IRF5:RelA interaction targets inflammatory genes in macrophages.

Interferon Regulatory Factor 5 (IRF5) plays a major role in setting up an inflammatory macrophage phenotype, but the molecular basis of its transcriptional activity is not fully understood. In this study, we conduct a comprehensive genome-wide analysis of IRF5 recruitment in macrophages stimulated with bacterial lipopolysaccharide and discover that IRF5 binds to regulatory elements of highly transcribed genes. Analysis of protein:DNA microarrays demonstrates that IRF5 recognizes the canonical IRF-binding (interferon-stimulated response element [ISRE]) motif in vitro. However, IRF5 binding in vivo appears to rely on its interactions with other proteins. IRF5 binds to a noncanonical composite PU.1:ISRE motif, and its recruitment is aided by RelA. Global gene expression analysis in macrophages deficient in IRF5 and RelA highlights the direct role of the RelA:IRF5 cistrome in regulation of a subset of key inflammatory genes. We map the RelA:IRF5 interaction domain and suggest that interfering with it would offer selective targeting of macrophage inflammatory activities.

Intrinsic danger: activation of Toll-like receptors in rheumatoid arthritis.

RA is a debilitating disorder that manifests as chronic localized synovial and systemic inflammation leading to progressive joint destruction. Recent advances in the molecular basis of RA highlight the role of both the innate and adaptive immune system in disease pathogenesis. Specifically, data obtained from in vivo animal models and ex vivo human tissue explants models has confirmed the central role of Toll-like receptors (TLRs) in RA. TLRs are pattern recognition receptors (PRRs) that constitute one of the primary host defence mechanisms against infectious and non-infectious insult. This receptor family is activated by pathogen-associated molecular patterns (PAMPs) and by damage-associated molecular patterns (DAMPs). DAMPs are host-encoded proteins released during tissue injury and cell death that activate TLRs during sterile inflammation. DAMPs are also proposed to drive aberrant stimulation of TLRs in the RA joint resulting in increased expression of cytokines, chemokines and proteases, perpetuating a vicious inflammatory cycle that constitutes the hallmark chronic inflammation of RA. In this review, we discuss the signalling mechanisms of TLRs, the central function of TLRs in the pathogenesis of RA, the role of endogenous danger signals in driving TLR activation within the context of RA and the current preclinical and clinical strategies available to date in therapeutic targeting of TLRs in RA.

Beyond the enhanceosome: cluster of novel κB sites downstream of the human IFN-ß gene is essential for lipopolysaccharide-induced gene activation.

The expression of interferon-ß (IFN-ß) in virus-infected HeLa cells established a paradigm of multifactorial gene regulation, in which cooperative assembly of transcription factors (TFs) at the composite DNA element (enhanceosome), is central for amplification of weak activating signals provided by individual TFs. However, whether the same TFs and the same DNA element are essential for IFN-ß induction in response to bacterial stimuli are less well understood. Here we report that rapid and transient transcription of IFN-ß in response to TLR4 stimulation with bacterial lipopolysaccharide (LPS) follows nuclear factor-κB (NF-κB) RelA activation and recruitment to the IFN-ß genomic locus at multiple spatially separated regulatory regions. We demonstrate that the IFN-ß enhanceosome region is not sufficient for maximal gene induction in response to LPS and identify an essential cluster of homotypic κB sites in the 3' downstream of the gene. The cluster is characterized by elevated levels of histone 3 lysine 4 mono-methylation, a chromatin signature of enhancers, and efficiently binds RelA-containing NF-κB complexes in vitro and in vivo. These findings demonstrate that IFN-ß gene activation via multifactorial enhanceosome assembly is potentiated in LPS-stimulated cells by NF-κB interactions with all functional κB sites in the locus.

Transcriptional regulation of the endogenous danger signal tenascin-C: a novel autocrine loop in inflammation.

Inappropriate expression of proinflammatory mediators underpins the pathogenesis of autoimmune disease and tumor metastasis. The extracellular matrix glycoprotein tenascin-C is an endogenous activator of innate immunity that promotes the synthesis of inflammatory cytokines via activation of TLR4. Little tenascin-C is observed in most healthy adult tissues, but expression is specifically upregulated at sites of inflammation. Moreover, high levels of tenascin-C are associated with chronic inflammation and found in the tumor stroma. In this study, we show that the expression of tenascin-C is induced in immune myeloid cells activated by a variety of inflammatory stimuli, including specific TLR ligands. Its synthesis is transcriptionally regulated and requires the specific activation of AKT/PI3K and NF-kappaB signaling pathways. Using a bioinformatic approach, we identified a large number of conserved noncoding regions throughout the tenascin-C genomic locus that may contribute to its transcriptional regulation during inflammation. We also demonstrate that tenascin-C expression is transient during acute inflammation. In contrast, persistently high levels of expression occur in the inflamed synovium of joints from rheumatoid arthritis patients. Thus, misregulated expression of this endogenous danger signal may promote an autocrine loop of inflammation and contribute to the persistence of inflammation in autoimmune diseases or to tumor egress and invasion during metastasis.

The role of transposable elements in the regulation of IFN-lambda1 gene expression.

IFNs lambda1, lambda2, and lambda3, or type III IFNs, are recently identified cytokines distantly related to type I IFNs. Despite an early evolutionary divergence, the 2 types of IFNs display similar antiviral activities, and both are produced primarily in dendritic cells. Although virus induction of the type I IFN-beta gene had served as a paradigm of gene regulation, relatively little is known about the regulation of IFN-lambda gene expression. Studies of virus induction of IFN-lambda1 identified an essential role of IFN regulatory factors (IRF) 3 and 7, which bind to a regulatory DNA sequence near the start site of transcription. Here, we report that the proximal promoter region of the IFN-lambda1 regulatory region is not sufficient for maximal gene induction in response to bacterial LPS, and we identify an essential cluster of homotypic NF-kappaB binding sites. Remarkably, these sites, which bind efficiently to NF-kappaB and function independently of the IRF3/7 binding sites, originate as transposable elements of the Alu and LTR families. We also show that depletion of the NF-kappaB RelA protein significantly reduces the level of the IFN-lambda1 gene expression. We conclude that IFN-lambda1 gene expression requires NF-kappaB, and we propose a model for IFN-lambda1 gene regulation, in which IRF and NF-kappaB activate gene expression independently via spatially separated promoter elements. These observations provide insights into the independent evolution of the IFN-lambda1 and IFN-beta promoters and directly implicate transposable elements in the regulation of the IFN-lambda1 gene by NF-kappaB.

Detecting and modulating the NF-kB activity in human immune cells: generation of human cell lines with altered levels of NF-kappaB.

NF-kappaB plays a pivotal role in immunity and inflammation and is considered to be a promising candidate for drug development. However, global suppression of NF-kappaB may have undesirable side-effects. Our data and the results of others suggest that each of the five NF-kappaB subunits may have a specific function in controlling the expression of inflammatory mediators in immune cells. Identifying the role for each NF-kappaB subunit in primary human immune cells will allow a more targeted approach to inhibiting NF-kappaB subunit-specific cellular functions. However, results obtained with primary human cells can often be inconsistent due to donor heterogeneity. Therefore one possible approach could be to generate human immune cell lines with stably inhibited expression of specific NF-kappaB subunit(s) as described in this chapter.