiology , Inflammation/metabolism , Mice , Mice, Knockout , Neutrophils/immunology , Neutrophils/metabolism , Phenotype , T-Lymphocytes/immunology , T-Lymphocytes/metabolism
12.
Nat Immunol ; 21(12): 1552-1562, 2020 12.
Article in English | MEDLINE | ID: mdl-33046887

ABSTRACT

T cell memory relies on the generation of antigen-specific progenitors with stem-like properties. However, the identity of these progenitors has remained unclear, precluding a full understanding of the differentiation trajectories that underpin the heterogeneity of antigen-experienced T cells. We used a systematic approach guided by single-cell RNA-sequencing data to map the organizational structure of the human CD8+ memory T cell pool under physiological conditions. We identified two previously unrecognized subsets of clonally, epigenetically, functionally, phenotypically and transcriptionally distinct stem-like CD8+ memory T cells. Progenitors lacking the inhibitory receptors programmed death-1 (PD-1) and T cell immunoreceptor with Ig and ITIM domains (TIGIT) were committed to a functional lineage, whereas progenitors expressing PD-1 and TIGIT were committed to a dysfunctional, exhausted-like lineage. Collectively, these data reveal the existence of parallel differentiation programs in the human CD8+ memory T cell pool, with potentially broad implications for the development of immunotherapies and vaccines.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Immunologic Memory , Lymphoid Progenitor Cells/metabolism , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Animals , Biomarkers , Cell Differentiation/immunology , Computational Biology/methods , Gene Expression Profiling , High-Throughput Nucleotide Sequencing , Humans , Immunophenotyping , Lymphoid Progenitor Cells/cytology , Lymphoid Progenitor Cells/immunology , Mice , Telomere Homeostasis
13.
Nat Immunol ; 21(11): 1359-1370, 2020 11.
Article in English | MEDLINE | ID: mdl-32929274

ABSTRACT

Elucidating the mechanisms that sustain asthmatic inflammation is critical for precision therapies. We found that interleukin-6- and STAT3 transcription factor-dependent upregulation of Notch4 receptor on lung tissue regulatory T (Treg) cells is necessary for allergens and particulate matter pollutants to promote airway inflammation. Notch4 subverted Treg cells into the type 2 and type 17 helper (TH2 and TH17) effector T cells by Wnt and Hippo pathway-dependent mechanisms. Wnt activation induced growth and differentiation factor 15 expression in Treg cells, which activated group 2 innate lymphoid cells to provide a feed-forward mechanism for aggravated inflammation. Notch4, Wnt and Hippo were upregulated in circulating Treg cells of individuals with asthma as a function of disease severity, in association with reduced Treg cell-mediated suppression. Our studies thus identify Notch4-mediated immune tolerance subversion as a fundamental mechanism that licenses tissue inflammation in asthma.


Subject(s)
Asthma/etiology , Asthma/metabolism , Growth Differentiation Factor 15/metabolism , Receptor, Notch4/metabolism , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Allergens/immunology , Analysis of Variance , Asthma/diagnosis , Biomarkers , Disease Susceptibility , Gene Expression , Hippo Signaling Pathway , Humans , Immune Tolerance , Immunophenotyping , Protein Serine-Threonine Kinases/metabolism , Severity of Illness Index , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism , Wnt Signaling Pathway
14.
Nat Immunol ; 21(11): 1397-1407, 2020 11.
Article in English | MEDLINE | ID: mdl-32989328

ABSTRACT

Antiviral CD8+ T cell responses are characterized by an initial activation/priming of T lymphocytes followed by a massive proliferation, subset differentiation, population contraction and the development of a stable memory pool. The transcription factor BATF3 has been shown to play a central role in the development of conventional dendritic cells, which in turn are critical for optimal priming of CD8+ T cells. Here we show that BATF3 was expressed transiently within the first days after T cell priming and had long-lasting T cell-intrinsic effects. T cells that lacked Batf3 showed normal expansion and differentiation, yet succumbed to an aggravated contraction and had a diminished memory response. Vice versa, BATF3 overexpression in CD8+ T cells promoted their survival and transition to memory. Mechanistically, BATF3 regulated T cell apoptosis and longevity via the proapoptotic factor BIM. By programing CD8+ T cell survival and memory, BATF3 is a promising molecule to optimize adoptive T cell therapy in patients.


Subject(s)
Basic-Leucine Zipper Transcription Factors/genetics , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/metabolism , Cellular Reprogramming/genetics , Immunologic Memory/genetics , Repressor Proteins/genetics , Animals , Basic-Leucine Zipper Transcription Factors/metabolism , Cell Differentiation , Cell Survival/genetics , Gene Expression , Humans , Immunophenotyping , Mice , Mice, Knockout , Mice, Transgenic , Repressor Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
15.
Nat Immunol ; 21(11): 1371-1383, 2020 11.
Article in English | MEDLINE | ID: mdl-32989331

ABSTRACT

Foxp3+ regulatory T (Treg) cells expressing the interleukin (IL)-33 receptor ST2 mediate tissue repair in response to IL-33. Whether Treg cells also respond to the alarmin IL-33 to regulate specific aspects of the immune response is not known. Here we describe an unexpected function of ST2+ Treg cells in suppressing the innate immune response in the lung to environmental allergens without altering the adaptive immune response. Following allergen exposure, ST2+ Treg cells were activated by IL-33 to suppress IL-17-producing γδ T cells. ST2 signaling in Treg cells induced Ebi3, a component of the heterodimeric cytokine IL-35 that was required for Treg cell-mediated suppression of γδ T cells. This response resulted in fewer eosinophil-attracting chemokines and reduced eosinophil recruitment into the lung, which was beneficial to the host in reducing allergen-induced inflammation. Thus, we define a fundamental role for ST2+ Treg cells in the lung as a negative regulator of the early innate γδ T cell response to mucosal injury.


Subject(s)
Immunomodulation , Interleukin-33/metabolism , Intraepithelial Lymphocytes/immunology , Intraepithelial Lymphocytes/metabolism , Lung/immunology , Lung/metabolism , T-Lymphocytes, Regulatory/immunology , T-Lymphocytes, Regulatory/metabolism , Allergens/immunology , Animals , Biomarkers , Immunophenotyping , Interleukin-1 Receptor-Like 1 Protein/metabolism , Leukocytes/immunology , Leukocytes/metabolism , Mice
16.
Nat Immunol ; 21(11): 1408-1420, 2020 11.
Article in English | MEDLINE | ID: mdl-32868930

ABSTRACT

B lymphocyte development and selection are central to adaptive immunity and self-tolerance. These processes require B cell receptor (BCR) signaling and occur in bone marrow, an environment with variable hypoxia, but whether hypoxia-inducible factor (HIF) is involved is unknown. We show that HIF activity is high in human and murine bone marrow pro-B and pre-B cells and decreases at the immature B cell stage. This stage-specific HIF suppression is required for normal B cell development because genetic activation of HIF-1α in murine B cells led to reduced repertoire diversity, decreased BCR editing and developmental arrest of immature B cells, resulting in reduced peripheral B cell numbers. HIF-1α activation lowered surface BCR, CD19 and B cell-activating factor receptor and increased expression of proapoptotic BIM. BIM deletion rescued the developmental block. Administration of a HIF activator in clinical use markedly reduced bone marrow and transitional B cells, which has therapeutic implications. Together, our work demonstrates that dynamic regulation of HIF-1α is essential for normal B cell development.


Subject(s)
B-Lymphocytes/metabolism , Hypoxia-Inducible Factor 1, alpha Subunit/genetics , Lymphopoiesis/genetics , Animals , B-Lymphocyte Subsets/immunology , B-Lymphocyte Subsets/metabolism , B-Lymphocytes/cytology , B-Lymphocytes/immunology , Biomarkers , Gene Expression Regulation , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Immunoglobulin Light Chains/genetics , Immunophenotyping , Mice , Mice, Knockout , RNA Editing , Receptors, Antigen, B-Cell/metabolism , Signal Transduction , Transcriptional Activation
17.
Nat Immunol ; 21(12): 1528-1539, 2020 12.
Article in English | MEDLINE | ID: mdl-33020661

ABSTRACT

Mutations that impact immune cell migration and result in immune deficiency illustrate the importance of cell movement in host defense. In humans, loss-of-function mutations in DOCK8, a guanine exchange factor involved in hematopoietic cell migration, lead to immunodeficiency and, paradoxically, allergic disease. Here, we demonstrate that, like humans, Dock8-/- mice have a profound type 2 CD4+ helper T (TH2) cell bias upon pulmonary infection with Cryptococcus neoformans and other non-TH2 stimuli. We found that recruited Dock8-/-CX3CR1+ mononuclear phagocytes are exquisitely sensitive to migration-induced cell shattering, releasing interleukin (IL)-1ß that drives granulocyte-macrophage colony-stimulating factor (GM-CSF) production by CD4+ T cells. Blocking IL-1ß, GM-CSF or caspase activation eliminated the type-2 skew in mice lacking Dock8. Notably, treatment of infected wild-type mice with apoptotic cells significantly increased GM-CSF production and TH2 cell differentiation. This reveals an important role for cell death in driving type 2 signals during infection, which may have implications for understanding the etiology of type 2 CD4+ T cell responses in allergic disease.


Subject(s)
Guanine Nucleotide Exchange Factors/deficiency , Lymphocyte Activation/genetics , Lymphocyte Activation/immunology , Th2 Cells/immunology , Th2 Cells/metabolism , Animals , Biomarkers , Caspases/metabolism , Cell Movement/genetics , Cell Movement/immunology , Cytokines/genetics , Cytokines/metabolism , Disease Susceptibility , Gene Expression , Granulocyte-Macrophage Colony-Stimulating Factor/metabolism , Humans , Immunophenotyping , Leukocytes, Mononuclear/immunology , Leukocytes, Mononuclear/metabolism , Mice , Mice, Knockout , Myeloid Cells/immunology , Myeloid Cells/metabolism , Phagocytes/immunology , Phagocytes/metabolism , Signal Transduction
18.
Nat Immunol ; 21(6): 636-648, 2020 06.
Article in English | MEDLINE | ID: mdl-32424365

ABSTRACT

Sepsis and trauma cause inflammation and elevated susceptibility to hospital-acquired pneumonia. As phagocytosis by macrophages plays a critical role in the control of bacteria, we investigated the phagocytic activity of macrophages after resolution of inflammation. After resolution of primary pneumonia, murine alveolar macrophages (AMs) exhibited poor phagocytic capacity for several weeks. These paralyzed AMs developed from resident AMs that underwent an epigenetic program of tolerogenic training. Such adaptation was not induced by direct encounter of the pathogen but by secondary immunosuppressive signals established locally upon resolution of primary infection. Signal-regulatory protein α (SIRPα) played a critical role in the establishment of the microenvironment that induced tolerogenic training. In humans with systemic inflammation, AMs and also circulating monocytes still displayed alterations consistent with reprogramming six months after resolution of inflammation. Antibody blockade of SIRPα restored phagocytosis in monocytes of critically ill patients in vitro, which suggests a potential strategy to prevent hospital-acquired pneumonia.


Subject(s)
Epigenesis, Genetic , Inflammation/etiology , Lung/immunology , Lung/metabolism , Macrophages, Alveolar/metabolism , Animals , Biomarkers , Cellular Reprogramming , Cytokines/metabolism , Humans , Immune Tolerance , Immunophenotyping , Inflammation/metabolism , Inflammation/pathology , Inflammation Mediators/metabolism , Lung/pathology , Macrophages/immunology , Macrophages/metabolism , Macrophages, Alveolar/immunology , Mice , Monocytes/immunology , Monocytes/metabolism , Phagocytosis/immunology , Pneumonia/etiology , Pneumonia/metabolism , Pneumonia/pathology , T-Lymphocyte Subsets/immunology , T-Lymphocyte Subsets/metabolism
19.
Nat Immunol ; 20(3): 301-312, 2019 03.
Article in English | MEDLINE | ID: mdl-30664737

ABSTRACT

The fetus is thought to be protected from exposure to foreign antigens, yet CD45RO+ T cells reside in the fetal intestine. Here we combined functional assays with mass cytometry, single-cell RNA sequencing and high-throughput T cell antigen receptor (TCR) sequencing to characterize the CD4+ T cell compartment in the human fetal intestine. We identified 22 CD4+ T cell clusters, including naive-like, regulatory-like and memory-like subpopulations, which were confirmed and further characterized at the transcriptional level. Memory-like CD4+ T cells had high expression of Ki-67, indicative of cell division, and CD5, a surrogate marker of TCR avidity, and produced the cytokines IFN-γ and IL-2. Pathway analysis revealed a differentiation trajectory associated with cellular activation and proinflammatory effector functions, and TCR repertoire analysis indicated clonal expansions, distinct repertoire characteristics and interconnections between subpopulations of memory-like CD4+ T cells. Imaging mass cytometry indicated that memory-like CD4+ T cells colocalized with antigen-presenting cells. Collectively, these results provide evidence for the generation of memory-like CD4+ T cells in the human fetal intestine that is consistent with exposure to foreign antigens.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , Fetus/immunology , Immunologic Memory/immunology , Intestines/immunology , Antigen-Presenting Cells/cytology , Antigen-Presenting Cells/immunology , Antigen-Presenting Cells/metabolism , CD4-Positive T-Lymphocytes/cytology , CD4-Positive T-Lymphocytes/metabolism , CD5 Antigens/genetics , CD5 Antigens/immunology , CD5 Antigens/metabolism , Cells, Cultured , Fetus/cytology , Fetus/metabolism , Flow Cytometry , Gene Expression Profiling/methods , Gene Expression Regulation, Developmental/immunology , High-Throughput Nucleotide Sequencing , Humans , Immunologic Memory/genetics , Immunophenotyping , Intestines/cytology , Intestines/embryology , Ki-67 Antigen/genetics , Ki-67 Antigen/immunology , Ki-67 Antigen/metabolism
20.
Nat Immunol ; 20(7): 902-914, 2019 07.
Article in English | MEDLINE | ID: mdl-31209404

ABSTRACT

Lupus nephritis is a potentially fatal autoimmune disease for which the current treatment is ineffective and often toxic. To develop mechanistic hypotheses of disease, we analyzed kidney samples from patients with lupus nephritis and from healthy control subjects using single-cell RNA sequencing. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid cells, T cells, natural killer cells and B cells that demonstrated both pro-inflammatory responses and inflammation-resolving responses. We found evidence of local activation of B cells correlated with an age-associated B-cell signature and evidence of progressive stages of monocyte differentiation within the kidney. A clear interferon response was observed in most cells. Two chemokine receptors, CXCR4 and CX3CR1, were broadly expressed, implying a potentially central role in cell trafficking. Gene expression of immune cells in urine and kidney was highly correlated, which would suggest that urine might serve as a surrogate for kidney biopsies.


Subject(s)
Kidney/immunology , Lupus Nephritis/immunology , Biomarkers , Biopsy , Cluster Analysis , Computational Biology/methods , Epithelial Cells/metabolism , Flow Cytometry , Gene Expression Profiling , Gene Expression Regulation , Humans , Immunophenotyping , Interferons/metabolism , Kidney/metabolism , Kidney/pathology , Leukocytes/immunology , Leukocytes/metabolism , Lupus Nephritis/genetics , Lupus Nephritis/metabolism , Lupus Nephritis/pathology , Lymphocytes/immunology , Lymphocytes/metabolism , Molecular Sequence Annotation , Myeloid Cells/immunology , Myeloid Cells/metabolism , Single-Cell Analysis , Transcriptome
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