The Innate Immune Database (IIDB)

<p>Abstract</p> <p>Background</p> <p>As part of a National Institute of Allergy and Infectious Diseases funded collaborative project, we have performed over 150 microarray experiments measuring the response of C57/BL6 mouse bone marrow macrophages to toll-like receptor stimuli. These microarray expression profiles are available freely from our project web site <url>http://www.innateImmunity-systemsbiology.org</url>. Here, we report the development of a database of computationally predicted transcription factor binding sites and related genomic features for a set of over 2000 murine immune genes of interest. Our database, which includes microarray co-expression clusters and a host of web-based query, analysis and visualization facilities, is available freely via the internet. It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens.</p> <p>Description</p> <p>We constructed a database indexed on genes and annotations of the immediate surrounding genomic regions. To facilitate both gene-specific and systems biology oriented research, our database provides the means to analyze individual genes or an entire genomic locus. Although our focus to-date has been on mammalian toll-like receptor signaling pathways, our database structure is not limited to this subject, and is intended to be broadly applicable to immunology. By focusing on selected immune-active genes, we were able to perform computationally intensive expression and sequence analyses that would currently be prohibitive if applied to the entire genome. Using six complementary computational algorithms and methodologies, we identified transcription factor binding sites based on the Position Weight Matrices available in TRANSFAC. For one example transcription factor (ATF3) for which experimental data is available, over 50% of our predicted binding sites coincide with genome-wide chromatin immnuopreciptation (ChIP-chip) results. Our database can be interrogated via a web interface. Genomic annotations and binding site predictions can be automatically viewed with a customized version of the Argo genome browser.</p> <p>Conclusion</p> <p>We present the Innate Immune Database (IIDB) as a community resource for immunologists interested in gene regulatory systems underlying innate responses to pathogens. The database website can be freely accessed at <url>http://db.systemsbiology.net/IIDB</url>.</p

A Systems Biology Approach to Infectious Disease Research: Innovating the Pathogen-Host Research Paradigm

The twentieth century was marked by extraordinary advances in our understanding of microbes and infectious disease, but pandemics remain, food and waterborne illnesses are frequent, multidrug-resistant microbes are on the rise, and the needed drugs and vaccines have not been developed. The scientific approaches of the past—including the intense focus on individual genes and proteins typical of molecular biology—have not been sufficient to address these challenges. The first decade of the twenty-first century has seen remarkable innovations in technology and computational methods. These new tools provide nearly comprehensive views of complex biological systems and can provide a correspondingly deeper understanding of pathogen-host interactions. To take full advantage of these innovations, the National Institute of Allergy and Infectious Diseases recently initiated the Systems Biology Program for Infectious Disease Research. As participants of the Systems Biology Program, we think that the time is at hand to redefine the pathogen-host research paradigm

Waveforms and Sonic Boom Perception and Response (WSPR): Low-Boom Community Response Program Pilot Test Design, Execution, and Analysis

The Waveforms and Sonic boom Perception and Response (WSPR) Program was designed to test and demonstrate the applicability and effectiveness of techniques to gather data relating human subjective response to multiple low-amplitude sonic booms. It was in essence a practice session for future wider scale testing on naive communities, using a purpose built low-boom demonstrator aircraft. The low-boom community response pilot experiment was conducted in California in November 2011. The WSPR team acquired sufficient data to assess and evaluate the effectiveness of the various physical and psychological data gathering techniques and analysis methods

Prognostic and Predictive Biomarkers in Patients With Coronavirus Disease 2019 Treated With Tocilizumab in a Randomized Controlled Trial

OBJECTIVES: To explore candidate prognostic and predictive biomarkers identified in retrospective observational studies (interleukin-6, C-reactive protein, lactate dehydrogenase, ferritin, lymphocytes, monocytes, neutrophils, d-dimer, and platelets) in patients with coronavirus disease 2019 pneumonia after treatment with tocilizumab, an anti-interleukin-6 receptor antibody, using data from the COVACTA trial in patients hospitalized with severe coronavirus disease 2019 pneumonia. DESIGN: Exploratory analysis from a multicenter, randomized, double-blind, placebo-controlled, phase 3 trial. SETTING: Hospitals in North America and Europe. PATIENTS: Adults hospitalized with severe coronavirus disease 2019 pneumonia receiving standard care. INTERVENTION: Randomly assigned 2:1 to IV tocilizumab 8 mg/kg or placebo. MEASUREMENTS AND MAIN RESULTS: Candidate biomarkers were measured in 295 patients in the tocilizumab arm and 142 patients in the placebo arm. Efficacy outcomes assessed were clinical status on a seven-category ordinal scale (1, discharge; 7, death), mortality, time to hospital discharge, and mechanical ventilation (if not receiving it at randomization) through day 28. Prognostic and predictive biomarkers were evaluated continuously with proportional odds, binomial or Fine-Gray models, and additional sensitivity analyses. Modeling in the placebo arm showed all candidate biomarkers except lactate dehydrogenase and d-dimer were strongly prognostic for day 28 clinical outcomes of mortality, mechanical ventilation, clinical status, and time to hospital discharge. Modeling in the tocilizumab arm showed a predictive value of ferritin for day 28 clinical outcomes of mortality (predictive interaction, p = 0.03), mechanical ventilation (predictive interaction, p = 0.01), and clinical status (predictive interaction, p = 0.02) compared with placebo. CONCLUSIONS: Multiple biomarkers prognostic for clinical outcomes were confirmed in COVACTA. Ferritin was identified as a predictive biomarker for the effects of tocilizumab in the COVACTA patient population; high ferritin levels were associated with better clinical outcomes for tocilizumab compared with placebo at day 28

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics

Macrophages are versatile immune cells that can detect a variety of pathogen-associated molecular patterns through their Toll-like receptors (TLRs). In response to microbial challenge, the TLR-stimulated macrophage undergoes an activation program controlled by a dynamically inducible transcriptional regulatory network. Mapping a complex mammalian transcriptional network poses significant challenges and requires the integration of multiple experimental data types. In this work, we inferred a transcriptional network underlying TLR-stimulated murine macrophage activation. Microarray-based expression profiling and transcription factor binding site motif scanning were used to infer a network of associations between transcription factor genes and clusters of co-expressed target genes. The time-lagged correlation was used to analyze temporal expression data in order to identify potential causal influences in the network. A novel statistical test was developed to assess the significance of the time-lagged correlation. Several associations in the resulting inferred network were validated using targeted ChIP-on-chip experiments. The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation

N-3 Polyunsaturated Fatty Acids and the Resolution of Neuroinflammation

In the past few decades, as a result of their anti-inflammatory properties, n-3 long chain polyunsaturated fatty acids (n-3 LC-PUFAs), have gained greater importance in the regulation of inflammation, especially in the central nervous system (in this case known as neuroinflammation). If sustained, neuroinflammation is a common denominator of neurological disorders, including Alzheimer's disease and major depression, and of aging. Hence, limiting neuroinflammation is a real strategy for neuroinflammatory disease therapy and treatment. Recent data show that n-3 LC-PUFAs exert anti-inflammatory properties in part through the synthesis of specialized pro-resolving mediators (SPMs) such as resolvins, maresins and protectins. These SPMs are crucially involved in the resolution of inflammation. They could be good candidates to resolve brain inflammation and to contribute to neuroprotective functions and could lead to novel therapeutics for brain inflammatory diseases. This review presents an overview 1) of brain n-3 LC-PUFAs as precursors of SPMs with an emphasis on the effect of n-3 PUFAs on neuroinflammation, 2) of the formation and action of SPMs in the brain and their biological roles, and the possible regulation of their synthesis by environmental factors such as inflammation and nutrition and, in particular, PUFA consumption

Dissecting macrophage responses to Salmonella Typhimurium infection

Salmonella Typhimurium infection of murine macrophages provides a robust model for studying host-pathogen interactions at a molecular level. Gene array hybridization studies identified changes in the expression of numerous genes not previously recognized to be involved in macrophage response to infection. An overlapping spectrum of genes was expressed in response to virulent S. Typhimurium and purified S. Typhimurium lipopolysaccharide, reinforcing the major role of this bacterial component in stimulating the early response of macrophages to bacterial infection. The infected macrophage gene expression profile was further altered by priming with interferon-γ, indicating that host cell responses depend on the activation state of the cell. These studies identified upregulated expression of MEK1 kinase in macrophages infected by S. Typhimurium, which correlated with increased MEK1 kinase activity during infection. As this kinase plays a key role in regulating macrophage signal transduction and antimicrobial activities, the functional role of MEK1 in Salmonella-infected macrophages was characterized. Inhibiting MEK kinase activity significantly increased intracellular bacterial numbers. In addition, while macrophages exert stress on intracellular Salmonella and impair bacterial cell division to result in long filamentous bacteria, there was a significant decrease in the number of filamentous Salmonella when MEK1 kinase activity was impaired. This filamentous bacterial morphology was also dependent on the production of reactive oxygen intermediates, which function in parallel to MEK signaling. Experiments were performed to characterize the macrophage effector mechanism(s) responsible for impairing the replication of this intracellular pathogen and the consequent bacterial filamentation. Antimicrobial peptides play an important role in the defense against extracellular infections, but the expression of cationic peptides within macrophages as an antibacterial effector mechanism against intracellular pathogens has not been demonstrated. Macrophages indeed express the antimicrobial peptide CRAMP, and this expression was increased following infection and was dependent on the macrophage's production of reactive oxygen intermediates. Studies using CRAMP-deficient mice or synthetic CRAMP peptide determined that CRAMP impairs Salmonella cell division in vivo and in vitro, resulting in long filamentous bacteria. This impaired bacterial cell division was also dependent on intracellular elastase-like serine protease activity, which can proteolytically activate antimicrobial peptides. A peptide-sensitive Salmonella mutant showed enhanced survival within macrophages derived from CRAMP-deficient mice, indicating that Salmonella can sense and respond to cationic peptides in the intracellular environment. Together, these results show that intracellular ROIs and proteases regulate macrophage CRAMP expression and activity to impair the replication of an intracellular bacterial pathogen. In summary, profiling of macrophage gene expression led to characterization of host signal transduction pathways necessary for impairing bacterial replication and the elucidation of novel antibacterial effector mechanisms. These data begin to address the complexity of interactions between macrophage signaling and effector mechanisms triggered by bacterial infection.Science, Faculty ofMicrobiology and Immunology, Department ofGraduat