Irah L. King

Alveolar macrophages and type I IFN in airway homeostasis and immunity.

Globally, respiratory infections cause more than 4 million deaths per year, with influenza and tuberculosis (TB) in particular being major causes of mortality and morbidity. Although immune cell activation is critical for killing respiratory pathogens, this response must be tightly regulated to effectively control and eliminate invading microorganisms while minimizing immunopathology and maintaining pulmonary function. The distinct microenvironment of the lung is constantly patrolled by alveolar macrophages (Mφ), which are essential for tissue homeostasis, early pathogen recognition, initiation of the local immune response, and resolution of inflammation. Here, we focus on recent advances that have provided insight into the relation between pulmonary Mφ, type I interferon (IFN) signaling, and the delicate balance between protective and pathological immune responses in the lung.

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

Abstract 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.

Annexin1 regulates DC efferocytosis and cross-presentation during Mycobacterium tuberculosis infection

The phagocytosis of apoptotic cells and associated vesicles (efferocytosis) by DCs is an important mechanism for both self tolerance and host defense. Although some of the engulfment ligands involved in efferocytosis have been identified and studied in vitro, the contributions of these ligands in vivo remain ill defined. Here, we determined that during Mycobacterium tuberculosis (Mtb) infection, the engulfment ligand annexin1 is an important mediator in DC cross-presentation that increases efferocytosis in DCs and intrinsically enhances the capacity of the DC antigen-presenting machinery. Annexin1-deficient mice were highly susceptible to Mtb infection and showed an impaired Mtb antigen-specific CD8+ T cell response. Importantly, annexin1 expression was greatly downregulated in Mtb-infected human blood monocyte-derived DCs, indicating that reduction of annexin1 is a critical mechanism for immune evasion by Mtb. Collectively, these data indicate that annexin1 is essential in immunity to Mtb infection and mediates the power of DC efferocytosis and cross-presentation.

The Integrin LFA-1 Controls T Follicular Helper Cell Generation and Maintenance

T follicular helper (Tfh) cells are a CD4+ Txa0cell subset critical for long-lived humoral immunity. We hypothesized that integrins play a decisive role in Tfh cell biology. Here we show that Tfh cells expressed a highly active form of leukocyte function-associated antigen-1 (LFA-1) that was required for their survival within the germinal center niche. In addition, LFA-1 promoted expression of Bcl-6, a transcriptional repressor critical for Tfh cell differentiation, and inhibition of LFA-1 abolished Tfh cell generation and prevented protective humoral immunity to intestinal helminth infection. Furthermore, we demonstrated that expression of Talin-1, an adaptor protein that regulates LFA-1 affinity, dictated Tfh versus Th2 effector cell differentiation. Collectively, our results define unique functions for LFA-1 in the Tfh cell effector program and suggest that integrin activity is important in lineage decision-making events in the adaptive immune system.

Evolution of the Immune Response to Chronic Airway Colonization with Aspergillus fumigatus Hyphae

ABSTRACT Airway colonization by the mold Aspergillus fumigatus is common in patients with underlying lung disease and is associated with chronic airway inflammation. Studies probing the inflammatory response to colonization with A. fumigatus hyphae have been hampered by the lack of a model of chronic colonization in immunocompetent mice. By infecting mice intratracheally with conidia embedded in agar beads (Af beads), we have established an in vivo model to study the natural history of airway colonization with live A. fumigatus hyphae. Histopathological examination and galactomannan assay of lung homogenates demonstrated that hyphae exited beads and persisted in the lungs of mice up to 28 days postinfection without invasive disease. Fungal lesions within the airways were surrounded by a robust neutrophilic inflammatory reaction and peribronchial infiltration of lymphocytes. Whole-lung cytokine analysis from Af bead-infected mice revealed an increase in proinflammatory cytokines and chemokines early in infection. Evidence of a Th2 type response was observed only early in the course of colonization, including increased levels of interleukin-4 (IL-4), elevated IgE levels in serum, and a mild increase in airway responsiveness. Pulmonary T cell subset analysis during infection mirrored these results with an initial transient increase in IL-4-producing CD4+ T cells, followed by a rise in IL-17 and Foxp3+ cells by day 14. These results provide the first report of the evolution of the immune response to A. fumigatus hyphal colonization.

Lifelong memory responses perpetuate humoral TH2 immunity and anaphylaxis in patients with food allergy

Background: A number of food allergies (eg, fish, shellfish, and nuts) are lifelong, without any disease‐transforming therapies, and unclear in their underlying immunology. Clinical manifestations of food allergy are largely mediated by IgE. Although persistent IgE titers have been attributed conventionally to long‐lived IgE+ plasma cells (PCs), this has not been directly and comprehensively tested. Objective: We sought to evaluate mechanisms underlying persistent IgE and allergic responses to food allergens. Methods: We used a model of peanut allergy and anaphylaxis, various knockout mice, adoptive transfer experiments, and in vitro assays to identify mechanisms underlying persistent IgE humoral immunity over almost the entire lifespan of the mouse (18–20 months). Results: Contrary to conventional paradigms, our data show that clinically relevant lifelong IgE titers are not sustained by long‐lived IgE+ PCs. Instead, lifelong reactivity is conferred by allergen‐specific long‐lived memory B cells that replenish the IgE+ PC compartment. B‐cell reactivation requires allergen re‐exposure and IL‐4 production by CD4 T cells. We define the half‐lives of antigen‐specific germinal centers (23.3 days), IgE+ and IgG1+ PCs (60 and 234.4 days, respectively), and clinically relevant cell‐bound IgE (67.3 days). Conclusions: These findings can explain lifelong food allergies observed in human subjects as the consequence of allergen exposures that recurrently activate memory B cells and identify these as a therapeutic target with disease‐transforming potential.

Identification of mouse T follicular helper cells by flow cytometry.

T follicular helper (Tfh) cells are a subset of CD4(+) T cells that accumulate in the B cell-rich regions of secondary lymphoid organs and provide activation signals essential for long-lived humoral immunity. Herein, we describe a flow cytometric cell-based approach to identify Tfh cells within the total leukocyte population isolated from the spleen, lymph nodes, and Peyers patches of mice. This protocol focuses on markers that have established relevance in Tfh cell differentiation and function allowing its use across varied settings of infection and immunity.

Suppression of CYP1 members of the AHR response by pathogen-associated molecular patterns

The aryl hydrocarbon receptor (AHR) is a ligand‐activated transcription factor that triggers a broad response, which includes the regulation of proinflammatory cytokine production by monocytes and macrophages. AHR is negatively regulated by a set of genes that it transcriptionally activates, including the AHR repressor (Ahrr) and the cytochrome P450 1 (Cyp1) family, which are critical for preventing exacerbated AHR activity. An imbalance in these regulatory mechanisms has been shown to cause severe defects in lymphoid cells. Therefore, we wanted to assess how AHR activation is regulated in monocytes and macrophages in the context of innate immune responses induced by pathogen‐associated molecular patterns (PAMPs). We found that concomitant stimulation of primary human monocytes with PAMPs and the AHR agonist 6‐formylindolo(3,2‐b)carbazole (FICZ) led to a selective dose‐dependent inhibition of Cyp1 family members induction. Two other AHR‐dependent genes [Ahrr and NADPH quinone dehydrogenase 1 (Nqo1)] were not affected under these conditions, suggesting a split in the AHR regulation by PAMPs. This down‐regulation of Cyp1 family members did not require de novo protein production nor signaling through p38, ERK, or PI3K‐Akt‐mammalian target of rapamycin (mTOR) pathways. Furthermore, such a split regulation of the AHR response was more apparent in GM‐CSF‐derived macrophages, a finding corroborated at the functional level by decreased CYP1 activity and decreased proinflammatory cytokine production in response to FICZ and LPS. Collectively, our findings identify a role for pattern recognition receptor (PRR) signaling in regulating the AHR response through selective down‐regulation of Cyp1 expression in human monocytes and macrophages.

Lifelong memory responses perpetuate humoral TH2 immunity and anaphylaxis in food allergy

Background: A number of food allergies (eg, fish, shellfish, and nuts) are lifelong, without any disease‐transforming therapies, and unclear in their underlying immunology. Clinical manifestations of food allergy are largely mediated by IgE. Although persistent IgE titers have been attributed conventionally to long‐lived IgE+ plasma cells (PCs), this has not been directly and comprehensively tested. Objective: We sought to evaluate mechanisms underlying persistent IgE and allergic responses to food allergens. Methods: We used a model of peanut allergy and anaphylaxis, various knockout mice, adoptive transfer experiments, and in vitro assays to identify mechanisms underlying persistent IgE humoral immunity over almost the entire lifespan of the mouse (18–20 months). Results: Contrary to conventional paradigms, our data show that clinically relevant lifelong IgE titers are not sustained by long‐lived IgE+ PCs. Instead, lifelong reactivity is conferred by allergen‐specific long‐lived memory B cells that replenish the IgE+ PC compartment. B‐cell reactivation requires allergen re‐exposure and IL‐4 production by CD4 T cells. We define the half‐lives of antigen‐specific germinal centers (23.3 days), IgE+ and IgG1+ PCs (60 and 234.4 days, respectively), and clinically relevant cell‐bound IgE (67.3 days). Conclusions: These findings can explain lifelong food allergies observed in human subjects as the consequence of allergen exposures that recurrently activate memory B cells and identify these as a therapeutic target with disease‐transforming potential.

An introduction to the microbiome and MS

The human microbiota is composed of diverse forms of microorganisms that live on or in us and plays a crucial role in the health and development. Commensal species that reside in the intestine particularly influence host physiology at local and systemic levels. Multiple sclerosis (MS) is a debilitating autoimmune disorder of the central nervous system for which there is currently no cure. While the cause of MS is unknown, there is a growing body of evidence suggesting that the microbiota can play both pathogenic and protective roles in disease progression. In this review, we provide a brief overview, based on both animal and clinical studies, of the current understanding by which the microbiota may influence MS and discuss opportunities for therapeutic intervention that may alleviate the symptoms associated with this debilitating neuroimmunological disease.