Dual ligand stimulation of RAW 264.7 cells uncovers feedback mechanisms that regulate TLR-mediated gene expression

Nonadditive transcriptional change analysis identifies regulators for ginsenoside Rg3 to alleviate synergistic cytokine production in TLR2/3 dual-stimulated macrophages

Cytokine synergy induced by the activation of multiple Toll-like receptors (TLRs) may result in uncontrollable life-threatening inflammation, the so-called cytokine storm. Owing to the complexity of the crosstalk for individual TLR signaling pathways, analyses of transcriptional changes in addition to differentially expression genes (DEGs) are needed. In the present study, we aimed to create algorithms to obtain a profile of synergistic cytokine production and to evaluate the anti-cytokine synergistic activity of ginsenoside Rg3. RAW264.7 macrophages were activated by TLR2/3 dual ligands; Rg3 was used as an intervention. After interleukin (IL)-6 secretion was detected as a preliminary readout for cytokine synergy, RNA sequencing-based bioinformatic analysis was performed, followed by qPCR and western blotting verification. Specifically, nonadditive transcriptional responses (DIFs) were applied as a measure of synergistic genes, and an anti-synergy score was created as a measure of the antagonistic effect of Rg3. A mouse model of TLR2/3 costimulation was subsequently established to evaluate the anti-cytokine synergistic effect of Rg3 in vivo. The results show that Rg3 alleviates synergistic cytokine production both in vitro and in vivo. Nuclear factor kappa B (NF-κB) and interferon regulatory factor 3 (IRF3) are novel targets of Rg3 related to its anti-cytokine synergistic effects. Our strategy of nonadditive transcriptional change analysis will be helpful for performing high-throughput screening for drugs with anti-cytokine synergy activities.

A genome-wide screen uncovers multiple roles for mitochondrial nucleoside diphosphate kinase D in inflammasome activation

Noncanonical inflammasome activation by cytosolic lipopolysaccharide (LPS) is a critical component of the host response to Gram-negative bacteria. Cytosolic LPS recognition in macrophages is preceded by a Toll-like receptor (TLR) priming signal required to induce transcription of inflammasome components and facilitate the metabolic reprograming that fuels the inflammatory response. Using a genome-scale arrayed siRNA screen to find inflammasome regulators in mouse macrophages, we identified the mitochondrial enzyme nucleoside diphosphate kinase D (NDPK-D) as a regulator of both noncanonical and canonical inflammasomes. NDPK-D was required for both mitochondrial DNA synthesis and cardiolipin exposure on the mitochondrial surface in response to inflammasome priming signals mediated by TLRs, and macrophages deficient in NDPK-D had multiple defects in LPS-induced inflammasome activation. In addition, NDPK-D was required for the recruitment of TNF receptor-associated factor 6 (TRAF6) to mitochondria, which was critical for reactive oxygen species (ROS) production and the metabolic reprogramming that supported the TLR-induced gene program. NDPK-D knockout mice were protected from LPS-induced shock, consistent with decreased ROS production and attenuated glycolytic commitment during priming. Our findings suggest that, in response to microbial challenge, NDPK-D-dependent TRAF6 mitochondrial recruitment triggers an energetic fitness checkpoint required to engage and maintain the transcriptional program necessary for inflammasome activation.

Systematic Investigation of Multi-TLR Sensing Identifies Regulators of Sustained Gene Activation in Macrophages

A typical pathogen presents a combination of Toll-like receptor (TLR) ligands during infection. Although individual TLR pathways have been well characterized, the nature of this "combinatorial code" in pathogen sensing remains unclear. Here, we conducted a comprehensive transcriptomic analysis of primary macrophages stimulated with all possible pairwise combinations of four different TLR ligands to understand the requirements, kinetics, and outcome of combined pathway engagement. We find that signal integration between TLR pathways leads to non-additive responses for a subset of immune mediators with sustained expression (>6 hr) properties and T cell polarizing function. To identify the underlying regulators, we conducted a focused RNAi screen and identified four genes-Helz2, Phf11d, Sertad3, and Zscan12-which preferentially affect the late phase response of TLR-induced immune effector expression. This study reveals key molecular details of how contemporaneous signaling through multiple TLRs, as would often be the case with pathogen infection, produce biological outcomes distinct from the single ligands typically used to characterize TLR pathways.

Myeloid Cell Prostaglandin E2 Receptor EP4 Modulates Cytokine Production but Not Atherogenesis in a Mouse Model of Type 1 Diabetes

Type 1 diabetes mellitus (T1DM) is associated with cardiovascular complications induced by atherosclerosis. Prostaglandin E2 (PGE2) is often raised in states of inflammation, including diabetes, and regulates inflammatory processes. In myeloid cells, a key cell type in atherosclerosis, PGE2 acts predominately through its Prostaglandin E Receptor 4 (EP4; Ptger4) to modulate inflammation. The effect of PGE2-mediated EP4 signaling specifically in myeloid cells on atherosclerosis in the presence and absence of diabetes is unknown. Because diabetes promotes atherosclerosis through increased arterial myeloid cell accumulation, we generated a myeloid cell-targeted EP4-deficient mouse model (EP4M-/-) of T1DM-accelerated atherogenesis to investigate the relationship between myeloid cell EP4, inflammatory phenotypes of myeloid cells, and atherogenesis. Diabetic mice exhibited elevated plasma PGE metabolite levels and elevated Ptger4 mRNA in macrophages, as compared with non-diabetic littermates. PGE2 increased Il6, Il1b, Il23 and Ccr7 mRNA while reducing Tnfa mRNA through EP4 in isolated myeloid cells. Consistently, the stimulatory effect of diabetes on peritoneal macrophage Il6 was mediated by PGE2-EP4, while PGE2-EP4 suppressed the effect of diabetes on Tnfa in these cells. In addition, diabetes exerted effects independent of myeloid cell EP4, including a reduction in macrophage Ccr7 levels and increased early atherogenesis characterized by relative lesional macrophage accumulation. These studies suggest that this mouse model of T1DM is associated with increased myeloid cell PGE2-EP4 signaling, which is required for the stimulatory effect of diabetes on IL-6, markedly blunts the effect of diabetes on TNF-α and does not modulate diabetes-accelerated atherogenesis.

Stimulus-selective crosstalk via the NF-κB signaling system reinforces innate immune response to alleviate gut infection

Tissue microenvironment functions as an important determinant of the inflammatory response elicited by the resident cells. Yet, the underlying molecular mechanisms remain obscure. Our systems-level analyses identified a duration code that instructs stimulus specific crosstalk between TLR4-activated canonical NF-κB pathway and lymphotoxin-β receptor (LTβR) induced non-canonical NF-κB signaling. Indeed, LTβR costimulation synergistically enhanced the late RelA/NF-κB response to TLR4 prolonging NF-κB target gene-expressions. Concomitant LTβR signal targeted TLR4-induced newly synthesized p100, encoded by Nfkb2, for processing into p52 that not only neutralized p100 mediated inhibitions, but potently generated RelA:p52/NF-κB activity in a positive feedback loop. Finally, Nfkb2 connected lymphotoxin signal within the intestinal niche in reinforcing epithelial innate inflammatory RelA/NF-κB response to Citrobacter rodentium infection, while Nfkb2^−/− mice succumbed to gut infections owing to stromal defects. In sum, our results suggest that signal integration via the pleiotropic NF-κB system enables tissue microenvironment derived cues in calibrating physiological responses.

DOI:http://dx.doi.org/10.7554/eLife.05648.001

The innate immune system is the body's first line of defense against infection and disease. Innate immune cells are found in every tissue type, poised to respond immediately to damaged, stressed, or infected host cells. When innate immune cells recognize any injury or infection, one of the first things they do is trigger the inflammatory response. Fluid and other immune cells then move from the blood into the injured tissues. This movement can cause redness and swelling. But the response helps to establish a physical barrier against the spread of infection, promotes the elimination of both invading microbes and damaged host cells, and encourages the repair of the tissue.

Inflammation is tightly controlled. If the response is too weak, it could leave an individual prone to serious infection. On the other hand, excessive inflammation can severely damage healthy cells and tissues. Inflammation is regulated differently in different tissue types, and the environment within the tissue itself influences the activity of local innate immune cells and the inflammatory response. However, the molecular mechanisms responsible for receiving and interpreting the signals derived from the host tissue remain unknown.

Now, Banoth et al., have revealed that the integration of inflammation-provoking signals, such as injury or infection and cues from the tissue environment occurs via the so-called ‘NF-κB signaling system’. NF-κB is a protein found in almost all cell types, and when activated it is able to switch on the expression of many different genes. Banoth et al. explain that signal integration via the NF-κB system enables cues from the tissue environment to tune a cell's responses. Further experiments confirmed the importance of this signal integration by showing how a signal coming from intestinal tissue can influence the activity of innate immune cells and inflammation in the gut.

These findings suggest that a breakdown in the NF-κB signaling system's ability to integrate multiple signals, including those derived from the tissue environment, may be responsible for many inflammatory disorders, and in particular those that involve the gut. Future work is now needed to explore this possibility.

DOI:http://dx.doi.org/10.7554/eLife.05648.002

Combinatorial code governing cellular responses to complex stimuli

Cells adapt to their environment through the integration of complex signals. Multiple signals can induce synergistic or antagonistic interactions, currently considered as homogenous behaviours. Here, we use a systematic theoretical approach to enumerate the possible interaction profiles for outputs measured in the conditions 0 (control), signals X, Y, X+Y. Combinatorial analysis reveals 82 possible interaction profiles, which we biologically and mathematically grouped into five positive and five negative interaction modes. To experimentally validate their use in living cells, we apply an original computational workflow to transcriptomics data of innate immune cells integrating physiopathological signal combinations. Up to 9 of the 10 defined modes coexisted in context-dependent proportions. Each interaction mode was preferentially used in specific biological pathways, suggesting a functional role in the adaptation to multiple signals. Our work defines an exhaustive map of interaction modes for cells integrating pairs of physiopathological and pharmacological stimuli.

Cells constantly integrate information from multiple stimuli. By considering every possible means by which two stimuli can interact, Cappuccio et al. define 10 interaction modes and demonstrate their preferential use by dendritic cells responding to different combinations of microbial and host inflammatory cues.

Rapid temporal dynamics of transcription, protein synthesis, and secretion during macrophage activation

Macrophages provide the first line of host defense with their capacity to react to an array of cytokines and bacterial components requiring tight regulation of protein expression and secretion to invoke a properly tuned innate immune response. To capture the dynamics of this system, we introduce a novel method combining pulsed stable isotope labeling with amino acids in cell culture (SILAC) with pulse labeling using the methionine analog azidohomoalanine that allows the enrichment of newly synthesized proteins via click-chemistry followed by their identification and quantification by mass spectrometry. We show that this permits the analysis of proteome changes on a rapid time scale, as evidenced by the detection of 4852 newly synthesized proteins after only a 20-min SILAC pulse. We have applied this methodology to study proteome response during macrophage activation in a time-course manner. We have combined this with full proteome, transcriptome, and secretome analyses, producing an integrative analysis of the first 3 h of lipopolysaccharide-induced macrophage activation. We observed the rapid induction of multiple processes well known to TLR4 signaling, as well as anti-inflammatory proteins and proteins not previously associated with immune response. By correlating transcriptional, translational, and secretory events, we derived novel mechanistic principles of processes specifically induced by lipopolysaccharides, including ectodomain shedding and proteolytic processing of transmembrane and extracellular proteins and protein secretion independent of transcription. In conclusion, we demonstrate that the combination of pulsed azidohomoalanine and pulsed SILAC permits the detailed characterization of proteomic events on a rapid time scale. We anticipate that this approach will be very useful in probing the immediate effects of cellular stimuli and will provide mechanistic insight into cellular perturbation in multiple biological systems. The data have been deposited in ProteomeXchange with the identifier PXD000600.

Systems Biological Approaches Reveal Non-additive Responses and Multiple Crosstalk Mechanisms between TLR and GPCR Signaling

A variety of ligands differ in their capacity to bind the receptor, elicit gene expression, and modulate physiological responses. Such receptors include Toll-like receptors (TLRs), which recognize various patterns of pathogens and lead to primary innate immune activation against invaders, and G-protein coupled receptors (GPCRs), whose interaction with their cognate ligands activates heterotrimeric G proteins and regulates specific downstream effectors, including immuno-stimulating molecules. Once TLRs are activated, they lead to the expression of hundreds of genes together and bridge the arm of innate and adaptive immune responses. We characterized the gene expression profile of Toll-like receptor 4 (TLR4) in RAW 264.7 cells when it bound with its ligand, 2-keto-3-deoxyoctonate (KDO), the active part of lipopolysaccharide. In addition, to determine the network communications among the TLR, Janus kinase (JAK)/signal transducer and activator of transcription (STAT), and GPCR, we tested RAW 264.7 cells with KDO, interferon-β, or cAMP analog 8-Br. The ligands were also administered as a pair of double and triple combinations.

Selective enrichment of newly synthesized proteins for quantitative secretome analysis

Secreted proteins constitute a large and biologically important subset of proteins that are involved in cellular communication, adhesion and migration. Yet secretomes are understudied because of technical limitations in the detection of low-abundance proteins against a background of serum-containing media. Here we introduce a method that combines click chemistry and pulsed stable isotope labeling with amino acids in cell culture to selectively enrich and quantify secreted proteins. The combination of these two labeling approaches allows cells to be studied irrespective of the complexity of the background proteins. We provide an in-depth and differential secretome analysis of various cell lines and primary cells, quantifying secreted factors, including cytokines, chemokines and growth factors. In addition, we reveal that serum starvation has a marked effect on secretome composition. We also analyze the kinetics of protein secretion by macrophages in response to lipopolysaccharides.

RahU: an inducible and functionally pleiotropic protein in Pseudomonas aeruginosa modulates innate immunity and inflammation in host cells

The aim of this study was to define the functional role of a recently identified RahU protein from Pseudomonas aeruginosa in macrophages and its role in bacterial defense. Recombinant (r)-RahU had no significant effect on cell apoptosis or cell viability in human monocytic THP-1 cells. Gene expression array of murine macrophage cells (RAW 264.7) stimulated with LPS showed modulation of common transcripts (by r-RahU and predisone) involved in inflammation. Functional cellular analysis showed RAW cells incubated with r-RahU at 1.0-10 μg/ml (0.06-0.6 μM) inhibited accumulation of nitric oxide (NO) in the presence of LPS by 10-50%. The IC(50) of r-RahU (0.6 μM) was distinct from the known inhibitors of NO production: prednisone (50 μM) and L-NMMA (100 μM). r-RahU also significantly inhibited chemotactic activity of THP-1 cells toward CCL2 or chemotactic supernatants from apoptotic T-cells. These reports show previously unknown pleiotropic properties of RahU in modulating both microbial physiology and host innate immunity.

Drugs targeting Toll-like receptors

Animals and plants are exposed to myriads of potential microbial invaders. In case of animals, Toll-like receptors (TLRs) act as the primary defense against infection by pathogens. Arguably, less is known regarding the activation of TLRs that connect the innate and adaptive immune systems. Some TLR ligands have been used as adjuvants in various vaccines and have gained a great deal of attention due to their ability to elicit an effective immune response. Understanding the intricate relationships between various molecules involved in TLR signaling and their positive or negative regulation is a key focus for the development of effective therapeutics. In this review, recent developments in TLR signaling that will be very important in providing new drug target molecules and a better understanding of molecular regulation of innate immunity are discussed.

Francisella tularensis induces ubiquitin-dependent major histocompatibility complex class II degradation in activated macrophages

The intracellular bacterium Francisella tularensis survives and replicates within macrophages, ultimately killing the host cell. Resolution of infection requires the development of adaptive immunity through presentation of F. tularensis antigens to CD4+ and CD8+ T cells. We have previously established that F. tularensis induces macrophage prostaglandin E2 (PGE2) production, leading to skewed T-cell responses. PGE2 can also downregulate macrophage major histocompatibility complex (MHC) class II expression, suggesting that F. tularensis-elicited PGE2 may further alter T-cell responses via inhibition of class II expression. To test this hypothesis, gamma interferon (IFN-gamma)-activated reporter macrophages were exposed to supernatants from F. tularensis-infected macrophages, and the class II levels were measured. Exposure of macrophages to infection supernatants results in essentially complete clearance of surface class II and CD86, compromising the macrophage's ability to present antigens to CD4 T cells. Biochemical analysis revealed that infection supernatants elicit ubiquitin-dependent class II downregulation and degradation within intracellular acidic compartments. By comparison, exposure to PGE2 alone only leads to a minor decrease in macrophage class II expression, demonstrating that a factor distinct from PGE2 is eliciting the majority of class II degradation. However, production of this non-PGE2 factor is dependent on macrophage cyclooxygenase activity and is induced by PGE2. These results establish that F. tularensis induces the production of a PGE2-dependent factor that elicits MHC class II downregulation in IFN-gamma-activated macrophages through ubiquitin-mediated delivery of class II to lysosomes, establishing another mechanism for the modulation of macrophage antigen presentation during F. tularensis infection.

H89, an inhibitor of PKA and MSK, inhibits cyclic-AMP response element binding protein-mediated MAPK phosphatase-1 induction by lipopolysaccharide

OBJECTIVE

Lipopolysaccharide (LPS) stimulates the production of inflammatory cytokines and the amplification of immune responses via MAPK pathways. MAPK phosphatases (MKPs) feedback-regulate the activities of MAPKs to prevent excessive immunological functions. H89 has been used as an inhibitor of the protein kinase A (PKA) and mitogen- and stress-activated protein kinase (MSK) pathways. In view of the potential roles of PKA and MSK for MKP-1 induction and the ability of H89 to inhibit these kinases, this study examined the effect of H89 on MKP-1 induction by LPS and the role of cyclic-AMP response element binding protein (CREB) in the MKP-1 induction.

RESULTS

H89 treatment inhibited increases in MKP-1 protein and mRNA levels, and gene transcription by LPS in Raw264.7 cells. Immunoblot, gel-shift, and chromatin-immunoprecipitation assays showed the activation of CREB by LPS, and the ability of H89 to inhibit it, suggesting that H89's inhibition of CREB may affect MKP-1 induction. In addition, H89 prevented the ability of LPS to induce other MKP genes (Dusp-2, 4, 8, and 16). Experiments using MAPK inhibitors showed that MAPKs are involved in CREB phosphorylation and MKP-1 induction, suggesting that CREB-mediated MKP-1 induction serves in part as a feedback-inhibitory loop of MAPKs.

CONCLUSION

Our results demonstrate that H89 inhibits the activation of CREB and the CREB-mediated MKP-1 induction by LPS, which may result from its inhibition of PKA and MSK.

Isoflavone effect on gene expression profile and biomarkers of inflammation

The use of high throughput techniques to find differences in gene expression profiles between related samples (transcriptomics) that underlie changes in physiological states can be applied in medicine, drug development and nutrition. Transcriptomics can be used to provide novel biomarkers of a future pathologic state and to study how bioactive food compounds or drugs can modulate them in the early stages. In this study, we examine the expression pattern in order to determine the effect of the pathological-inflammatory state on the RAW 264.7 cell model and to ascertain how isoflavones and their active functional metabolites alleviate the inflammatory burst and the extent of gene modulation due to the presence of polyphenols. Results demonstrated that genistein (20 microM) and equol (10 microM) significantly inhibited the overproduction of NO and PGE(2) induced by LPS plus INF-gamma when a pre-treatment was performed or when administered during activation. Daidzein, however, did not exert similar effects. Moreover, both isoflavone treatments regulated gene transcription of cytokines and inflammatory markers, among others. The transcriptomic changes provide clues firstly into defining a differential expression profile in inflammation in order to select putative biomarkers of the inflammatory process, and secondly into understanding the isoflavone action mechanism at the transcriptional level. In conclusion, isoflavone modulates the inflammatory response in activated macrophages by inhibiting NO and PGE(2) and by modulating the expression of key genes defined by transcriptomic profiling.

The identification of C/EBPbeta as a transcription factor necessary for the induction of MAPK phosphatase-1 by toll-like receptor-4 ligand

Toll-like receptor activates mitogen-activated protein kinases (MAPKs), which contributes to inflammatory responses. The activities of MAPKs are counter-balanced by MAPK phosphatases (MKPs). Because the transcriptional regulatory mechanism of mkp-1 has not been completely established, this study investigated the effect of toll-like receptor-4 ligand (TLR4L, lipopolysaccharide) on CCAAT/enhancer binding protein-beta (C/EBP beta)-dependent induction of MKP-1 in Raw264.7 cells. TLR4L treatment induced MKP-1 through gene transcription. Other TLRLs also transactivated mkp-1. Gel-shift, immunoblot and chromatin immunoprecipitation assays identified the activation of C/EBPbeta by TLR4L. Consistently, C/EBP beta transfection promoted mkp-1 transactivation, which was reversed by its dominant-negative mutant (AC/EBP). Experiments using chemical inhibitors or dominant-negative mutants of MAPKs indicated that both C/EBP beta activation and MKP-1 induction depend on the activation of MAPKs. TLR4L activation of C/EBP beta also contributed to the induction of dusp-2,dusp-4,dusp-8 and dusp-16. These results identify C/EBP beta as a transcription factor necessary for the induction of MKP-1 by TLRL.

A versatile approach to multiple gene RNA interference using microRNA-based short hairpin RNAs

Background

Effective and stable knockdown of multiple gene targets by RNA interference is often necessary to overcome isoform redundancy, but it remains a technical challenge when working with intractable cell systems.

Results

We have developed a flexible platform using RNA polymerase II promoter-driven expression of microRNA-like short hairpin RNAs which permits robust depletion of multiple target genes from a single transcript. Recombination-based subcloning permits expression of multi-shRNA transcripts from a comprehensive range of plasmid or viral vectors. Retroviral delivery of transcripts targeting isoforms of cAMP-dependent protein kinase in the RAW264.7 murine macrophage cell line emphasizes the utility of this approach and provides insight to cAMP-dependent transcription.

Conclusion

We demonstrate functional consequences of depleting multiple endogenous target genes using miR-shRNAs, and highlight the versatility of the described vector platform for multiple target gene knockdown in mammalian cells.