Macrophages.com: an on-line community resource for innate immunity research

Stepwise target controllability identifies dysregulations of macrophage networks in multiple sclerosis

Identifying the nodes able to drive the state of a network is crucial to understand, and eventually control, biological systems. Despite recent advances, such identification remains difficult because of the huge number of equivalent controllable configurations, even in relatively simple networks. Based on the evidence that in many applications it is essential to test the ability of individual nodes to control a specific target subset, we develop a fast and principled method to identify controllable driver-target configurations in sparse and directed networks. We demonstrate our approach on simulated networks and experimental gene networks to characterize macrophage dysregulation in human subjects with multiple sclerosis.

Cardiac macrophage biology in the steady-state heart, the aging heart, and following myocardial infarction

Macrophages play critical roles in homeostatic maintenance of the myocardium under normal conditions and in tissue repair after injury. In the steady-state heart, resident cardiac macrophages remove senescent and dying cells and facilitate electrical conduction. In the aging heart, the shift in macrophage phenotype to a proinflammatory subtype leads to inflammaging. Following myocardial infarction (MI), macrophages recruited to the infarct produce both proinflammatory and anti-inflammatory mediators (cytokines, chemokines, matrix metalloproteinases, and growth factors), phagocytize dead cells, and promote angiogenesis and scar formation. These diverse properties are attributed to distinct macrophage subtypes and polarization status. Infarct macrophages exhibit a proinflammatory M1 phenotype early and become polarized toward an anti-inflammatory M2 phenotype later post-MI. Although this classification system is oversimplified and needs to be refined to accommodate the multiple different macrophage subtypes that have been recently identified, general concepts on macrophage roles are independent of subtype classification. This review summarizes current knowledge about cardiac macrophage origins, roles, and phenotypes in the steady state, with aging, and after MI, as well as highlights outstanding areas of investigation.

Transcriptional Regulation and Macrophage Differentiation

Monocytes and macrophages are professional phagocytes that occupy specific niches in every tissue of the body. Their survival, proliferation, and differentiation are controlled by signals from the macrophage colony-stimulating factor receptor (CSF-1R) and its two ligands, CSF-1 and interleukin-34. In this review, we address the developmental and transcriptional relationships between hematopoietic progenitor cells, blood monocytes, and tissue macrophages as well as the distinctions from dendritic cells. A huge repertoire of receptors allows monocytes, tissue-resident macrophages, or pathology-associated macrophages to adapt to specific microenvironments. These processes create a broad spectrum of macrophages with different functions and individual effector capacities. The production of large transcriptomic data sets in mouse, human, and other species provides new insights into the mechanisms that underlie macrophage functional plasticity.

Colony-stimulating factor-1-induced AIF1 expression in tumor-associated macrophages enhances the progression of hepatocellular carcinoma

M2-polarized (alternatively activated) macrophages play an important role in the progression of hepatocellular carcinoma (HCC). Allograft inflammatory factor 1 (AIF1) is overexpressed in M2-polarized macrophages. This study explored the role of AIF1 in tumor-associated macrophages in HCC. Macrophages were stimulated with colony-stimulating factor 1 (CSF1) to characterize the regulatory pathway of AIF1 in macrophages. The chromatin immunoprecipitation and luciferase reporter gene assay were conducted to examine transcription factors associated with AIF1 expression. AIF1 was down or upregulated, and the effects on tumor progression were evaluated by using in vitro and in vivo co-culture systems. A cytokine array was performed to screen the downstream functional components of AIF1. Tumor tissue from 206 patients with HCC were used to explore the clinical significance of AIF1. AIF1 induced a M2-like phenotype of macrophages. By facilitating the binding of c-Jun to the promoter of AIF1, CSF1 secreted from hepatoma cells increased AIF1 expression through the CSF1R-MEK1/2-Erk1/2-c-Jun axis. AIF1 expressed in macrophages promoted the migration of hepatoma cells in co-culture system of RAW264.7 and Hepa1-6 and tumor growth in an animal model. The cytokine array showed that CXCL16 was increased in RAW264.7 cells with overexpressed AIF1, leading to enhanced tumor cell migration. In human HCC tissue, AIF1-positive macrophages in the adjacent microenvironment was associated with microvascular invasion and advanced TNM stages and with patients' overall and disease-free survival (p = 0.002 for both). AIF1 expression in macrophages plays a pivotal role in the interaction between macrophages and hepatoma cells.

Ultrasonic-electrodeposition of PtPd alloy nanoparticles on ionic liquid-functionalized graphene paper: towards a flexible and versatile nanohybrid electrode

Here we fabricate a new type of flexible and versatile nanohybrid paper electrode by ultrasonic-electrodeposition of PtPd alloy nanoparticles on freestanding ionic liquid (IL)-functionalized graphene paper, and explore its multifunctional applications in electrochemical catalysis and sensing systems. The graphene-based paper materials demonstrate intrinsic flexibility, exceptional mechanical strength and high electrical conductivity, and therefore can serve as an ideal freestanding flexible electrode for electrochemical devices. Furthermore, the functionalization of graphene with IL (i.e., 1-butyl-3-methylimidazolium tetrafluoroborate) not only increases the electroactive surface area of a graphene-based nanohybrid paper electrode, but also improves the adhesion and dispersion of metal nanoparticles on the paper surface. These unique attributes, combined with the merits of an ultrasonic-electrodeposition method, lead to the formation of PtPd alloy nanoparticles on IL-graphene paper with high loading, uniform distribution, controlled morphology and favourable size. Consequently, the resultant nanohybrid paper electrode exhibits remarkable catalytic activity as well as excellent cycle stability and improved anti-poisoning ability towards electrooxidation of fuel molecules such as methanol and ethanol. Furthermore, for nonenzymatic electrochemical sensing of some specific biomarkers such as glucose and reactive oxygen species, the nanohybrid paper electrode shows high selectivity, sensitivity and biocompatibility in these bio-catalytic processes, and can be used for real-time tracking hydrogen peroxide secretion by living human cells. All these features demonstrate its promising application as a versatile nanohybrid electrode material in flexible and lightweight electrochemical energy conversion and biosensing systems such as bendable on-chip power sources, wearable/implantable detectors and in vivo micro-biosensors.

The macrophage and its role in inflammation and tissue repair: mathematical and systems biology approaches

Macrophages are central to the inflammatory response and its ability to resolve effectively. They are complex cells that adopt a range of subtypes depending on the tissue type and stimulus that they find themselves under. This flexibility allows them to play multiple, sometimes opposing, roles in inflammation and tissue repair. Their central role in the inflammatory process is reflected in macrophage dysfunction being implicated in chronic inflammation and poorly healing wounds. In this study, we discuss recent attempts to model mathematically and computationally the macrophage and how it partakes in the complex processes of inflammation and tissue repair. There are increasing data describing the variety of macrophage phenotypes and their underlying transcriptional programs. Dynamic mathematical and computational models are an ideal way to test biological hypotheses against experimental data and could aid in understanding this multi-functional cell and its potential role as an attractive therapeutic target for inflammatory conditions and tissue repair.

The Many Alternative Faces of Macrophage Activation

Monocytes and macrophages provide the first line of defense against pathogens. They also initiate acquired immunity by processing and presenting antigens and provide the downstream effector functions. Analysis of large gene expression datasets from multiple cells and tissues reveals sets of genes that are co-regulated with the transcription factors that regulate them. In macrophages, the gene clusters include lineage-specific genes, interferon-responsive genes, early inflammatory genes, and genes required for endocytosis and lysosome function. Macrophages enter tissues and alter their function to deal with a wide range of challenges related to development and organogenesis, tissue injury, malignancy, sterile, or pathogenic inflammatory stimuli. These stimuli alter the gene expression to produce "activated macrophages" that are better equipped to eliminate the cause of their influx and to restore homeostasis. Activation or polarization states of macrophages have been classified as "classical" and "alternative" or M1 and M2. These proposed states of cells are not supported by large-scale transcriptomic data, including macrophage-associated signatures from large cancer tissue datasets, where the supposed markers do not correlate with other. Individual macrophage cells differ markedly from each other, and change their functions in response to doses and combinations of agonists and time. The most studied macrophage activation response is the transcriptional cascade initiated by the TLR4 agonist lipopolysaccharide. This response is reviewed herein. The network topology is conserved across species, but genes within the transcriptional network evolve rapidly and differ between mouse and human. There is also considerable divergence in the sets of target genes between mouse strains, between individuals, and in other species such as pigs. The deluge of complex information related to macrophage activation can be accessed with new analytical tools and new databases that provide access for the non-expert.

Transcriptomic analysis of mononuclear phagocyte differentiation and activation

Monocytes and macrophages differentiate from progenitor cells under the influence of colony-stimulating factors. Genome-scale data have enabled the identification of the sets of genes that are associated with specific functions and the mechanisms by which thousands of genes are regulated in response to pathogen challenge. In large datasets, it is possible to identify large sets of genes that are coregulated with the transcription factors that regulate them. They include macrophage-specific genes, interferon-responsive genes, early inflammatory genes, and those associated with endocytosis. Such analyses can also extract macrophage-associated signatures from large cancer tissue datasets. However, cluster analysis provides no support for a signature that distinguishes macrophages from antigen-presenting dendritic cells, nor the classification of macrophage activation states as classical versus alternative, or M1 versus M2. Although there has been a focus on a small subset of lineage-enriched transcription factors, such as PU.1, more than half of the transcription factors in the genome can be expressed in macrophage lineage cells under some state of activation, and they interact in a complex network. The network architecture is conserved across species, but many of the target genes evolve rapidly and differ between mouse and human. The data and publication deluge related to macrophage biology require the development of new analytical tools and ways of presenting information in an accessible form.

Transcriptional programming of human macrophages: on the way to systems immunology

Many of the major common diseases such as atherosclerosis, diabetes, obesity, numerous autoimmune diseases, as well as neurodegenerative diseases such as Alzheimer's disease and many cancer types are characterised by a chronic inflammatory component termed sterile inflammation. Myeloid cells, particularly macrophages, are an important cellular component of chronic inflammation in these diseases. For almost all of these disease conditions, previous reports suggested that macrophages can exert either so-called pro-inflammatory or anti-inflammatory functions, thereby either fighting or feeding the disease. This apparent dichotomy of reactions of macrophages led to a dichotomous definition of macrophage activation classified as macrophage polarisation. However, analysis of large transcriptomics data derived from human and murine macrophages show that macrophage functions are shaped in a very tissue- and signal-input specific manner, allowing these cells to develop extremely specific functional programmes. Integrating global views on macrophage activation on the transcriptome, the epigenome, the proteome or the metabolome will finally lead to a data-driven approach to understand macrophage biology in context of major diseases. We are indeed on the way to a systems immunology approach that integrates -omics data with mathematical and bioinformatical modelling as the pre-requisite to generate data-driven hypotheses. This approach opens completely new avenues for the development of tailored diagnostics and therapies targeting macrophages in sterile inflammations of the major common diseases. I will also discuss some of the next developments that will be necessary to reach these important goals.

Immunomodulatory effect of an isolated fraction from Tinospora crispa on intracellular expression of INF-γ, IL-6 and IL-8

Background

Immunomodulators are substances that modify immune system response to a threat. Immunomodulators modulate and potentiate the immune system, keeping it highly prepared for any threat. The immunomodulatory effect of the traditional medicine Tinospora crispa is investigated in this work.

Methods

T. crispa ethanol extract was fractionated by using different solvents. The ethanol extract and effective isolated fraction were used to investigate the potential immunomodulatory effect of different T. crispa doses ranging from 25 μg/mL to 1000 μg/mL on RAW 246.7 cells by detecting intracellular INF-γ, IL-6, and IL-8 expressions. The antioxidant activity of T. crispa was evaluated through FRAP and DPPH. The total phenolic and total flavonoid contents were also quantified.

Results

Results show that T. crispa extract has higher antioxidant potential than ascorbic acid. The FRAP value of T. crispa extract is 11011.11 ± 1145.42 μmol Fe⁺²/g, and its DPPH inhibition percentage is 55.79 ± 7.9, with 22 μg/mL IC50. The results also reveal that the total phenolic content of T. crispa extract is 213.16- ± 1.31 mg GAE/g dry stem weight, and the total flavonoid content is 62.07- ± 39.76 mg QE/g dry stem weight. T. crispa crude extract and its isolated fraction significantly stimulate RAW264.7 cell viability (P ≤ 0.05) and intracellular INF-γ, IL-6, and IL-8 expressions. The results of LC-MS show that four of the active compounds detected in the T. crispa isolated fraction are cordioside, quercetin, eicosenoic acid (paullinic acid), and boldine.

Conclusions

The results of this study obviously indicate that T. crispa has immunomodulatory effects through the stimulation of INF-γ, IL-6, and IL-8 expressions. LC-MS phytochemical analysis showed that the T. crispa fraction has cordioside, quercetin, eicosenoic acid (paullinic acid), and boldine, which may be responsible for the immunostimulator effect of T. crispa.

Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro

Monocytes/macrophages are key players in all phases of physiological and pathological inflammation. To understanding the regulation of macrophage functional differentiation during inflammation, we designed an in vitro model that recapitulates the different phases of the reaction (recruitment, initiation, development, and resolution), based on human primary blood monocytes exposed to sequential changes in microenvironmental conditions. All reaction phases were profiled by transcriptomic microarray analysis. Distinct clusters of genes were identified that are differentially regulated through the different phases of inflammation. The gene sets defined by GSEA analysis revealed that the inflammatory phase was enriched in inflammatory pathways, while the resolution phase comprised pathways related to metabolism and gene rearrangement. By comparing gene clusters differentially expressed in monocytes vs. M1 and vs. M2 macrophages extracted from an in-house created meta-database, it was shown that cells in the model resemble M1 during the inflammatory phase and M2 during resolution. The validation of inflammatory and transcriptional factors by qPCR and ELISA confirmed the transcriptomic profiles in the different phases of inflammation. The accurate description of the development of the human inflammatory reaction provided by this in vitro kinetic model can help in identifying regulatory mechanisms in physiological conditions and during pathological derangements.

Systems biology of host-mycobiota interactions: dissecting Dectin-1 and Dectin-2 signalling in immune cells with DC-ATLAS

Modelling the networks sustaining the fruitful coexistence between fungi and their mammalian hosts is becoming increasingly important to control emerging fungal pathogens. The C-type lectins Dectin-1 and Dectin-2 are involved in host defense mechanisms against fungal infection driving inflammatory and adaptive immune responses and complement in containing fungal burdens. Recognizing carbohydrate structures in pathogens, their engagement induces maturation of dendritic cells (DCs) into potent immuno-stimulatory cells endowed with the capacity to efficiently prime T cells. Owing to these properties, Dectin-1 and Dectin-2 agonists are currently under investigation as promising adjuvants in vaccination procedures for the treatment of fungal infection. Thus, a detailed understanding of events' cascade specifically triggered in DCs upon engagement is of great interest in translational research. Here, we summarize the current knowledge on Dectin-1 and Dectin-2 signalling in DCs highlighting similarities and differences. Detailed maps are annotated, using the Biological Connection Markup Language (BCML) data model, and stored in DC-ATLAS, a versatile resource for the interpretation of high-throughput data generated perturbing the signalling network of DCs.

Transfusion-Related Acute Lung Injury: The Work of DAMPs

Current notions in immunology hold that not only pathogen-mediated tissue injury but any injury activates the innate immune system. In principle, this evolutionarily highly conserved, rapid first-line defense system responds to pathogen-induced injury with the creation of infectious inflammation, and non-pathogen-induced tissue injury with 'sterile' tissue inflammation. In this review, evidence has been collected in support of the notion that the transfusion-related acute lung injury induces a 'sterile' inflammation in the lung of transfused patients in terms of an acute innate inflammatory disease. The inflammatory response is mediated by the patient's innate immune cells including lung-passing neutrophils and pulmonary endothelial cells, which are equipped with pattern recognition receptors. These receptors are able to sense injury-induced, damage-associated molecular patterns (DAMPs) generated during collection, processing, and storage of blood/blood components. The recognition process leads to activation of these innate cells. A critical role for a protein complex known as the NLRP3 inflammasome has been suggested to be at the center of such a scenario. This complex undergoes an initial 'priming' step mediated by 1 class of DAMPs and then an 'activating' step mediated by another class of DAMPs to activate interleukin-1beta and interleukin-18. These 2 cytokines then promote, via transactivation, the formation of lung inflammation.

Plenary perspective: the complexity of constitutive and inducible gene expression in mononuclear phagocytes

Monocytes and macrophages differentiate from progenitor cells under the influence of colony-stimulating factors. Genome-scale data have enabled the identification of the set of genes that distinguishes macrophages from other cell types and the ways in which thousands of genes are regulated in response to pathogen challenge. Although there has been a focus on a small subset of lineage-enriched transcription factors, such as PU.1, more than one-half of the transcription factors in the genome can be expressed in macrophage lineage cells under some state of activation, and they interact in a complex network. The network architecture is conserved across species, but many of the target genes evolve rapidly and differ between mouse and human. The data and publication deluge related to macrophage biology require the development of new analytical tools and ways of presenting information in an accessible form.

Systems biology approaches to toll-like receptor signaling

Toll-like receptor (TLR) signaling pathways constitute an evolutionarily conserved host defense system that protects against a broad range of infectious agents. Modeling of TLR signaling has been carried out at several levels. Structural models of TLRs and their adaptors, which utilize a small number of structural domains to recognize a diverse range of pathogens, provide a starting point for understanding how pathogens are recognized and signaling events initiated. Various experimental and computational techniques have been used to construct models of downstream signal transduction networks from the measurements of gene expression and chromatin structure under resting and perturbed conditions along with predicted regulatory sequence motifs. Although a complete and accurate mathematical model of all TLR signaling pathways has yet to be derived, many important modules have been identified and investigated, enhancing our understanding of innate immune responses. Extensions of these models based on emerging experimental techniques are discussed. © 2012 Wiley Periodicals, Inc.