NFkappa B interacts with serum amyloid A3 enhancer factor to synergistically activate mouse serum amyloid A3 gene transcription

Osteocytes/Osteoblasts Produce SAA3 to Regulate Hepatic Metabolism of Cholesterol

Hypercholesterolaemia is a systemic metabolic disease, but the role of organs other than liver in cholesterol metabolism is unappreciated. The phenotypic characterization of the Tsc1Dmp1 mice reveal that genetic depletion of tuberous sclerosis complex 1 (TSC1) in osteocytes/osteoblasts (Dmp1-Cre) triggers progressive increase in serum cholesterol level. The resulting cholesterol metabolic dysregulation is shown to be associated with upregulation and elevation of serum amyloid A3 (SAA3), a lipid metabolism related factor, in the bone and serum respectively. SAA3, elicited from the bone, bound to toll-like receptor 4 (TLR4) on hepatocytes to phosphorylate c-Jun, and caused impeded conversion of cholesterol to bile acids via suppression on cholesterol 7 α-hydroxylase (Cyp7a1) expression. Ablation of Saa3 in Tsc1Dmp1 mice prevented the CYP7A1 reduction in liver and cholesterol elevation in serum. These results expand the understanding of bone function and hepatic regulation of cholesterol metabolism and uncover a potential therapeutic use of pharmacological modulation of SAA3 in hypercholesterolaemia.

Balanophora polyandra Griff. prevents dextran sulfate sodium-induced murine experimental colitis via the regulation of NF-κB and NLRP3 inflammasome

Balanophora polyandra Griff. (B. polyandra) is a folk medicine used as an antipyretic, antidote, haemostatic, dressing and haematic tonic, for the treatment of gonorrhea, syphilis, wounds, and the bleeding of the alimentary tract by the local people in China.

Serum amyloid A - a review

Serum amyloid A (SAA) proteins were isolated and named over 50 years ago. They are small (104 amino acids) and have a striking relationship to the acute phase response with serum levels rising as much as 1000-fold in 24 hours. SAA proteins are encoded in a family of closely-related genes and have been remarkably conserved throughout vertebrate evolution. Amino-terminal fragments of SAA can form highly organized, insoluble fibrils that accumulate in “secondary” amyloid disease. Despite their evolutionary preservation and dynamic synthesis pattern SAA proteins have lacked well-defined physiologic roles. However, considering an array of many, often unrelated, reports now permits a more coordinated perspective. Protein studies have elucidated basic SAA structure and fibril formation. Appreciating SAA’s lipophilicity helps relate it to lipid transport and metabolism as well as atherosclerosis. SAA’s function as a cytokine-like protein has become recognized in cell-cell communication as well as feedback in inflammatory, immunologic, neoplastic and protective pathways. SAA likely has a critical role in control and possibly propagation of the primordial acute phase response. Appreciating the many cellular and molecular interactions for SAA suggests possibilities for improved understanding of pathophysiology as well as treatment and disease prevention.

Airway epithelial regulation of allergic sensitization in asthma

While many of the contributing cell types and mediators of allergic asthma are known, less well understood are the factors that influence the development of allergic responses that lead to the development of allergic asthma. As the first airway cell type to respond to inhaled factors, the epithelium orchestrates downstream interactions between dendritic cells (DCs) and CD4⁺ T cells that quantitatively and qualitatively dictate the degree and type of the allergic asthma phenotype, making the epithelium of critical importance for the genesis of allergies that later manifest in allergic asthma. Amongst the molecular processes of critical importance in airway epithelium is the transcription factor, nuclear factor-kappaB (NF-κB). This review will focus primarily on the genesis of pulmonary allergies and the participation of airway epithelial NF-κB activation therein, using examples from our own work on nitrogen dioxide (NO₂) exposure and genetic modulation of airway epithelial NF-κB activation. In addition, the mechanisms through which Serum Amyloid A (SAA), an NF-κB-regulated, epithelial-derived mediator, influences allergic sensitization and asthma severity will be presented. Knowledge of the molecular and cellular processes regulating allergic sensitization in the airways has the potential to provide powerful insight into the pathogenesis of allergy, as well as targets for the prevention and treatment of asthma.

Imbalance of Clara cell-mediated homeostatic inflammation is involved in lung metastasis

We have previously shown that tumor necrosis factor (TNF)α produced from primary tumor-induced expression of two endogenous Toll-like receptor 4 (TLR4) ligands, S100A8 and serum amyloid A3 (SAA3), in pre-metastatic lungs. However, mechanistic details of the signaling network and relevance to pulmonary physiology are poorly understood. Here, we identify Clara cells as a control tower of the network. Clara cell ablation by naphthalene suppressed pulmonary recruitment of CD11b+TLR4+ cells and spontaneous lung metastasis. Clara cells turned out to express TLR4 through which SAA3 was auto-amplified. Reciprocal bone marrow transplantation between wild-type and TLR4 knockout mice demonstrated that pulmonary TLR4+ Clara cells could be derived from bone marrow. SAA3-induced TNFα expression in both alveolar type II cells and macrophages. Primary co-cultures of alveolar type II cells and Clara cells revealed that the induction of TNFα in alveolar type II cells was dependent on the Clara cell-mediated amplification of SAA3. SAA3 induction by bacterial endotoxin also required both Clara cells and TLR4. Thus, pulmonary metastatic soil may feature deregulation of homeostatic inflammatory responses to constant assaults of microbes with endotoxin.

Toll-like receptor 4 signalling is specifically TGF-beta-activated kinase 1 independent in synovial fibroblasts

OBJECTIVE

Activated synovial fibroblasts are key players in the pathogenesis of RA by driving inflammation and joint destruction. Numerous molecules including cytokines and Toll-like receptor (TLR) ligands induce pro-inflammatory signalling and gene expression through a hierarchical network of kinases. Upstream mitogen-activated protein kinase kinase kinases (MAP3Ks) represent an attractive target for RA treatment. In this study, we sought to determine the role of the MAP3K TGF-β-activated kinase 1 (TAK1) in cytokine and TLR-mediated signalling.

METHODS

TAK1 activity was inhibited using either a small molecule inhibitor or lentivirally overexpressed kinase-inactive TAK1-K63W mutant in murine embryonic and human dermal and synovial fibroblasts. Fibroblasts were stimulated with IL-1, TNF, TLR2 or TLR4 agonists and responses were evaluated using transcriptional reporters, western blotting and analysis of gene expression of collagenases (MMP3 and MMP13), cytokines (IL-1β and IL-6) and chemokines (IL-8 and MCP-1).

RESULTS

TAK1 inhibition abrogated cytokine- and TLR-induced nuclear factor-κB (NF-κB) and Saa3-promoter reporter activation in murine and human dermal fibroblasts. In synovial fibroblasts, TAK1 regulated IL-1 and TNF-mediated NF-κB, but not Saa3-promoter reporter activation. Inducible mRNA expression of cytokines, collagenases and chemokines, except MCP-1, was TAK1 dependent for IL-1, TNF and TLR2 signalling. Unexpectedly, TLR4-mediated NF-κB reporter activation and inducible mRNA expression was fully TAK1 independent. Accordingly, NF-κB p65 and p38 MAPK phosphorylation was unaffected by TAK1 inhibition.

CONCLUSION

In general, TAK1 crucially regulates IL-1 and TNF signalling in fibroblasts. Interestingly, TLR4 signalling is specifically TAK1 independent in synovial fibroblasts. Consequently, therapeutic TAK1 inhibition in arthropathies may not dampen the damage-associated molecular pattern-mediated TLR4 activation of synovial fibroblasts.

Transcription factor Late SV40 Factor (LSF) functions as an oncogene in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a highly aggressive cancer with no currently available effective treatment. Understanding of the molecular mechanism of HCC development and progression is imperative for developing novel, effective, and targeted therapies for this lethal disease. In this article, we document that the cellular transcription factor Late SV40 Factor (LSF) plays an important role in HCC pathogenesis. LSF protein was significantly overexpressed in human HCC cells compared to normal hepatocytes. In 109 HCC patients, LSF protein was overexpressed in >90% cases, compared to normal liver, and LSF expression level showed significant correlation with the stages and grades of the disease. Forced overexpression of LSF in less aggressive HCC cells resulted in highly aggressive, angiogenic, and multiorgan metastatic tumors in nude mice. Conversely, inhibition of LSF significantly abrogated growth and metastasis of highly aggressive HCC cells in nude mice. Microarray studies revealed that as a transcription factor, LSF modulated specific genes regulating invasion, angiogenesis, chemoresistance, and senescence. The expression of osteopontin (OPN), a gene regulating every step in tumor progression and metastasis, was robustly up-regulated by LSF. It was documented that LSF transcriptionally up-regulates OPN, and loss-of-function studies demonstrated that OPN plays an important role in mediating the oncogenic functions of LSF. Together, these data establish a regulatory role of LSF in cancer, particularly HCC pathogenesis, and validate LSF as a viable target for therapeutic intervention.

A role for PKR in hematologic malignancies

The double-stranded RNA-dependent kinase PKR has been described for many years as strictly a pro-apoptotic kinase. Recent data suggest that the main purpose of this kinase is damage control and repair following stress and, if all else fails, apoptosis. Aberrant activation of PKR has been reported in numerous neurodegenerative diseases and cancer. Although a subset of myelodysplastic syndromes (MDS) and chronic lymphocytic leukemia contain low levels of PKR expression and activity, elevated PKR activity and/or expression have been detected in a wide range of hematologic malignancies, from bone marrow failure disorders to acute leukemia. With the recent findings that cancers containing elevated PKR activity are highly sensitive to PKR inhibition, we explore the role of PKR in hematologic malignancies, signal transduction pathways affected by PKR, and how PKR may contribute to leukemic transformation.

The evolutionary diversification of LSF and Grainyhead transcription factors preceded the radiation of basal animal lineages

Background

The transcription factors of the LSF/Grainyhead (GRH) family are characterized by the possession of a distinctive DNA-binding domain that bears no clear relationship to other known DNA-binding domains, with the possible exception of the p53 core domain. In triploblastic animals, the LSF and GRH subfamilies have diverged extensively with respect to their biological roles, general expression patterns, and mechanism of DNA binding. For example, Grainyhead (GRH) homologs are expressed primarily in the epidermis, and they appear to play an ancient role in maintaining the epidermal barrier. By contrast, LSF homologs are more widely expressed, and they regulate general cellular functions such as cell cycle progression and survival in addition to cell-lineage specific gene expression.

Results

To illuminate the early evolution of this family and reconstruct the functional divergence of LSF and GRH, we compared homologs from 18 phylogenetically diverse taxa, including four basal animals (Nematostella vectensis, Vallicula multiformis, Trichoplax adhaerens, and Amphimedon queenslandica), a choanoflagellate (Monosiga brevicollis) and several fungi. Phylogenetic and bioinformatic analyses of these sequences indicate that (1) the LSF/GRH gene family originated prior to the animal-fungal divergence, and (2) the functional diversification of the LSF and GRH subfamilies occurred prior to the divergence between sponges and eumetazoans. Aspects of the domain architecture of LSF/GRH proteins are well conserved between fungi, choanoflagellates, and metazoans, though within the Metazoa, the LSF and GRH families are clearly distinct. We failed to identify a convincing LSF/GRH homolog in the sequenced genomes of the algae Volvox carteri and Chlamydomonas reinhardtii or the amoebozoan Dictyostelium purpureum. Interestingly, the ancestral GRH locus has become split into two separate loci in the sea anemone Nematostella, with one locus encoding a DNA binding domain and the other locus encoding the dimerization domain.

Conclusions

In metazoans, LSF and GRH proteins play a number of roles that are essential to achieving and maintaining multicellularity. It is now clear that this protein family already existed in the unicellular ancestor of animals, choanoflagellates, and fungi. However, the diversification of distinct LSF and GRH subfamilies appears to be a metazoan invention. Given the conserved role of GRH in maintaining epithelial integrity in vertebrates, insects, and nematodes, it is noteworthy that the evolutionary origin of Grh appears roughly coincident with the evolutionary origin of the epithelium.

Modulation of ozone-sensitive genes in alpha-tocopherol transfer protein null mice

Alpha-tocopherol transfer protein (ATTP) null mice (ATTP-/-) have a systemic alpha-tocopherol (AT) deficiency, with their lung AT levels being < 10% of those in AT-replete ATTP(+/+) mice when fed a standard rodent chow diet. ATTP(+/+) and ATTP(-/-) mice (4 wk old male mice, n = 16 per group) were fed a standard diet (35 IU AT/kg diet) for 8-12 wk, exposed 6 h/day for 3 days to either to O(3) (0.5 ppm) or filtered air, then sacrificed. No significant differences in plasma or lung AT concentrations were observed in response to this level of O(3) exposure. Lung genomic responses of the lungs to O(3) were determined using Affymetrix 430A 2.0 arrays containing over 22,600 probe sets representing 14,000 well-characterized mouse genes. As compared with filtered air exposure, O(3) exposure resulted in 99 genes being differentially expressed in ATTP(-/-) mice, as compared to 52 differentially expressed genes in ATTP(+/+) mice. The data revealed an O(3)-induced upregulation of genes related to cell proliferation/DNA repair and inflammatory-immune responses in both ATTP(+/+) and ATTP(-/-) mice, with the expression of 22 genes being common to both, whereas 30 and 77 genes were unique to ATTP(+/+) and ATTP(-/-) mice, respectively. The expressions of O(3) sensitive genes-Timp1, Areg, Birc5 and Tnc-were seen to be further modulated by AT status. The present study reveals AT modulation of adaptive response of lung genome to O(3) exposure.

Cloning and characterization of DULP, a novel ubiquitin-like molecule from human dendritic cells

We identified a novel ubiquitin-like molecule DULP from human dendritic cells. DULP contains a domain that shares 26% identity and 34% similarity with ubiquitin, and it possesses the corresponding Ile-44 hydrophobic patch used by mono- or poly-ubiquitin to interact with a ubiquitin-interaction motif (UIM) or ubiquitin-associated domain (UBA). Lysine residue corresponding to 6 of ubiquitin, which is involved in the formation of a multi-ubiquitin chain that can bind proteasomal subunit Rpn10/S5a, is also conserved in its ubiquitin-homology domain. However, DULP does not possess the highly conserved C-terminus Gly-Gly required for ubiquitin conjugation or the Lys-48 required for the formation of polyubiquitin chain to target substrates for degradation, suggesting it might be a novel ubiquitin-domain protein (UDP). DULP was found widely expressed in many cells and the ubiquitin-homology domain was not cleaved. We also confirmed that DULP expression was enriched in the nucleus and much weaker in the cytosol. Besides, we found that overexpression of DULP in 293T cells induced apoptosis, which might not be associated with the mitochondrial or proteasome pathway, with the specific mechanism remaining unclear. Further investigations are needed to identify the precise biological functions of DULP.

Insulin exhibits short-term anti-inflammatory but long-term proinflammatory effects in vitro

Although insulin is indispensable for maintaining glucose homeostasis, it is still controversial whether or not a high concentration of insulin is deleterious. We examined the effect of insulin on the transcriptional activity of NF-kappaB, which mediates the expression of a variety of inflammation/coagulation-related genes using hepatocyte cell lines in vitro. We found that insulin (1 nM) alone caused minimal increase in NF-kappaB-mediated transcription. On the other hand, when cells were simultaneously treated with proinflammatory cytokines such as TNFalpha, the following dual effect of insulin was observed: short-term (6h) suppressive, and long-term (36 h or later) stimulatory effects. The former effect was transient and appears to be mediated by the phosphatidylinositol 3 kinase (PI(3)K) signaling pathway. The latter effect, in contrast, was more pronounced, enhancing the TNFalpha-stimulated NF-kappaB-dependent transcription by more than sevenfold. This positive effect was NF-kappaB-specific, and was eliminated by mitogen-activated protein kinase (MAPK) inhibitors. Altogether, our data suggest that insulin has short-term anti-inflammatory but long-term proinflammatory effects. From a clinical standpoint, this implies that low basal and periodically high plasma insulin is beneficial, whereas a sustained rise in plasma insulin, as often seen in patients with obesity, may induce atherothrombotic disorders, because of the NF-kappaB-mediated overexpression of proinflammatory/procoagulant/antifibrinolytic proteins in the liver.

Induction of serum amyloid A genes is associated with growth and apoptosis of HC11 mammary epithelial cells

In this study, we examined the expression and functions of serum amyloid A (SAA) isoforms during apoptosis of HC11 mammary gland epithelial cells. Expression of SAA mRNAs and apoptosis were increased in HC11 cells by serum withdrawal and gradually decreased upon the addition of serum, or epidermal growth factor (EGF). TNFalpha treatment of HC11 cells also induced expression of SAA genes, and the effect on SAA1 and SAA2 expression was suppressed by treatment with MG132, and in cells transfected with a dominant negative mutant form of IkappaBalpha. Similar results were observed in response to interleukin-1 (IL-1), IL-6 and interferon gamma (IFNgamma). Furthermore, overexpression of the SAA1 and SAA2 isoforms suppressed growth and accelerated apoptosis of HC11 cells by increasing caspase 3/7 and caspase 8 activities, but the apoptotic effect of tumor necrosis factor alpha (TNFalpha) on HC11 cells was not enhanced. We found that expression of SAA1 and SAA2, but not SAA3, was regulated by an NFkappaB-dependent pathway, and that overexpression of SAA isoforms accelerated the apoptosis of HC11 cells.

High glucose alone, as well as in combination with proinflammatory cytokines, stimulates nuclear factor kappa-B-mediated transcription in hepatocytes in vitro

Diabetes mellitus is frequently associated with coagulation disorders such as coronary heart disease and stroke. We aimed to clarify the molecular mechanism whereby hyperglycemia causes the procoagulant state. HuH7 human hepatocyte cells were treated with high glucose alone or in combination with proinflammatory cytokines, and the effects on the activity of the transcription factor nuclear factor kappa-B (NF-kappaB), which mediates the expression of acute-phase and coagulation-related genes, were examined. The results showed that increasing the medium glucose concentration from 3 to 24 mM significantly enhanced NF-kappaB-luciferase activity by 40% in the presence of insulin. The effect was promoter specific and not mimicked by comparable hyperosmolality with L-glucose. Proinflammatory cytokines such as interleukin-1 and tumor necrosis factor-alpha (TNF-alpha) also stimulated NF-kappaB-dependent transcription and showed an additive effect with high glucose. Similar effects were obtained on acute-phase or coagulation/fibrinolysis-related gene promoters such as fibrinogen or plasminogen activator inhibitor-1, all of which are shown to have NF-kappaB-mediated transcription. Finally, pretreatment of the cells with an antioxidant PDTC completely abolished the effect of high glucose and markedly attenuated that of TNF-alpha, suggesting the involvement of reactive oxygen species. These results suggest that (1) high glucose as well as proinflammatory cytokines have positive effects on NF-kappaB-mediated transcription in an additive manner and enhance coagulation-related gene expression and (2) the effects are mediated, at least partly, by the generation of oxidative stress and may be responsible for the high prevalence of thrombotic disorders in the metabolic syndrome with diabetes, hyperinsulinemia, obesity, and/or inflammation.

Systemic responses to inhaled ozone in mice: cachexia and down-regulation of liver xenobiotic metabolizing genes

Rats or mice acutely exposed to high concentrations of ozone show an immediate and significant weight loss, even when allowed free access to food and water. The mechanisms underlying this systemic response to ozone have not been previously elucidated. We have applied the technique of global gene expression analysis to the livers of C57BL mice acutely exposed to ozone. Mice lost up to 14% of their original body weight, with a 42% decrease in total food consumption. We previously had found significant up-regulation of genes encoding proliferative enzymes, proteins related to acute phase reactions and cytoskeletal functions, and other biomarkers of a cachexia-like inflammatory state in lungs of mice exposed to ozone. These results are consistent with a general up-regulation of different gene families responsive to NF-kappaB in the lungs of the exposed mice. In the present study, we observed significant down-regulation of different families of mRNAs in the livers of the exposed mice, including genes related to lipid and fatty acid metabolism, and to carbohydrate metabolism in this tissue, consistent with a systemic cachexic response. Several interferon-dependent genes were down-regulated in the liver, suggesting a possible role for interferon as a signaling molecule between lung and liver. In addition, transcription of several mRNAs encoding enzymes of xenobiotic metabolism in the livers of mice exposed to ozone was decreased, suggesting cytokine-mediated suppression of cytochrome P450 expression. This finding may explain a previously controversial report from other investigators more than 20 years ago of prolongation of pentobarbital sleeping time in mice exposed to ozone.

Lineage-specific and ubiquitous biological roles of the mammalian transcription factor LSF

Transcriptional regulation in mammalian cells is driven by a complex interplay of multiple transcription factors that respond to signals from either external or internal stimuli. A single transcription factor can control expression of distinct sets of target genes, dependent on its state of post-translational modifications, interacting partner proteins, and the chromatin environment of the cellular genome. Furthermore, many transcription factors can act as either transcriptional repressors or activators, depending on promoter and cellular contexts [Alvarez, M., Rhodes, S.J., Bidwell, J.P., 2003. Context-dependent transcription: all politics is local. Gene 313, 43-57]. Even in this light, the versatility of LSF (Late SV40 Factor) is remarkable. A hallmark of LSF is its unusual DNA binding domain, as evidenced both by lack of homology to any other established DNA-binding domains and by its DNA recognition sequence. Although a dimer in solution, LSF requires additional multimerization with itself or partner proteins in order to interact with DNA. Transcriptionally, LSF can function as an activator or a repressor. It is a direct target of an increasing number of signal transduction pathways. Biologically, LSF plays roles in cell cycle progression and cell survival, as well as in cell lineage-specific functions, shown most strikingly to date in hematopoietic lineages. This review discusses how the unique aspects of LSF DNA-binding activity may make it particularly susceptible to regulation by signal transduction pathways and may relate to its distinct biological roles. We present current progress in elucidation of both tissue-specific and more universal cellular roles of LSF. Finally, we discuss suggestive data linking LSF to signaling by the amyloid precursor protein and to Alzheimer's disease, as well as to the regulation of latency of the human immunodeficiency virus (HIV).

Changes in intestinal and liver global gene expression in response to a phytosterol-enriched diet

BACKGROUND

Dietary phytosterols are a recommended therapeutic option for decreasing plasma cholesterol. The increased activity of ATP-binding cassette (ABC) transporters ABCA1, ABCG5 and ABCG8, or, alternatively, a decrease in Niemann-Pick C1 Like 1 (NPC1L1) could mediate the reduction in intestinal cholesterol absorption caused by phytosterols. Other biological properties such as a direct immune modulatory activity have recently been ascribed to these plant compounds.

METHODS

To gain insight into the molecular effects of phytosterols, global genome-wide gene profiling and real-time RT-PCR studies were conducted in small intestines and livers of phytosterol-treated apolipoprotein E-deficient (apoE(-/-)) mice. Re-testing of the main results was performed in C57BL/6J and LDL receptor-deficient (LDLR(-/-)) mice.

RESULTS

Intestinal cholesterol absorption was decreased in all mouse models but plasma cholesterol was only decreased in apoE(-/-) and LDLR(-/-) mice. ABCA1, ABCG5, ABCG8 and NPC1L1 mRNA levels were slightly reduced in the intestine of phytosterol-treated apoE(-/-) and LDLR(-/-) mice, but increased in C57BL/6J-treated mice. Phytosterols changed genes involved in immune regulation in apoE(-/-) mice. However, these changes were less extensive in LDLR(-/-) mice and were not found in C57BL/6J mice.

CONCLUSIONS

Inhibition of intestinal cholesterol absorption by phytosterols is not mediated via transcriptional changes in ABCA1, ABCG5, ABCG8 or NPC1L1. Changes suggestive of immunomodulation are associated with the hypocholesterolemic effect of phytosterols and with apoE deficiency.

Adipocyte differentiation induces dynamic changes in NF-kappaB expression and activity

The adipocyte exerts an important role in energy homeostasis, both as depot for energy-rich triglycerides and as a source for metabolic hormones. Adipocytes also contribute to inflammation and the innate immune response. Although it can be physiologically beneficial to combine these two functions in a single cell type under some circumstances, the proinflammatory signals emanating from adipocytes in the obese state can have local and systemic effects that promote atherosclerosis and insulin resistance. The transcriptional machinery in the adipocyte that mediates these pro-inflammatory responses has remained poorly characterized to date. In particular, no information is currently available on the NF-kappaB family of transcription factors. Here, we show that adipogenesis is associated with changes in amount and subunit composition of the NF-kappaB complexes. NF-kappaB subunits p65 (RelA), p68 (RelB), and IkappaB are upregulated during fat cell differentiation. Correspondingly, basal NF-kappaB nuclear gel shift and luciferase reporter assays are induced in parallel during differentiation. Surprisingly, endotoxin sensitivity of the classical NF-kappaB pathway is substantially delayed and attenuated despite increased overall inflammatory response in the mature adipocyte, as judged by induction of IL-6 and TNF-alpha. As a reflection of the constitutively elevated NF-kappaB activity in the mature adipocyte, adipocytes (but not preadipocytes) exert a strong inflammatory stimulus on macrophages in vitro, suggesting a cross talk between adipocytes and interstitial macrophages in adipose tissue in vivo. These effects are mediated by a secretory product of adipocytes that is unlikely to be IL-6 or TNF-alpha.

Detection of functional DNA motifs via statistical over-representation

The interaction of proteins with DNA recognition motifs regulates a number of fundamental biological processes, including transcription. To understand these processes, we need to know which motifs are present in a sequence and which factors bind to them. We describe a method to screen a set of DNA sequences against a precompiled library of motifs, and assess which, if any, of the motifs are statistically over- or under-represented in the sequences. Over-represented motifs are good candidates for playing a functional role in the sequences, while under-representation hints that if the motif were present, it would have a harmful dysregulatory effect. We apply our method (implemented as a computer program called Clover) to dopamine-responsive promoters, sequences flanking binding sites for the transcription factor LSF, sequences that direct transcription in muscle and liver, and Drosophila segmentation enhancers. In each case Clover successfully detects motifs known to function in the sequences, and intriguing and testable hypotheses are made concerning additional motifs. Clover compares favorably with an ab initio motif discovery algorithm based on sequence alignment, when the motif library includes only a homolog of the factor that actually regulates the sequences. It also demonstrates superior performance over two contingency table based over-representation methods. In conclusion, Clover has the potential to greatly accelerate characterization of signals that regulate transcription.

Minireview: The adipocyte--at the crossroads of energy homeostasis, inflammation, and atherosclerosis

Adipose tissue evolved to efficiently store energy for times of caloric restriction. The large caloric excess common in many Western diets has negated the need for this thrifty function, leaving adipose tissue ill-equipped to handle this increased load. An excess of adipose tissue increases risk for a number of conditions including coronary artery disease, hypertension, dyslipidemias, type 2 diabetes, and even cancer. Indeed, the ability of the adipocyte to function properly when engorged with lipid can lead to lipid accumulation in other tissues, reducing their ability to function and respond normally. The role of adipose tissue as an endocrine organ capable of secreting a number of adipose tissue-specific or enriched hormones, known as adipokines, is gaining appreciation. The normal balance of these adipose tissue secretory proteins is perturbed in obesity. Paradoxically, the lack of normal adipose tissue, as seen in cases of lipodystrophy and lipoatrophy, is also associated with pathologic sequelae similar to what is seen with obesity. The pathologic findings associated with lack of adipose tissue, largely due to inability to properly store lipids, may also be due to a lack of adipokines. In this review, we highlight the role of adipose tissue as an endocrine organ focusing on some of the recent advances in the identification and pharmacological characterization of adipokines as well as their regulation in the context of obesity and insulin-resistant states.

Ozone-induced disruptions of lung transcriptomes

We have analyzed changes in approximately 4000 lung mRNAs, with GeneChips, in mice exposed to 1 ppm O(3) for three consecutive nights (8 h per night). Differential gene expression analysis identified approximately 260 O(3) sensitive genes; approximately 80% of these were repressed and approximately 20% were induced in O(3)-exposed mice compared to the air-exposed controls. A 20-fold induction of serum amyloid A3 mRNA by O(3) suggested activation of NF-kappaB and CCAAT/enhancer binding protein-mediated pathways by inflammatory cytokines. Induction (up to 14-fold) of 12 genes that increase DNA synthesis and cell cycle progression, and increase (approximately 7-fold) in CD44 mRNA and macrophage metalloelastase suggested a state of O(3)-induced hyperplasia and lung remodeling. Several mRNAs encoding enzymes of xenobiotic metabolism and cytoskeletal functions were repressed and may suggest cytokine mediated suppression of cytochrome P450 expression and cachexia-like inflammatory state in ozone-exposed lungs. The expressions of approximately 30 genes of immune response were also repressed. Collectively this genome-wide analysis of lungs identified ozone-induced disruption of gene transcriptional profile indicative of increased cellular proliferation under suppressed immune surveillance and xenobiotic metabolism.

Differential transcription of the mouse acute phase serum amyloid A genes in response to pro-inflammatory cytokines

The acute phase members of the mouse serum amyloid A (Saa) family, Saa1, Saa2 and Saa3, are highly similar at both the nucleotide and protein sequence levels. Saa1 and Saa2 in the BALB/c strain are 72% identical over the first 500 bp upstream of their transcription start sites and to date have been considered to be coordinately regulated. Furthermore, based on their homology with the upstream regions of the human SAA1 and SAA2 genes, it has been assumed that they are Type I acute phase proteins (APPs), i.e. they are primarily regulated by IL-1 and TNF. Here we establish that the BALB/c Saa1, Saa2 and Saa3 genes, in fact, respond differently to IL-1, TNF and IL-6. The Saa1 and Saa2 promoters are strongly induced by IL-6, with synergistic upregulation of Saa2, but not of Saa1, by IL-1 or TNF. In contrast, the Saa3 promoter is strongly induced by IL-1, moderately induced by TNF and only minimally induced by IL-6. We also define important sequence differences between the Saa promoters of Type A (BALB/c and ICR/Swiss) and Type B (129/Ola) strains of mice, that have dramatic qualitative and quantitative consequences for Saa1 and Saa2 regulation. These findings mandate careful strain selection prior to embarking on studies involving mouse models of secondary amyloidosis or cytokine inactivation.

IL-4 dependent alternatively-activated macrophages have a distinctive in vivo gene expression phenotype

BACKGROUND

"Alternatively-activated" macrophages are found in Th2-mediated inflammatory settings such as nematode infection and allergic pulmonary inflammation. Due in part to a lack of markers, these cells have not been well characterized in vivo and their function remains unknown.

RESULTS

We have used murine macrophages elicited by nematode infection (NeM(phi)) as a source of in vivo derived alternatively activated macrophages. Using three distinct yet complementary molecular approaches we have established a gene expression profile of alternatively activated macrophages and identified macrophage genes that are regulated in vivo by IL-4. First, genes abundantly expressed were identified by an expressed sequence tag strategy. Second, an array of 1176 known mouse genes was screened for differential expression between NeM(phi) from wild type or IL-4 deficient mice. Third, a subtractive library was screened to identify novel IL-4 dependent macrophage genes. Differential expression was confirmed by real time RT-PCR analysis.

CONCLUSIONS

Our data demonstrate that alternatively activated macrophages generated in vivo have a gene expression profile distinct from any macrophage population described to date. Several of the genes we identified, including those most abundantly expressed, have not previously been associated with macrophages and thus this study provides unique new information regarding the phenotype of macrophages found in Th2-mediated, chronic inflammatory settings. Our data also provide additional in vivo evidence for parallels between the inflammatory processes involved in nematode infection and allergy.

Differential glucocorticoid enhancement of the cytokine-driven transcriptional activation of the human acute phase serum amyloid A genes, SAA1 and SAA2

The human acute phase serum amyloid A (A-SAA) genes, SAA1 and SAA2, have a high degree of sequence identity that extends approximately 450 bp upstream of their transcription start sites. Each promoter contains analogously positioned functional binding sites for the transcription factors NF-kappaB and NF-IL6. In human HepG2 hepatoma cells transfected with SAA promoter luciferase reporter constructs, administration of IL-1 and IL-6, singly or in combination, induced SAA1 and SAA2 transcriptional readouts that were qualitatively indistinguishable. However, under induced conditions, the SAA2 promoter had a significant quantitative transcriptional advantage over the SAA1 promoter. The application of the synthetic glucocorticoid dexamethasone in the context of cytokine stimulation enhanced the transcriptional activity of the SAA1, but not the SAA2, promoter such that readout from the former became equivalent to that from the latter. A putative glucocorticoid response element (GRE) is present (between residues -208 and -194) only in the SAA1 gene; a similar sequence in the corresponding region of the SAA2 gene is disrupted by a nine-residue insertion. The SAA1 GRE was shown to be functionally active and the SAA2 disrupted GRE was shown to be functionally inactive in experiments using reporter constructs carrying SAA1 and SAA2 promoters that had been modified by site-specific mutagenesis. Quantitative analysis of transcript-specific RT-PCR products, derived from SAA1 and SAA2 mRNAs after treatment of HepG2 cells with cytokines in the presence or absence of dexamethasone, confirmed that the endogenous SAA1 gene has a cytokine-driven transcriptional disadvantage that is superseded by a marginal transcriptional advantage when glucocorticoids are present.

Nuclear factor kappa B signaling in catabolic disorders

The nuclear factor kappa B family of inducible transcription factors regulates the expression of many genes. Nuclear factor kappa B has been implicated in autoimmune and inflammatory diseases, infection, cell survival, and cell transformation with subsequent promotion of cancer. In this review, we summarize features of nuclear factor kappa B regulation in several catabolic disorders, and describe its role in normal cellular function as well as provide an important link to the role of scaffold proteins, cellular receptors, and other cell signaling pathway kinases that converge on the nuclear factor kappa B signaling cascade. Subsequently, we focus on the role of nuclear factor kappa B in cell survival and oxidative stress. Finally, potential therapeutic strategies are discussed that may modify nuclear factor kappa B activity including endogenous antioxidant systems and the Fas/FasL system. However, challenges still remain in developing new therapeutic strategies that not only include identifying novel agents, but also by improving clinical endpoint definitions and by defining biological efficacy.

Activators and target genes of Rel/NF-kappaB transcription factors

The vertebrate transcription factor NF-kappaB is induced by over 150 different stimuli. Active NF-kappaB, in turn, participates in the control of transcription of over 150 target genes. Because a large variety of bacteria and viruses activate NF-kappaB and because the transcription factor regulates the expression of inflammatory cytokines, chemokines, immunoreceptors, and cell adhesion molecules, NF-kappaB has often been termed a 'central mediator of the human immune response'. This article contains a complete listing of all NF-kappaB inducers and target genes described to date. The collected data argue that NF-kappaB functions more generally as a central regulator of stress responses. In addition, NF-kappaB activation blocks apoptosis in several cell types. Coupling stress responsiveness and anti-apoptotic pathways through the use of a common transcription factor may result in increased cell survival following stress insults.