The widespread application of next-generation sequencing technologies has revolutionized microbiome research by enabling high-throughput profiling of the genetic contents of microbial communities. ...How to analyze the resulting large complex datasets remains a key challenge in current microbiome studies. Over the past decade, powerful computational pipelines and robust protocols have been established to enable efficient raw data processing and annotation. The focus has shifted toward downstream statistical analysis and functional interpretation. Here, we introduce MicrobiomeAnalyst, a user-friendly tool that integrates recent progress in statistics and visualization techniques, coupled with novel knowledge bases, to enable comprehensive analysis of common data outputs produced from microbiome studies. MicrobiomeAnalyst contains four modules - the Marker Data Profiling module offers various options for community profiling, comparative analysis and functional prediction based on 16S rRNA marker gene data; the Shotgun Data Profiling module supports exploratory data analysis, functional profiling and metabolic network visualization of shotgun metagenomics or metatranscriptomics data; the Taxon Set Enrichment Analysis module helps interpret taxonomic signatures via enrichment analysis against >300 taxon sets manually curated from literature and public databases; finally, the Projection with Public Data module allows users to visually explore their data with a public reference data for pattern discovery and biological insights. MicrobiomeAnalyst is freely available at http://www.microbiomeanalyst.ca.
The dogma that adaptive immunity is the only arm of the immune response with memory capacity has been recently challenged by several studies demonstrating evidence for memory-like innate immune ...training. However, the underlying mechanisms and location for generating such innate memory responses in vivo remain unknown. Here, we show that access of Bacillus Calmette–Guérin (BCG) to the bone marrow (BM) changes the transcriptional landscape of hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs), leading to local cell expansion and enhanced myelopoiesis at the expense of lymphopoiesis. Importantly, BCG-educated HSCs generate epigenetically modified macrophages that provide significantly better protection against virulent M. tuberculosis infection than naïve macrophages. By using parabiotic and chimeric mice, as well as adoptive transfer approaches, we demonstrate that training of the monocyte/macrophage lineage via BCG-induced HSC reprogramming is sustainable in vivo. Our results indicate that targeting the HSC compartment provides a novel approach for vaccine development.
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•Access of BCG to the bone marrow expands HSCs and promotes myelopoiesis•BCG educates HSCs to generate trained monocytes/macrophages•BCG induces a unique epigenetic and transcriptomic signature in macrophages•BCG-trained macrophages are highly protective against pulmonary M. tuberculosis infection
BCG induces trained immunity through education of hematopoietic stem cells.
Interleukin (IL)-4 is the quintessential T helper type 2 (Th2) cytokine produced by CD4(+) T cells in response to helminth infection. IL-4 not only promotes the differentiation of Th2 cells but is ...also critical for immunoglobulin (Ig) G1 and IgE isotype-switched antibody responses. Despite the IL-4-mediated link between Th2 cells and B lymphocytes, the location of IL-4-producing T cells in the lymph nodes is currently unclear. Using IL-4 dual reporter mice, we examined the Th2 response and IL-4 production in the draining mesenteric lymph nodes during infection with the enteric nematode Heligmosomoides polygyrus. We show that although IL-4-competent Th2 cells are found throughout the B and T cell areas, IL-4-producing Th2 cells are restricted to the B cell follicles and associate with germinal centers. Consistent with their localization, IL-4 producers express high levels of CXCR5, ICOS, PD-1, IL-21, and BCL-6, a phenotype characteristic of T follicular helper (Tfh) cells. Although IL-4 was dispensable for the generation of Th2 and Tfh cells, its deletion resulted in defective B cell expansion and maturation. Our report reveals the compartmentalization of Th2 priming and IL-4 production in the lymph nodes during infection, and identifies Tfh cells as the dominant source of IL-4 in vivo.
Highlights • The airways are constantly patrolled by alveolar macrophages. • Alveolar macrophages are indispensable for tissue homeostasis and host defense. • Alveolar macrophages are the major ...source of type I IFN following immune challenge. • Type I IFNs regulate antimicrobial and inflammatory responses of pulmonary macrophages. • Eicosanoids modulate type I IFN signaling and production following pathogen invasion.
Mature myeloid cells (macrophages and CD11b+ dendritic cells) form a prominent component of neuroinflammatory infiltrates in multiple sclerosis and experimental autoimmune encephalomyelitis (EAE). ...The mechanism by which these cells are replenished during relapsing and chronic neuroinflammation is poorly understood. Here we demonstrate that CD11b+CD62L+Ly6Chi monocytes with colony-forming potential are mobilized into the bloodstream by a granulocyte-macrophage colony-stimulating factor-dependent pathway immediately before EAE relapses. Circulating Ly6Chi monocytes traffic across the blood-brain barrier, up-regulate proinflammatory molecules, and differentiate into central nervous system dendritic cells and macrophages. Enrichment of Ly6Chi monocytes in the circulating pool is associated with an earlier onset and increased severity of clinical EAE. Our studies indicate that granulocyte-macrophage colony-stimulating factor–driven release of Ly6Chi precursors from the bone marrow prevents exhaustion of central nervous system myeloid populations during relapsing or chronic autoimmune demyelination, suggesting a novel pathway for therapeutic targeting.
Innate Lymphocytes in Psoriasis Polese, Barbara; Zhang, Hualin; Thurairajah, Bavanitha ...
Frontiers in immunology,
02/2020, Volume:
11
Journal Article, Web Resource
Peer reviewed
Open access
Skin is a fundamental component of our host defense system that provides a dynamic physical and chemical barrier against pathogen invasion and environmental insults. Cutaneous barrier function is ...mediated by complex interactions between structural cells such as keratinocytes and diverse lineages of immune cells. In contrast to the protective role of these intercellular interactions, uncontrolled immune activation can lead to keratinocyte dysfunction and psoriasis, a chronic inflammatory disease affecting 2% of the global population. Despite some differences between human and murine skin, animal models of psoriasiform inflammation have greatly informed clinical approaches to disease. These studies have helped to identify the interleukin (IL)-23-IL-17 axis as a central cytokine network that drives disease. In addition, they have led to the recent description of long-lived, skin-resident innate lymphocyte and lymphoid cells that accumulate in psoriatic lesions. Although not completely defined, these populations have both overlapping and unique functions compared to antigen-restricted αβ T lymphocytes, the latter of which are well-known to contribute to disease pathogenesis. In this review, we describe the diversity of innate lymphocytes and lymphoid cells found in mammalian skin with a special focus on αβ T cells, Natural Killer T cells and Innate Lymphoid cells. In addition, we discuss the effector functions of these unique leukocyte subsets and how each may contribute to different stages of psoriasis. A more complete understanding of these cell types that bridge the innate and adaptive immune system will hopefully lead to more targeted therapies that mitigate or prevent disease progression.
IgE production plays a crucial role in protective as well as pathogenic type 2 immune responses. Although the cytokine IL-4 is required for the development of IgE-producing plasma cells, the source ...of IL-4 and cellular requirements for optimal IgE responses remain unclear. Recent evidence suggests that T follicular helper (Tfh) cells are the primary producer of IL-4 in the reactive lymph node during type 2 immune responses. As Tfh cells are also required for the development of plasmablasts derived from germinal center and extrafollicular sources, we hypothesized that this cell subset is essential for the IgE plasmablast response. In this study, we show that during intestinal helminth infection, IL-4 derived from Tfh cells is required for IgE class switching and plasmablast formation. Notably, early IgE class switching did not require germinal center formation. Additionally, Tfh cell-derived IL-4 was required to maintain the Th2 response in the mesenteric lymph nodes of infected mice. Collectively, our results indicate that IL-4-producing Tfh cells are central orchestrators of the type 2 immune response in the reactive lymph nodes during parasitic helminth infection.
Parasitic helminths are among the most pervasive pathogens of the animal kingdom. To complete their life cycle, these intestinal worms migrate through host tissues causing significant damage in their ...wake. As a result, infection can lead to malnutrition, anemia and increased susceptibility to co-infection. Despite repeated deworming treatment, individuals living in endemic regions remain highly susceptible to re-infection by helminths, but rarely succumb to excessive tissue damage. The chronicity of infection and inability to resist numerous species of parasitic helminths that have co-evolved with their hosts over millenia suggests that mammals have developed mechanisms to tolerate this infectious disease. Distinct from resistance where the goal is to destroy and eliminate the pathogen, disease tolerance is an active process whereby immune and structural cells restrict tissue damage to maintain host fitness without directly affecting pathogen burden. Although disease tolerance is evolutionary conserved and has been well-described in plant systems, only recently has this mode of host defense, in its strictest sense, begun to be explored in mammals. In this review, we will examine the inter- and intracellular networks that support disease tolerance during enteric stages of parasitic helminth infection and why this alternative host defense strategy may have evolved to endure the presence of non-replicating pathogens and maintain the essential functions of the intestine.
Current treatments for tuberculosis (TB) are effective in controlling Mycobacterium tuberculosis (Mtb) growth, yet have significant side effects and do not prevent reinfection. Therefore, it is ...critical to understand why our host defense system is unable to generate permanent immunity to Mtb despite prolonged anti-tuberculosis therapy (ATT). Here, we demonstrate that treatment of mice with the most widely used anti-TB drugs, rifampicin (RIF) or isoniazid (INH) and pyrazinamide (PYZ), significantly altered the composition of the gut microbiota. Unexpectedly, treatment of mice with the pro-Mtb drugs INH and PYZ, but not RIF, prior to Mtb infection resulted in an increased bacterial burden, an effect that was reversible by fecal transplantation from untreated animals. Mechanistically, susceptibility of INH/PYZ-treated mice was associated with impaired metabolism of alveolar macrophages and defective bactericidal activity. Collectively, these data indicate that dysbiosis induced by ATT administered to millions of individuals worldwide may have adverse effects on the anti-Mtb response of alveolar macrophages.
...a fraction of TB patients (5% to 10%) still maintain a lifetime risk of developing active disease. ...Mtb has coevolved with humans to achieve an evolutionary trade-off that infrequently ...compromises host health for survival. By contrast, other studies have shown that helminth infection can be protective during the early stages of Mycobacterium bovis BCG infection 13. ...definitive data that these parasites promote progression from asymptomatic TB to active disease via T-cell immunomodulation are lacking. ...both have evolved mechanisms to modulate host immunity. In this Pearl, we suggest helminth-associated intestinal microbiota modulation as a potential mechanism underlying disease tolerance to Mtb infection or, at the very least, confound studies examining the impact of helminth infection on TB outcomes. ...investigating changes in the composition and/or functional output of the intestinal microbiota, with its far-reaching regulatory capacity (via immune suppression, metabolite processing, and niche competition), is needed to determine the relative contribution of diverse intestinal residents on Mtb infection.
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