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Ernst, J. D.

Publications and source records attributed to Ernst, J. D..

16 recordsLinked to original sources

The lung tissue environment in Mycobacterium tuberculosis infection determines local monocyte differentiation

Infection by Mycobacterium tuberculosis (Mtb) is characterized by pathogen persistence in lung cells derived from blood monocytes. Since monocyte-derived lung subsets differ in their ability to restrict the growth of intracellular Mtb in mice, understanding the ontogeny of these subsets can inform development of host-directed therapies. Circulating monocytes are proposed to be heterogeneous, arising from distinct bone marrow or spleen progenitors that direct local differentiation. However, the role of the Mtb-infected lung environment in this process has not been addressed. We found that infected and uninfected mice had similar bone marrow monopoiesis, resulting in equivalent monocyte differentiation within the infected lung. While pulmonary Mtb infection also induced splenic monopoiesis, we found no impact on lung monocyte differentiation in splenectomized mice. However, when wildtype monocytes were transferred into Mtb-infected Sp140-/- recipients, in which excess Type I interferons and neutrophils alter the lung environment, we observed that donor-derived lung subsets resembled recipient-derived cells. In the lungs of Mtb-infected mice, we identified monocyte-derived lung subsets with unique gene expression, associated with specific spatial distributions and cell neighborhoods. These findings suggest that the local lung environment has a larger influence on the phenotypic diversity of monocyte-derived lung cells than does the peripheral environment.

immunology↗

Impaired IFNγ responsiveness of lung monocyte-derived cells limits immunity to Mycobacterium tuberculosis

Lung mononuclear phagocyte (MNP) subsets differ in their ability to restrict Mycobacterium tuberculosis (Mtb) during chronic infection, yet the mechanisms underlying this difference are not well defined. Here, we show that CD11clo monocyte-derived cells (MNC1), the subset of lung cells that is most permissive for Mtb viability during chronic infection, express lower levels of interferon-gamma (IFN{gamma}) signaling proteins, resulting in reduced responses to IFN{gamma} compared to alveolar macrophages (AM) and CD11chi MNC2. Moreover, type I IFN signaling suppresses IFN{gamma}-mediated MHC-II expression, impairing antigen-specific CD4 T cell activation by MNC1 cells. Importantly, prior immunity conferred by contained Mtb infection enhances IFN{gamma} responsiveness of monocyte-derived cells, reducing bacterial burdens in lungs and within MNC subsets. Our findings indicate that heterogeneous IFN{gamma} responsiveness is exploited by Mtb for persistence in vivo. Overcoming or bypassing impaired IFN{gamma} responsiveness may guide the development of more effective TB vaccines and host-directed therapies.

immunology↗

A Mycobacterium tuberculosis rare variable antigen vaccine reduces lung pathology without affecting bacterial burdens

Mycobacterium tuberculosis is the leading cause of death globally due to a single infectious agent. Currently, no reliable vaccine against pulmonary tuberculosis, the primary adult disease caused by Mtb infection, exists. CD4 T cells are essential in protection against Mtb infection and inducing a protective CD4 T cell response remains the goal of most Mtb vaccines currently in testing. However, most Mtb T cell antigens do not exhibit antigenic variation, suggesting that T cell recognition does not drive selection of escape mutants. We utilized a set of antigens that do exhibit sequence diversity within human T cell epitopes and tested the impact of vaccination with these rare variable antigens (RVMA) using a DNA vaccine platform. We found vaccination with RVMA significantly alters the immune response to Mtb infection in both C57BL/6 and hypersusceptible SP140-/- mice without reducing bacterial burdens. RVMA vaccination of hypersusceptible SP140-/- animals prevented necrosis and altered the lesion composition reducing tissue damage and increasing CD4 T cell distribution. Reductions in pathology were associated with increases in ROR{gamma}t-expressing CD4 T cells and decreases in monocyte-derived cells in the lungs prior to the development of necrotic lesions. These results suggest T cell responses to certain antigens may be involved in preventing pathology without significantly changing bacterial burdens. SignificanceMtb is the leading cause of death worldwide due to an infectious agent, a title it has held for most of human history. Despite significant efforts, an effective vaccine that prevents the morbidity associated with pulmonary tuberculosis, the most prevalent form of adult TB disease, has yet to be developed. A lack of correlates of protection and ideal antigen targets have hampered the development of a subunit vaccine. Mtb is unique in that the CD4 T cell epitope sequences of Mtb are predominantly under purifying selection. Targeting antigens that are an exception to this T cell epitope sequence conservation can inform our understanding of what the most optimal antigens are for inclusion in an effective vaccine against Mtb. Our study describes the effects of a vaccine consisting solely of antigens that exhibit epitope sequence diversity on the outcome of infection and identifies possible benefits to lung pathology. Given the ongoing interest in prevention of disease (POD) vaccines for TB, these results can inform future vaccine design and the search for correlates of protection.

immunology↗

Tissue-wide profiling of human lungs reveals spatial sequestration of macrophages in tuberculosis

The immune response to human tuberculosis (TB), particularly in the context of complex lung pathology, remains incompletely understood. Here, we employed whole-slide spatial proteomics to map immune cell organization in TB-affected human lung tissues. Our analysis revealed pronounced spatial segregation of major immune cell populations in non-necrotizing TB lesions. At the tissue level, macrophages and lymphocytes formed distinct cellular communities associated with specific pathological features. At the lesion level, macrophages and B cells showed an inverse relationship in both abundance and spatial distribution. Proinflammatory T cells preferentially accumulated in macrophage-rich lesions but remained largely separated from macrophages. Interestingly, lesions exhibiting clear segregation between T cells and macrophages were more common in subclinical TB than in active disease. These findings suggest that spatial isolation of macrophages from effector lymphocytes may help temper inflammation and potentially prevent lesion progression to necrosis, while also enabling immune evasion by Mycobacterium tuberculosis. One Sentence SummaryXiao et al. reveal spatial segregation of immune cells in TB-lung tissue and link the microenvironmental dynamics to disease states of tuberculosis.

immunology↗

CCR2 recruits monocytes to the lung, while CX3CR1 modulates positioning of monocyte-derived CD11cpos cells in the lymph node during pulmonary tuberculosis

Infection by Mycobacterium tuberculosis (Mtb) continues to cause more than 1 million deaths annually, due to pathogen persistence in lung macrophages and dendritic cells derived from blood monocytes. While accumulation of monocyte-derived cells in the Mtb-infected lung partially depends on the chemokine receptor CCR2, the other chemoattractant receptors regulating trafficking remain undefined. We used mice expressing knock-in/knockout reporter alleles of Ccr2 and Cx3cr1 to interrogate their expression and function in monocyte-derived populations of the lungs and draining mediastinal lymph nodes during Mtb infection. CCR2 and CX3CR1 expression varied across monocyte-derived subsets stratified by cell surface Ly6C expression in both organs. We found that expression of CCR2 predicted dependence of monocyte-derived cells on the receptor for lung and lymph node accumulation. CCR2-deficient mice were also observed to have worsened lung and lymph node Mtb burden. While CX3CR1 deficiency, alone or in combination with CCR2 deficiency, did not affect cell frequencies or lung Mtb control, its absence was associated with altered positioning of monocyte-derived dendritic cells in mediastinal lymph nodes. We found that combined loss of Ccr2 and Cx3cr1 also worsened Mtb control in the mediastinal lymph node, suggesting a rationale for the persistent expression of CX3CR1 among monocyte-derived cells in pulmonary tuberculosis. IMPORTANCEMycobacterium tuberculosis is the respiratory pathogen responsible for the deadliest infectious disease worldwide. Susceptible humans exhibit ineffective immune responses, in which infected phagocytes are not able to eliminate the pathogen. Since recruited monocyte-derived cells serve as reservoirs for persistent infection, understanding how these phagocytes accumulate in the lung and why they are unable to eliminate Mtb can inform development of therapies that can synergize with antimicrobials to achieve faster and more durable Mtb elimination. Monocyte-derived cells express the chemokine receptors CCR2 and CX3CR1, but the role of the latter in Mtb infection remains poorly defined. The significance of our study is in elucidating the roles of these receptors in the trafficking of monocyte-derived cells in the infected lung and mediastinal lymph node. These data shed light on the host response in tuberculosis and in other pulmonary infections.

immunology↗

Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages

Crosstalk between autophagy, host cell death, and inflammatory host responses to bacterial pathogens enables effective innate immune responses that limit bacterial growth while minimizing coincidental host damage. Mycobacterium tuberculosis (Mtb) thwarts innate immune defense mechanisms in alveolar macrophages (AMs) during the initial stages of infection and in recruited bone marrow-derived cells during later stages of infection. However, how protective inflammatory responses are achieved during Mtb infection and the variation of the response in different macrophage subtypes remain obscure. Here, we show that the autophagy receptor Tax1bp1 plays a critical role in enhancing inflammatory cytokine production and increasing the susceptibility of mice to Mtb infection. Surprisingly, although Tax1bp1 restricts Mtb growth during infection of bone marrow-derived macrophages (BMDMs) (Budzik et al. 2020) and terminates cytokine production in response to cytokine stimulation or viral infection, Tax1bp1 instead promotes Mtb growth in AMs, neutrophils, and a subset of recruited monocyte-derived cells from the bone marrow. Tax1bp1 also leads to increases in bacterial growth and inflammatory responses during infection of mice with Listeria monocytogenes, an intracellular pathogen that is not effectively targeted to canonical autophagy. In Mtb-infected AMs but not BMDMs, Tax1bp1 enhances necrotic-like cell death early after infection, reprogramming the mode of host cell death to favor Mtb replication in AMs. Tax1bp1s impact on host cell death is a mechanism that explains Tax1bp1s cell type-specific role in the control of Mtb growth. Similar to Tax1bp1-deficiency in AMs, the expression of phosphosite-deficient Tax1bp1 restricts Mtb growth. Together, these results show that Tax1bp1 plays a crucial role in linking the regulation of autophagy, cell death, and pro-inflammatory host responses and enhancing susceptibility to bacterial infection. Author SummaryAlthough macrophages are the first innate immune cells to encounter Mycobacterium tuberculosis during infection, M. tuberculosis has evolved the ability to persist in them. Recent studies highlight that some types of macrophages are more permissive to M. tuberculosis replication and survival than others, but the mechanisms for cell type-specific differences in M. tuberculosis growth are only beginning to be understood. We found that the host factor, Tax1bp1 (Tax-1 binding protein 1), supports M. tuberculosis growth during animal infection and in specific subsets of innate immune cells, including alveolar macrophages while restricting M. tuberculosis in bone marrow-derived macrophages. We also found that Tax1bp1 has a similar phenotype in enhancing the pathogenesis of another intracellular pathogen, Listeria monocytogenes. Compared to bone marrow-derived macrophages, in alveolar macrophages, Tax1bp1 enhances the release of inflammatory mediators and leads to necrotic-like host cell death, which is known to enhance M. tuberculosis growth. Phosphorylation of Tax1bp1 in alveolar macrophages promotes M. tuberculosis growth. Our research highlights that Tax1bp1 is a host target for host-directed therapy against M. tuberculosis and controls host responses to M. tuberculosis in a cell type-specific manner.

microbiology↗

Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis

Immunity to Mycobacterium tuberculosis (Mtb), like many pathogens, is encoded jointly by the antigen specificities and functions of responding CD4 T cells. However, these features span a large two-dimensional possibility space - defined on one axis by the Mtb proteome, and on the other by the T cell transcriptome - that exceeds the dimensionality of existing technologies. Here we present an approach ("CRESTA") that combines highly-multiplexed DNA-barcoded epitope probes, single cell sequencing, and clonal analysis of T Cell Receptors (TCRs) to robustly detect rare antigen-specific CD4 T cells across hundreds of epitopes simultaneously and reveal their transcriptome-wide phenotypes. By comprehensively assaying known epitopes in Mtb-infected participants, we reveal polyclonal and multi-epitope responses across a spectrum of differentiation states, uncover previously-unobserved phenotypic diversity within and between epitopes, and increase the total number of known Mtb epitope-mapped TCR:{beta}s by [~]8-fold. We expect CRESTA to enable high-dimensional analyses of CD4 T cell responses in various settings, including infection, cancer, autoimmunity and allergy.

immunology↗

Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restriction.

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a leading cause of death by an infectious disease globally, with no efficacious vaccine. Antibodies are implicated in Mtb control, but the mechanisms of antibody action remain poorly understood. We assembled a library of TB monoclonal antibodies (mAb) and screened for the ability to restrict Mtb in mice, identifying protective antibodies targeting known and novel antigens. To dissect the mechanism of mAb-mediated Mtb restriction, we optimized a protective lipoarabinomannan-specific mAb through Fc-swapping. In vivo analysis of these Fc-variants revealed a critical role for Fc-effector function in Mtb restriction. Restrictive Fc-variants altered distribution of Mtb across innate immune cells. Single-cell transcriptomics highlighted distinctly activated molecular circuitry within innate immune cell subpopulations, highlighting early activation of neutrophils as a key signature of mAb-mediated Mtb restriction. Therefore, improved antibody-mediated restriction of Mtb is associated with reorganization of the tissue-level immune response to infection and depends on the collaboration of antibody Fab and Fc.

immunology↗

Immunopeptidomics informs discovery and delivery of Mycobacterium tuberculosis MHC-II antigens for vaccine design

No currently licensed vaccine reliably prevents pulmonary tuberculosis (TB), a leading cause of infectious disease mortality. Developing effective new vaccines will require identifying which of the roughly 4000 proteins in the Mycobacterium tuberculosis (Mtb) proteome are presented on MHC class II (MHC-II) by infected human phagocytes and can be recognized by CD4+ T cells to mediate protective immunity. Vaccines must also elicit T cell responses recognizing the same peptide-MHC complexes presented by infected cells, and successful presentation of target human MHC-II peptides is currently challenging to evaluate and optimize. Here, we define antigenic targets for TB vaccine development by using mass spectrometry (MS) for proteome-wide discovery of Mtb epitopes presented on MHC-II by infected human cells. We next iteratively design and evaluate candidate mRNA vaccine immunogens, revealing design principles that enhance presentation of target MHC-II peptides. Our results will inform the development of new TB vaccine candidates.

microbiology↗

Rare Variable M. tuberculosis Antigens induce predominant Th17 responses in human infection

CD4 T cells are essential for immunity to M. tuberculosis (Mtb), and emerging evidence indicates that IL-17-producing Th17 cells contribute to immunity to Mtb. While identifying protective T cell effector functions is important for TB vaccine design, T cell antigen specificity is also likely to be important. To identify antigens that induce protective immunity, we reasoned that as in other pathogens, effective immune recognition drives sequence diversity in individual Mtb antigens. We previously identified Mtb genes under evolutionary diversifying selection pressure whose products we term Rare Variable Mtb Antigens (RVMA). Here, in two distinct human cohorts with recent exposure to TB, we found that RVMA preferentially induce CD4 T cells that express RoR{gamma}t and produce IL-17, in contrast to classical Mtb antigens that induce T cells that produce IFN{gamma}. Our results suggest that RVMA can be valuable antigens in vaccines for those already infected with Mtb to amplify existing antigen-specific Th17 responses to prevent TB disease.

immunology↗

Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during persistent infection

Mycobacterium tuberculosis (Mtb) infects cells in multiple lung myeloid cell subsets and causes chronic infection despite innate and adaptive immune responses. However, the mechanisms allowing Mtb to evade elimination are not fully understood. Here, using new methods, we determined that after T cell responses have developed, CD11clo monocyte-derived lung cells termed MNC1 (mononuclear cell subset 1), harbor more live Mtb compared to alveolar macrophages (AM), neutrophils, and less permissive CD11chi MNC2. Bulk RNA sequencing of sorted cells revealed that the lysosome biogenesis pathway is underexpressed in MNC1. Functional assays confirmed that Mtb-permissive MNC1 have less lysosome content, acidification, and proteolytic activity than AM, and less nuclear TFEB, a master regulator of lysosome biogenesis. Mtb infection does not drive lysosome deficiency in MNC1 in vivo. Instead, Mtb recruits MNC1 and MNC2 to the lungs for its spread from AM to these cell subsets as a virulence mechanism that requires the Mtb ESX-1 secretion system. The c-Abl tyrosine kinase inhibitor nilotinib activates TFEB and enhances lysosome function of primary macrophages in vitro and MNC1 and MNC2 in vivo, improving control of Mtb infection. Our results indicate that Mtb exploits lysosome-poor monocyte-derived cells for in vivo persistence, suggesting a potential target for host-directed tuberculosis therapy. One Sentence SummaryVirulent Mtb recruits and exploits intrinsically lysosome-deficient lung mononuclear cell subsets to resist elimination during chronic infection.

immunology↗

M. tuberculosis antigen-responsive IL17+ CD4 T cells are disproportionately spared in ART-suppressed HIV

BackgroundInterleukin 17 producing CD4 T cells contribute to the control of Mycobacterium tuberculosis (Mtb) infection in humans; whether infection with Human Immunodeficiency Virus (HIV) disproportionately affects distinct Th17 cell subsets that respond to Mtb is incompletely defined. MethodsWe performed high-definition characterization of circulating Mtb-specific Th17 cells by spectral flow cytometry in people with latent TB and treated HIV (HIV-ART). We also measured kynurenine pathway activity by LC/MS on plasma and tested the hypothesis that tryptophan catabolism influences Th17 cell frequencies in this context. ResultsWe identified two subsets of Th17 cells: subset 1 defined as CD4+V7.2-CD161+CD26+ and subset 2 defined as CD4+V7.2-CCR6+CXCR3- cells of which subset 1 was significantly reduced in LTBI with HIV-ART, yet Mtb-responsive IL17-producing CD4 T cells were preserved; we found that IL17-producing CD4 T cells dominate the response to Mtb antigen but not CMV antigen or staphylococcal enterotoxin B (SEB); and tryptophan catabolism negatively correlates with both subset 1 and subset 2 Th17 cell frequencies. ConclusionsWe found differential effects of ART-suppressed HIV on distinct subsets of Th17 cells, that IL17-producing CD4 T cells dominate responses to Mtb but not CMV antigen or SEB, and that kynurenine pathway activity is associated with decreases of circulating Th17 cells that may contribute to tuberculosis immunity.

immunology↗

Spatial mapping of human lung tissue reveals granuloma diversity and histopathological superstructure in tuberculosis

The histopathological hallmark of tuberculosis (TB) is the formation of immune cell enriched aggregates called granulomas, but the scope of granuloma heterogeneity in human TB is unknown. By spatially mapping individual immune cells across large regions of TB lung tissue, we report that in addition to necrotizing granulomas, the human TB lung contains abundant non-necrotizing leukocyte aggregates surrounding areas of necrotizing tissue. These cellular lesions were more diverse in composition than necrotizing lesions and could be stratified into four general classes based on cellular composition and spatial distribution of B cells and macrophages, indicating there are foci of distinct immune reactions adjacent to necrotizing granulomas. We further show that the specific cellular composition of non-necrotizing structures correlates with their proximity to necrotizing lesions. Together, our study shows that during tuberculosis diseased lung tissue develops a histopathological superstructure comprising at least four different types of non-necrotizing cellular aggregates organized as satellites of necrotizing granulomas.

immunology↗

Towards comprehensive plasma proteomics by orthogonal protease digestion

Rapid and consistent protein identification across large clinical cohorts is an important goal for clinical proteomics. With the development of data-independent technologies (DIA/SWATH-MS), it is now possible to analyze hundreds of samples with great reproducibility and quantitative accuracy. However, this technology benefits from empirically derived spectral libraries that define the detectable set of peptides and proteins. Here we apply a simple and accessible tip-based workflow for the generation of spectral libraries to provide a comprehensive overview on the plasma proteome in individuals with and without active tuberculosis (TB). To boost protein coverage, we utilized non-conventional proteases such as GluC and AspN together with the gold standard trypsin, identifying more than 30,000 peptides mapping to 3,309 proteins. Application of this library to quantify plasma proteome differences in TB infection recovered more than 400 proteins in 50 minutes of MS-acquisition, including diagnostic Mycobacterium tuberculosis (Mtb) proteins that have previously been detectable primarily by antibody-based assays and intracellular proteins not previously described to be in plasma.

systems biology↗

Efficient Generation of Isogenic Primary Human Myeloid Cells using CRISPR-Cas9 Ribonucleoproteins

Genome engineering of primary human cells with CRISPR-Cas9 has revolutionized experimental and therapeutic approaches to cell biology, but human myeloid-lineage cells have remained largely genetically intractable. We present a method for delivery of CRISPR-Cas9 ribonucleoprotein (RNP) complexes by nucleofection directly into CD14+ human monocytes purified from peripheral blood, leading to high rates of precise gene knockout. These cells can be efficiently differentiated into monocyte-derived macrophages or dendritic cells. This process yields genetically-edited cells that retain critical markers of both myeloid differentiation and phagocytic function. Genetic ablation of the restriction factor SAMHD1 increased HIV-1 infection more than fifty-fold, demonstrating the power of this system for genotype-phenotype interrogation. This fast, flexible and scalable platform can be used for genetic studies of human myeloid cells in immune signaling, inflammation, cancer immunology, host-pathogen interactions, and beyond, and could facilitate development of novel myeloid cellular therapies.

genetics↗

Mononuclear cell dynamics in M. tuberculosis infection provide opportunities for therapeutic intervention

Mycobacterium tuberculosis causes chronic infection of mononuclear phagocytes, especially resident (alveolar) macrophages, recruited macrophages, and dendritic cells. Despite the importance of these cells in tuberculosis (TB) pathogenesis and immunity, little is known about the population dynamics of these cells at the sites of infection. We used a combination of congenic monocyte adoptive transfer, and pulse-chase labeling of DNA, to determine the kinetics and characteristics of trafficking, differentiation, and infection of mononuclear phagocytes during the chronic, adaptive immune phase of M. tuberculosis infection in mice. We found that Ly6Chi monocytes traffic rapidly to the lungs, where a subpopulation become Ly6Clo and remain in the lung vascular space, while the remainder migrate into the lung parenchyma and differentiate into Ly6Chi dendritic cells, CD11b+ dendritic cells, and recruited macrophages. As in humans with TB, M. tuberculosis-infected mice have increased numbers of blood monocytes; this is due to increased egress from the bone marrow, and not delayed egress from the blood. Pulse-chase labeling of dividing cells and flow cytometry analysis revealed a T1/2 of [~]15 hrs for Ly6Chi monocytes, indicating that they differentiate rapidly upon entry to the parenchyma of infected lungs; in contrast, cells that differentiate from Ly6Chi monocytes turn over more slowly, but diminish in frequency in less than one week. New cells (identified by pulse-chase labeling) acquire bacteria within 1-3 days of appearance in the lungs, indicating that bacteria regularly encounter new cellular niches, even during the chronic stage of infection. Our findings that mononuclear phagocyte populations at the site of M. tuberculosis infection are highly dynamic provide support for specific approaches for host-directed therapies directed at monocytes, including trained immunity, as potential interventions in TB, by replacing cells with limited antimycobacterial capabilities with newly-recruited cells better able to restrict and kill M. tuberculosis.\n\nAuthor summaryDuring certain chronic infections such as tuberculosis, inflammatory cells, including macrophages and dendritic cells, are recruited to infected tissues where they aggregate to form tissue lesions known as granulomas. Although granulomas can persist long term, the dynamics of the cell populations that comprise granulomas are not well understood. We used a combination of methods to discover that, during chronic infection of mice with Mycobacterium tuberculosis, the monocyte, macrophage, and dendritic cell populations are highly dynamic: recently-proliferated cells traffic rapidly to infected lung tissues, yet they persist with a half-life of less than one week. We also found that recently-proliferated cells become infected with M. tuberculosis as soon as one day after their arrival in the lungs, indicating that the bacteria are regularly moving to new cellular niches, even during the chronic stage of infection. The dynamic nature of the cell populations that encounter M. tuberculosis suggests that interventions such as trained immunity have potential therapeutic roles, by replacing cells that have poor antimycobacterial activity with cells with enhanced antimycobacterial activity. These interventions could improve the outcomes of treatment of drug resistant tuberculosis.

immunology↗