HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons

Multi-omics delineation of cytokine-induced endothelial inflammatory states

Vascular endothelial cells (ECs) form a dynamic interface between blood and tissue and play a crucial role in the progression of vascular inflammation. Here, we aim to dissect the system-wide molecular mechanisms of inflammatory endothelial-cytokine responses. Applying an unbiased cytokine library, we determined that TNFα and IFNγ induced the largest EC response resulting in distinct proteomic inflammatory signatures. Notably, combined TNFα + IFNγ stimulation induced an additional synergetic inflammatory signature. We employed a multi-omics approach to dissect these inflammatory states, combining (phospho-) proteome, transcriptome and secretome and found, depending on the stimulus, a wide-array of altered immune-modulating processes, including complement proteins, MHC complexes and distinct secretory cytokines. Synergy resulted in cooperative activation of transcript induction. This resource describes the intricate molecular mechanisms that are at the basis of endothelial inflammation and supports the adaptive immunomodulatory role of the endothelium in host defense and vascular inflammation.

The New Kid on the Block: HLA-C, a Key Regulator of Natural Killer Cells in Viral Immunity

The human leukocyte antigen system (HLA) is a cluster of highly polymorphic genes essential for the proper function of the immune system, and it has been associated with a wide range of diseases. HLA class I molecules present intracellular host- and pathogen-derived peptides to effector cells of the immune system, inducing immune tolerance in healthy conditions or triggering effective immune responses in pathological situations. HLA-C is the most recently evolved HLA class I molecule, only present in humans and great apes. Differentiating from its older siblings, HLA-A and HLA-B, HLA-C exhibits distinctive features in its expression and interaction partners. HLA-C serves as a natural ligand for multiple members of the killer-cell immunoglobulin-like receptor (KIR) family, which are predominately expressed by natural killer (NK) cells. NK cells are crucial for the early control of viral infections and accumulating evidence indicates that interactions between HLA-C and its respective KIR receptors determine the outcome and progression of viral infections. In this review, we focus on the unique role of HLA-C in regulating NK cell functions and its consequences in the setting of viral infections.

HLA Expression in Uveal Melanoma: An Indicator of Malignancy and a Modifiable Immunological Target

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults, and gives rise to metastases in 50% of cases. The presence of an inflammatory phenotype is a well-known risk factor for the development of metastases. This inflammatory phenotype is characterized by the presence of high numbers of lymphocytes and macrophages, and a high expression of the HLA Class I and II antigens. An abnormal expression of HLA Class I may influence cytotoxic T lymphocyte (CTL) as well as Natural Killer (NK) cell responses. We provide a comprehensive review regarding the inflammatory phenotype in UM and the expression of locus- and allele-specific HLA Class I and of Class II antigens in primary UM and its metastases. Furthermore, we describe the known regulators and the role of genetics (especially chromosome 3 and BRCA-Associated Protein 1 (BAP1 status)), and, last but not least, the effect of putative therapeutic treatments on HLA expression.

Cell Type-Specific Roles of NF-κB Linking Inflammation and Thrombosis

The transcription factor NF-κB is a central mediator of inflammation with multiple links to thrombotic processes. In this review, we focus on the role of NF-κB signaling in cell types within the vasculature and the circulation that are involved in thrombo-inflammatory processes. All these cells express NF-κB, which mediates important functions in cellular interactions, cell survival and differentiation, as well as expression of cytokines, chemokines, and coagulation factors. Even platelets, as anucleated cells, contain NF-κB family members and their corresponding signaling molecules, which are involved in platelet activation, as well as secondary feedback circuits. The response of endothelial cells to inflammation and NF-κB activation is characterized by the induction of adhesion molecules promoting binding and transmigration of leukocytes, while simultaneously increasing their thrombogenic potential. Paracrine signaling from endothelial cells activates NF-κB in vascular smooth muscle cells and causes a phenotypic switch to a “synthetic” state associated with a decrease in contractile proteins. Monocytes react to inflammatory situations with enforced expression of tissue factor and after differentiation to macrophages with altered polarization. Neutrophils respond with an extension of their life span—and upon full activation they can expel their DNA thereby forming so-called neutrophil extracellular traps (NETs), which exert antibacterial functions, but also induce a strong coagulatory response. This may cause formation of microthrombi that are important for the immobilization of pathogens, a process designated as immunothrombosis. However, deregulation of the complex cellular links between inflammation and thrombosis by unrestrained NET formation or the loss of the endothelial layer due to mechanical rupture or erosion can result in rapid activation and aggregation of platelets and the manifestation of thrombo-inflammatory diseases. Sepsis is an important example of such a disorder caused by a dysregulated host response to infection finally leading to severe coagulopathies. NF-κB is critically involved in these pathophysiological processes as it induces both inflammatory and thrombotic responses.

Molecular evolution of elements controlling HLA-C expression: Adaptation to a role as a killer-cell immunoglobulin-like receptor ligand regulating natural killer cell function

The regulatory elements controlling the transcription of the HLA-A, HLA-B, and HLA-C genes have been extensively studied and compared. However, few studies have considered regulatory differences in the HLA genes from the perspective of their role as ligands for the killer-cell immunoglobulin-like receptor (KIR) family of HLA receptors expressed by natural killer (NK) cells. HLA-C is the most recently evolved gene, and there is considerable evidence pointing to its emergence as a specialized KIR ligand playing a major role in the missing-self recognition system of NK cells. Here I evaluate gene-specific differences in regulatory elements of the HLA genes, showing alterations that are consistent with the adaptation of HLA-C to a role in NK cell regulation.

Immunobiology of Inherited Muscular Dystrophies

The immune response to acute muscle damage is important for normal repair. However, in chronic diseases such as many muscular dystrophies, the immune response can amplify pathology and play a major role in determining disease severity. Muscular dystrophies are inheritable diseases that vary tremendously in severity, but share the progressive loss of muscle mass and function that can be debilitating and lethal. Mutations in diverse genes cause muscular dystrophy, including genes that encode proteins that maintain membrane strength, participate in membrane repair, or are components of the extracellular matrix or the nuclear envelope. In this article, we explore the hypothesis that an important feature of many muscular dystrophies is an immune response adapted to acute, infrequent muscle damage that is misapplied in the context of chronic injury. We discuss the involvement of the immune system in the most common muscular dystrophy, Duchenne muscular dystrophy, and show that the immune system influences muscle death and fibrosis as disease progresses. We then present information on immune cell function in other muscular dystrophies and show that for many muscular dystrophies, release of cytosolic proteins into the extracellular space may provide an initial signal, leading to an immune response that is typically dominated by macrophages, neutrophils, helper T-lymphocytes, and cytotoxic T-lymphocytes. Although those features are similar in many muscular dystrophies, each muscular dystrophy shows distinguishing features in the magnitude and type of inflammatory response. These differences indicate that there are disease-specific immunomodulatory molecules that determine response to muscle cell damage caused by diverse genetic mutations. © 2018 American Physiological Society. Compr Physiol 8:1313-1356, 2018.

Expression of classical HLA class I molecules: regulation and clinical impacts: Julia Bodmer Award Review 2015

Human leukocyte antigen (HLA) class I genes are ubiquitously expressed, but in a tissue specific-manner. Their expression is primarily regulated at the transcriptional level and can be modulated both positively and negatively by different stimuli. Advances in sequencing technologies led to the identification of new regulatory variants located in the untranslated regions (UTRs), which could influence the expression. After a brief description of the mechanisms underlying the transcriptional regulation of HLA class I genes expression, we will review how the expression levels of HLA class I genes could affect biological and pathological processes. Then, we will discuss on the differential expression of HLA class I genes according to the locus, allele and UTR polymorphisms and its clinical impact. This interesting field of study led to a new dimension of HLA typing, going beyond a qualitative aspect.

Radiation takes its Toll

The ability to recognize and respond to universal molecular patterns on invading microorganisms allows our immune system to stay on high alert, sensing danger to our self-integrity. Our own damaged cells and tissues in pathological situations activate similar warning systems as microbes. In this way, the body is able to mount a response that is appropriate to the danger. Toll-like receptors are at the heart of this pattern recognition system that initiates innate pro-oxidant, pro-inflammatory signaling cascades and ultimately bridges recognition of danger to adaptive immunity. The acute inflammatory lesions that are formed segue into resolution of inflammation, repair and healing or, more dysfunctionally, into chronic inflammation, autoimmunity, excessive tissue damage and carcinogenesis. Redox is at the nexus of this decision making process and is the point at which ionizing radiation initially intercepts to trigger similar responses to self-damage. In this review we discuss our current understanding of how radiation-damaged cells interact with Toll-like receptors and how the immune systems interprets these radiation-induced danger signals in the context of whole-body exposures and during local tumor irradiation.

Radiation as an immune modulator

Radiation therapy is currently one of the most widely utilized treatment strategies in the clinical management of cancer. Classically, radiation therapy was developed as an anticancer treatment on the basis of its capacity to induce DNA double strand breaks in exposed cancer cells, ultimately resulting in tumor cell death. Recently, our understanding of radiation effects has expanded widely in terms of the consequences of radiation-induced tumor cell death and the pertinent cells, signaling pathways, and molecular sensors that modify the tumor response to radiation. It is now well accepted that inflammation plays a complex dual role in promoting or inhibiting tumor growth. The capacity of inflammatory responses to alter the tumor response to radiation therapy, and vice versa, is now the subject of intense scientific and clinical investigation. Herein, we review the concepts regarding the immunostimulatory properties of radiation therapy with particular focus on the effects of radiation therapy on the tumor microenvironment.

IRF-1 responsiveness to IFN-γ predicts different cancer immune phenotypes

BACKGROUND

Several lines of evidence suggest a dichotomy between immune active and quiescent cancers, with the former associated with a good prognostic phenotype and better responsiveness to immunotherapy. Central to such dichotomy is the master regulator of the acute inflammatory process interferon regulatory factor (IRF)-1. However, it remains unknown whether the responsiveness of IRF-1 to cytokines is able to differentiate cancer immune phenotypes.

METHODS

IRF-1 activation was measured in 15 melanoma cell lines at basal level and after treatment with IFN-γ, TNF-α and a combination of both. Microarray analysis was used to compare transcriptional patterns between cell lines characterised by high or low IRF-1 activation.

RESULTS

We observed a strong positive correlation between IRF-1 activation at basal level and after IFN-γ and TNF-α treatment. Microarray demonstrated that three cell lines with low and three with high IRF-1 inducible translocation scores differed in the expression of 597 transcripts. Functional interpretation analysis showed mTOR and Wnt/β-cathenin as the top downregulated pathways in the cell lines with low inducible IRF-1 activation, suggesting that a low IRF-1 inducibility recapitulates a cancer phenotype already described in literature characterised by poor prognosis.

CONCLUSION

Our findings support the central role of IRF-1 in influencing different tumour phenotypes.

Allele-specific cytokine responses at the HLA-C locus: implications for psoriasis

Psoriasis is an inflammatory skin disorder that is inherited as a complex trait. Genetic studies have repeatedly highlighted HLA-C as the major determinant for psoriasis susceptibility, with the Cw*0602 allele conferring significant disease risk in a wide range of populations. Despite the potential importance of HLA-C variation in psoriasis, either via an effect on peptide presentation or immuno-inhibitory activity, allele-specific expression patterns have not been investigated. Here, we used reporter assays to characterize two regulatory variants, which virtually abolished the response to tumor necrosis factor (TNF)-α (rs2524094) and IFN-γ (rs10657191) in HLA-Cw*0602 and a cluster of related alleles. We validated these findings through the analysis of HLA-Cw*0602 expression in primary keratinocytes treated with TNF-α and IFN-γ. Finally, we showed that HLA-Cw*0602 transcripts are not increased in psoriatic skin lesions, despite highly elevated TNF-α levels. Thus, our findings demonstrate the presence of allele-specific differences in HLA-C expression and indicate that HLA-Cw*0602 is unresponsive to upregulation by key proinflammatory cytokines in psoriasis. These data pave the way for functional studies into the pathogenic role of the major psoriasis susceptibility allele.

Involvement of NF-κB in changes of IFN-γ-induced CIITA/MHC-II and iNOS expression by influenza virus in macrophages

Type II interferon (IFN-γ) plays an important role in defense against viral infection. Although this cytokine is found during influenza virus infection, it seems to have no protective function against the virus, and the reasons for this are not clear. To determine how the influenza virus overcomes the antiviral effects of IFN-γ, we examined the effect of A/Puerto-Rico/8/34 (H1N1) (PR8) infection on the expression of various IFN-γ inducible genes involved in defense against virus infection. The results showed that PR8 selectively affects IFN-γ induced MHC-II and iNOS expression in both the murine macrophage-like cell line, Raw264.7, and in primary alveolar macrophages. Infection of IFN-γ treated macrophages with PR8 resulted in decreased expression of CIITA/MHC-II and increased production of iNOS/NO. These changes correlate with activation of NF-κB but not with JAK/STAT signaling. The data indicate one possible mechanism underlying the ineffectiveness of IFN-γ against influenza virus, and suggest that NF-κB may be a promising target for anti-influenza drugs.

Pathways and promoter networks analysis provides systems topology for systems biology approaches

Systems-level approaches provide help in characterizing the complexity of renal disease. In this review, we illustrate, using a series of recent examples of integrative studies based on pathway analysis and promoter networks, how new techniques allow the analysis of the layout of complex systems and, through this, help answer questions related to renal disease processes. These technologies include the identification of regulatory pathways dysregulated in the context of renal disease, and techniques for studying promoter networks. Both approaches make use of technologies applied to large-scale transcriptomics, transcriptomic profiling by DNA microarrays, or next-generation sequencing.

The tumor-immune microenvironment and response to radiation therapy

Chemotherapy and radiation therapy (RT) are standard therapeutic modalities for patients with cancer, including breast cancer. Historic studies examining tissue and cellular responses to RT have predominantly focused on damage caused to proliferating malignant cells leading to their death. However, there is increasing evidence that RT also leads to significant alterations in the tumor microenvironment, particularly with respect to effects on immune cells infiltrating tumors. This review focuses on tumor-associated immune cell responses following RT and discusses how immune responses may be modified to enhance durability and efficacy of RT.

Influence of apple polyphenols on inflammatory gene expression

Apples (Malus spp., Rosaceae) and products thereof contain high amounts of polyphenols which show diverse biological activities and may contribute to beneficial health effects, like protecting the intestine against inflammation initiated by chronic inflammatory bowel diseases (IBD). IBD are characterized by an excessive release of several proinflammatory cytokines and chemokines by different cell types which results consequently in an increased inflammatory response. In the present study we investigated the preventive effectiveness of polyphenolic juice extracts and single major constituents on inflammatory gene expression in immunorelevant human cell lines (DLD-1, T84, MonoMac6, Jurkat) induced with specific stimuli. Besides the influence on proinflammatory gene expression, the effect on NF-kappaB-, IP-10-, IL-8-promoter-, STAT1-dependent signal transduction, and the relative protein levels of multiple released cytokines and chemokines were studied. DNA microarray analysis of several genes known to be strongly regulated during gastrointestinal inflammation, combined with quantitative real-time PCR (qRT-PCR) revealed that the apple juice extract AE04 (100-200 microg/mL) significantly inhibited the expression of NF-kappaB regulated proinflammatory genes (TNF-alpha, IL-1beta, CXCL9, CXCL10), inflammatory relevant enzymes (COX-2, CYP3A4), and transcription factors (STAT1, IRF1) in LPS/IFN-gamma stimulated MonoMac6 cells without significant effects on the expression of house-keeping genes. A screening of some major compounds of AE04 revealed that the flavan-3-ol dimer procyanidin B(2 )is mainly responsible for the anti-inflammatory activity of AE04. Furthermore, the dihydrochalcone aglycone phloretin and the dimeric flavan-3-ol procyanidin B(1 )significantly inhibited proinflammatory gene expression and repressed NF-kappaB-, IP-10-, IL-8-promoter-, and STAT1-dependent signal transduction in a dose-dependent manner. The influence on proinflammatory gene expression by the applied polyphenols thereby strongly correlated with the increased protein levels investigated by human cytokine array studies. In summary, we evaluated selected compounds responsible for the anti-inflammatory activity of AE04. In particular, procyanidin B(1), procyanidin B(2), and phloretin revealed anti-inflammatory activities in vitro and therefore may serve as transcription-based inhibitors of proinflammatory gene expression.

Glucocorticoid suppression of CX3CL1 (fractalkine) by reduced gene promoter recruitment of NF-kappaB

Glucocorticoids are an important anti-inflammatory treatment of many inflammatory diseases including asthma. However, the mechanisms by which they mediate their suppressive effects are not fully understood. Respiratory epithelial cells are a source of CX(3)CL1 (fractalkine), which mediates cell adhesion and acts as a chemoattractant for monocytes, T cells, and mast cells. We show, in lung A549 epithelial cells, that the tumor necrosis factor-alpha (TNF-alpha) and IFNgamma synergistically induced protein release and mRNA expression of CX(3)CL1 is inhibited by dexamethasone, without interfering with cytokine-induced nuclear translocation of NF-kappaB, and by an inhibitor of IkappaB kinase 2, AS602868. DNA binding assays confirmed the ability of NF-kappaB to bind to the proximal CX(3)CL1 promoter. Chromatin immunoprecipitation assays showed a 5-fold increase in the recruitment of NF-kappaB to the CX(3)CL1 gene promoter in response to IFNgamma/TNF-alpha; this too was reversed by dexamethasone. In contrast, dexamethasone did not displace NF-kappaB from the granulocyte-macrophage colony-stimulating factor gene promoter. We conclude that CX(3)CL1 expression is regulated through the NF-kappaB pathway and that dexamethasone inhibits CX(3)CL1 expression through a glucocorticoid receptor-dependent (RU486 sensitive) mechanism. This study also provides support for the action of glucocorticoids mediating their suppressive effects on expression by interfering with the binding of transcriptional activators at native gene promoters.

Enhancing CTL responses to melanoma cell vaccines in vivo: synergistic increases obtained using IFNgamma primed and IFNbeta treated B7-1+ B16-F10 melanoma cells

Sequentially treating human melanoma cell lines by priming with interferon-gamma before adding interferon-beta was previously found to be the most efficient protocol for producing concurrently increased expression of the three surface antigens B7-1, intercellular adhesion molecule-1 and human histocompatibility leucocyte antigens Class I. The present study describes similar outcomes when the same sequential intercellular adhesion molecule-based protocol is applied to murine B16-F10 melanoma cells as well as preclinical studies using the B16-F10 model as a poorly immunogenic melanoma. Thus, treating B16-F10 cells or a highly expressing B7-1 transfected subline (B16-F10/B7-1 hi) by priming with interferon-gamma for 24 h before adding interferon-beta for a further 48 h (interferon-gamma 72/beta 48) increased expression of all three surface antigens, particularly major histocompatibility complex class I whose increased expression was sustained for several days. As a whole tumour cell vaccine, interferon-gamma 72/beta 48 treated B16-F10 cells produced greater levels of cytoxic T lymphocyte response compared to vaccines prepared from cells treated with a single type of interferon. Furthermore, B16-F10 cells expressing high levels of B7-1 and treated using the interferon-gamma 72/beta 48 protocol (interferon-gamma 72/beta 48-treated B16-F10/B7-1 hi) produced substantially increased cytoxic T lymphocyte responses with a fivefold greater synergy than the combined results of either interferon treated or B7-1 expressing cells tested individually. The resulting CD8+ cytoxic T lymphocyte showed greater specificity for B16-F10 cells with tenfold higher killing than for syngeneic EL-4 lymphoma cells. Killing proceeded via the perforin-mediated pathway. CTL responses were induced independent of CD4+ T helper cells. The majority of mice receiving interferon-gamma 72/beta 48-treated B16-F10/B7-1 hi vaccine in vivo remained tumour free after challenge with 5 x 105 live B16-F10 cells expressing intermediate B7-1 levels. The novel strategy described will help enhance vaccine potency when applied clinically to prepare whole cell based cancer vaccine therapies.

Interferon-β1afor the treatment of multiple sclerosis

At present, two types of recombinant human interferon (IFN)-beta are in clinical use. IFN-beta1a is produced in genetically engineered Chinese hamster ovary cells, and its amino acid sequence and glycosylation pattern are identical to those of endogenous human IFN-beta. The beneficial effect of IFN-beta in multiple sclerosis (MS) probably results from different mechanisms of action, such as a direct effect on plasma cells modulating IgG synthesis, an increase of interleukin (IL)-10 levels, the inhibition of IL-1beta and tumour necrosis factor alpha, the stimulation of IL-1 receptor antagonist production, the inhibition of proliferation of leukocytes, a decreased antigen presentation in microglia, a reduction of T cell migration into the brain by inhibition of the activity of T cell matrix metalloproteinases, and a downregulation of adhesion molecules. IFN-beta1a has been shown by several multicenter controlled trials to be effective in relapsing-remitting MS. It reduces relapse rate by 30-50%, magnetic resonance imaging signs of disease activity in 30-80% and disability progression by 30%. It is also effective in preventing conversion to clinically definite MS when given at the time of a first demyelinating event (i.e., at the very beginning of the clinical disease). No clear evidence of the persistence of the efficacy over the long-term has stood out from a systematic analysis of published trials. A Cochrane review concluded that, in fact, the clinical effect beyond the first year of treatment is not clear. Finally, no efficacy has been shown in secondary progressive or primary progressive MS. However, IFN-beta1a is very well tolerated and the most frequent side effects are mild (local skin reaction and flu-like symptoms) and decline in frequency or disappear after the first 3-6 months of treatment. Although the optimal frequency between once weekly or multiple weekly administrations is still controversial, all protocols require multiple monthly injections. Some patients might find it hard to cope with such a treatment regimen over the long term. Ongoing trials with new powerful immunomodulatory drugs, such as monoclonal antibodies, that require only monthly or bimonthly parenteral administrations will probably offer a better tolerated treatment option in the near future.

Modular activation of nuclear factor-kappaB transcriptional programs in human diabetic nephropathy

Diabetic nephropathy (DN) is the leading cause of end-stage renal failure and a major risk factor for cardiovascular mortality in diabetic patients. To evaluate the multiple pathogenetic factors implicated in DN, unbiased mRNA expression screening of tubulointerstitial compartments of human renal biopsies was combined with hypothesis-driven pathway analysis. Expression fingerprints obtained from biopsies with histological diagnosis of DN (n = 13) and from control subjects (pretransplant kidney donors [n = 7] and minimal change disease [n = 4]) allowed us to segregate the biopsies by disease state and stage by the specific expression signatures. Functional categorization showed regulation of genes linked to inflammation in progressive DN. Pathway mapping of nuclear factor-kappaB (NF-kappaB), a master transcriptional switch in inflammation, segregated progressive from mild DN and control subjects by showing upregulation of 54 of 138 known NF-kappaB targets. The promoter regions of regulated NF-kappaB targets were analyzed using ModelInspector, and the NF-kappaB module NFKB_IRFF_01 was found to be specifically enriched in progressive disease. Using this module, the induction of eight NFKB_IRFF_01-dependant genes was correctly predicted in progressive DN (B2M, CCL5/RANTES, CXCL10/IP10, EDN1, HLA-A, HLA-B, IFNB1, and VCAM1). The identification of a specific NF-kappaB promoter module activated in the inflammatory stress response of progressive DN has helped to characterize upstream pathways as potential targets for the treatment of progressive renal diseases such as DN.

Clinical relevance of soluble HLA-I and beta2-microglobulin levels in non-Hodgkin's lymphoma and Hodgkin's disease

Plasma levels of beta-2 microglobulin (beta2M), a subunit of the human leukocyte antigen-class I (HLA-I) molecule, correlate negatively with outcome in non-Hodgkin's lymphoma (NHL) and Hodgkin's disease (HD). We examined the clinical relevance of soluble HLA-I (sHLA-I) levels in NHL and HD. Sera from consecutive NHL (n=65) and HD (n=37) patients were analyzed in a blinded manner. NHL and HD patients had significantly higher levels of sHLA-1 and beta2M than control subjects. In NHL patients, sHLA-I levels correlated with clinical behavior in a fashion similar to that of beta2M. However, multivariate analysis incorporating beta2M, sHLA-I, and international prognostic index (IPI) indicated that NHL patients with elevated (>312.6mug/100mL) sHLA-I levels had significantly shorter survival, independent of IPI score as well as beta2M. In HD patients, beta2M but not sHLA-I levels were associated with clinical behavior. These findings not only establish the role of sHLA-I as an independent tumor marker in NHL that can be used to stratify patients, but also suggest that beta2M and sHLA-I may reflect different biological processes in HD and NHL. Further studies are needed to assess whether the immunomodulatory properties of sHLA-I may be responsible for its divergence from beta2M as an indicator of clinical behavior in HD.

Differential effects of TNF-alpha and IFN-gamma on gene transcription mediated by NF-kappaB-Stat1 interactions

Regulation of gene transcription by the cytokines tumor necrosis factor-alpha (TNF-alpha) and interferon-gamma (IFN-gamma) involves complex interactions between NF-kappaB and Stat families of transcription factors. The purpose of this study was to identify the spatial promoter requirements that govern cytokine synergy for gene transcription regulated by NF-kappaB and Stat factors. Using a set of transcription reporter-luciferase constructs, we show that the relative orientation of juxtaposed NF-kappaB-Stat (SIE) cis-elements determines the ability of TNF-alpha and IFN- gamma to induce gene transcription. Further, NF-kappaB and Stat1 proteins directly regulate transcription by interacting cooperatively on NF-kappaB-SIE DNA binding in response to TNF-alpha plus IFN-gamma. Coimmunoprecipitation provides evidence for a direct NF-kappaB/Stat1 protein-protein interaction. In contrast, IFN-gamma inhibits TNF-alpha-induced transcription of an NF-kappaB reporter gene in a Stat1-dependent mechanism in 2fTGH fibroblasts. Similarly, Stat1 is inhibitory to NF-kappaB overexpression-induced transcription. IFN-gamma and Stat1-dependent inhibition of NF-kappaB transcription occurs independent of TNF-alpha-induced NF-kappaB DNA binding. Interestingly, IFN-gamma pretreatment of 2fTGH fibroblasts potentiates TNF-alpha induction of Stat1 DNA binding. Further, ChIP analysis was applied to detect cytokine-induced in vivo binding and transcriptional regulation of the human inducible nitric oxide synthase (iNOS) gene by NF-kappaB and Stat1. These data demonstrate complex transcriptional regulatory mechanisms elicited by TNF-alpha and IFN-gamma and have potentially important implications for other genes differentially controlled by cytokines.

MatInspector and beyond: promoter analysis based on transcription factor binding sites

MOTIVATION

Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.

RESULTS

We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).

The role of tumor necrosis factor in modulating responses of murine embryo fibroblasts by flavivirus, West Nile

Murine embryo fibroblasts (MEF) transcribe tumor necrosis factor (TNF) mRNA and secrete soluble TNF in response to infection by West Nile virus (WNV) and TNF was demonstrated to be protective against WNV infection in vitro. TNF is not required for the WNV-induced upregulation of MHC-I expression on MEF, as TNF deficiency did not affect the upregulation of major histocompatibility complex class I (MHC-I) by WNV. Furthermore, NF-kappaB was activated by WNV in TNF-deficient MEF, demonstrating that WNV induces NF-kappaB activation in a TNF-independent manner. The subunits of NF-kappaB activated by TNF and WNV differed, WNV-activated a p65/p50 NF-kappaB complex while TNF-activated NF-kappaB was composed of p65, p50, and c-Rel. Furthermore, TNF-induced activation of NF-kappaB occurred earlier than WNV-induced NF-kappaB activation. The data demonstrate that WNV infection of MEF is associated with TNF production, but the WNV-induced activation of NF-kappaB and subsequent upregulation of MHC-I by WNV is TNF-independent.

Towards quantitative biology: integration of biological information to elucidate disease pathways and to guide drug discovery

Developing a new drug is a tedious and expensive undertaking. The recently developed high-throughput experimental technologies, summarised by the terms genomics, transcriptomics, proteomics and metabolomics provide for the first time ever the means to comprehensively monitor the molecular level of disease processes. The "-omics" technologies facilitate the systematic characterisation of a drug target's physiology, thereby helping to reduce the typically high attrition rates in discovery projects, and improving the overall efficiency of pharmaceutical research processes. Currently, the bottleneck for taking full advantage of the new experimental technologies are the rapidly growing volumes of automatically produced biological data. A lack of scalable database systems and computational tools for target discovery has been recognised as a major hurdle. In this review, an overview will be given on recent progress in computational biology that has an impact on drug discovery applications. The focus will be on novel in silico methods to reconstruct regulatory networks, signalling cascades, and metabolic pathways, with an emphasis on comparative genomics and microarray-based approaches. Promising methods, such as the mathematical simulation of pathway dynamics are discussed in the context of applications in discovery projects. The review concludes by exemplifying concrete data-driven studies in pharmaceutical research that demonstrate the value of integrated computational systems for drug target identification and validation, screening assay development, as well as drug candidate efficacy and toxicity evaluations.

STAT1 regulates lipopolysaccharide- and TNF-alpha-dependent expression of transporter associated with antigen processing 1 and low molecular mass polypeptide 2 genes in macrophages by distinct mechanisms

Transporter associated with Ag processing 1 and low molecular mass polypeptide 2 (LMP2) are essential for class I MHC function and share a common bidirectional promoter. In murine bone marrow-derived macrophages, LPS and TNF-alpha induced Tap1 and up-regulated Lmp2, which is constitutively expressed at low levels. These two genes are induced by LPS and TNF-alpha with distinct kinetics, at 6 and 12-24 h, respectively. Using macrophages derived from the TNF-alpha receptors of knockout mice, we found that induction by LPS is not due to the autocrine production of TNF-alpha. In macrophages from STAT-1 knockout mice, neither LPS nor TNF-alpha induced the expression of Tap1 or Lmp2. The shared promoter contains several areas that can be controlled by STAT-1, such as the proximal and distal IFN-gamma activation site (GAS) boxes in the direction of the Tap1 gene. By making deletions of the promoter, we determined that only the proximal GAS box is required for LPS induction of Tap1 and Lmp2. In contrast, TNF-alpha induction of these two genes is dependent on the IFN regulatory factor-1 and NF-kappaB boxes, and not on the GAS box. Our experiments using gel shift analysis and Abs indicated that STAT1 binds to the GAS box in nuclear extracts from LPS-treated macrophages. The nuclear extracts obtained from macrophages treated with TNF-alpha bound to the IFN regulatory factor-1 and NF-kappaB boxes. These results show that LPS and TNF-alpha regulate the induction of Tap1 and Lmp2 through STAT1, but use distinct areas of the promoter.

T lymphocyte-endothelial cell interactions

Human vascular endothelial cells (EC) basally display class I and II MHC-peptide complexes on their surface and come in regular contact with circulating T cells. We propose that EC present microbial antigens to memory T cells as a mechanism of immune surveillance. Activated T cells, in turn, provide both soluble and contact-dependent signals to modulate normal EC functions, including formation and remodeling of blood vessels, regulation of blood flow, regulation of blood fluidity, maintenance of permselectivity, recruitment of inflammatory leukocytes, and antigen presentation leading to activation of T cells. T cell interactions with vascular EC are thus bidirectional and link the immune and circulatory systems.

Tumour necrosis factor-α stimulates expression of TNF-α converting enzyme in endothelial cells

Tumor necrosis factor-alpha converting enzyme (ADAM17) is a major metalloproteinase involved in the shedding of several membrane-bound cytokines and cytokine receptors. Interplay of cytokines and their soluble receptors might be an important regulatory element in the network of interactions responsible for maintaining homeostasis in the immune system. ADAM17 thus has the potential to participate in a broad range of immune reactions. We studied the mechanisms of ADAM17 activation in endothelial cells and found that pro-inflammatory cytokines (tumor necrosis factor-alpha, interleukin-1beta, interferon-gamma) and growth factors (epidermal growth factor, vascular endothelial growth factor) are able to upregulate transcription of ADAM17 and expression of ADAM17 protein. This process might constitute an important mechanism of regulation of ADAM17 activity. Stimulation of transcription, rather than increased ADAM17 mRNA stability, was responsible for increased levels of ADAM17 mRNA. Importantly, the increase in ADAM17 was accompanied by increased shedding of TNF-Receptor I (p55) in tumor necrosis factor-alpha-stimulated endothelial cells. Therefore, ADAM17-dependent depletion of membrane-bound tumor necrosis factor receptors from endothelial cells might constitute a mechanism of self-protection in states of prolonged immunostimulation.

Leishmania donovani induces interferon regulatory factor in murine macrophages: a host defense response

Macrophages play a key role in directing the host immune response to infection. Interaction of Leishmania donovani with macrophages results in the antagonization of host defense mechanisms by interfering with a cascade of cell signaling processes in the macrophages. Macrophages secrete interferon (IFN), as well as other cytokines, following lipopolysaccharide (LPS) stimulation. The interferon regulatory factors (IRFs) comprise a family of DNA-binding proteins that have been implicated in the transcriptional regulation of IFN and certain IFN-inducible genes. IRF-1 is a transcription factor, which regulates induction of several macrophage effectors and is known to bind to IRF-E site in the inducible nitric oxide synthase (iNOS) promoter. We for the first time report that L. donovani and its surface molecule lipophosphoglycan (LPG) result in a dose- and time-dependent activation of IRF-DNA-binding activity in macrophages. The components of this novel LPG-stimulated IRF-like complex are unclear. The interaction of parasite with the macrophages and not the cellular uptake was important for IRF activation. The use of inhibitors selective for ERK (PD98059) and p38 (SB203580) mitogen-activated protein (MAP) kinase pathway showed that preincubation of cells with either SB203580 or PD98059 did not affect the binding activity of IRF-E, suggesting that both p38 and ERK MAP kinase activation are not necessary for IRF-E activation. It is likely that induction of IRF in response to infection by L. donovani represents a host defense mechanism.

Replacement of 198MQMDII203 of mouse IRF-1 by 197IPVEVV202 of human IRF-1 abrogates induction of IFN-β, iNOS, and COX-2 gene expression by IRF-1

Interferon regulatory factor-1 (IRF-1) is a transcription factor exhibiting functional diversity because of its ability to activate transcription from promoters of several IRF-1-dependent genes. It is a modular protein, where the overall structure is not essential for function of its individual domains. A comparison of the mouse and human IRF-1 amino acid sequences enabled us to identify a stretch of six amino acids (198-203) within the transactivation domain of mouse IRF-1, 198MQMDII(203) to be different from that of the human IRF-1, 197IPVEVV(202). This indicated a possible functional significance of the six amino acid stretches in the two IRF-1 molecules. The murine IRF-1 sequence at 198-203 (MQMDII) was replaced by IPVEVV. Recombinant wild type mouse IRF-1 with 198MQMDII(203) and its mutant form with 198IPVEVV(203), expressed as GST-IRF-1-fusion proteins, showed similar DNA-binding activity. However, ectopic expression of the wild type and mutant IRF-1 in the human embryonic kidney (HEK-293) cells showed the effect of replacement of this region on expression of a few chromosomal genes that are transcriptionally activated by IRF-1 viz. IFN-beta, iNOS, and COX-2 genes. In our study, expression of wild type IRF-1 activated these genes as judged by RT-PCR but the mutant IRF-1 did not show this effect. Thus, the MQMDII (198-203 a.a.) region of mouse IRF-1 has a functional context in relation to expression of IRF-1-inducible genes.

Locus-specific constitutive and cytokine-induced HLA class I gene expression

Cytokine induction of the MHC class I genes increases the nascent molecules available for binding potentially antigenic peptides. The human H chain loci, HLA-A, -B, and -C, encode highly homologous and polymorphic mRNAs. Here, these transcripts were resolved and measured by competitive PCR of cDNA using locus-specific primers. Endothelial cells expressed many HLA-A and -B, but fewer HLA-C, transcripts. In contrast, HeLa cells expressed many HLA-A and -C, but fewer HLA-B, transcripts. The inflammatory cytokines TNF-alpha, IFN-beta, and IFN-gamma induced HLA-B strongly, but HLA-A and -C weakly in both cell types. Combined treatment with IFNs and TNF further increased HLA-A and -B, but not HLA-C transcripts. The constitutive and inducible activities of transfected promoters correlated well with mRNA levels. The weak IFN response of the HLA-A2 promoter was not due to variations in the IFN consensus sequence, the site alpha, or a 3-bp insertion between them. The HLA-Cw6 promoter was less TNF responsive due to a variant kappaB enhancer, which also reduced the IFN responses. The NF-kappaB subunit RelA strongly activated the HLA-A2 and -B7 promoters but only weakly activated the HLA-Cw6 promoter due to the variant kappaB. Cotransfecting NF-kappaB1 with RelA further increased activity of the HLA-A2 and -B7, but not HLA-Cw6, promoters. All three promoters were activated by MHC class II trans-activator, but not CREB-binding protein, whereas IFN regulatory factor-1 and -2 weakly activated the HLA-B7 and -Cw6, but not HLA-A2, promoters. These studies illustrate common and locus-specific mechanisms that may be targeted to modulate immune reactions.

The transcriptional coactivator CREB-binding protein cooperates with STAT1 and NF-kappa B for synergistic transcriptional activation of the CXC ligand 9/monokine induced by interferon-gamma gene

Signal transducers and activators of transcription 1 (STAT1) and NF-kappaB cooperatively regulate the expression of many inflammatory genes. In the present study, we demonstrate that the transcriptional coactivator CREB-binding protein (CBP) mediated the STAT1/NF-kappaB synergy for transcription of the gene for CXC ligand 9 (CXCL9), an interferon-gamma (IFN-gamma)-inducible chemokine. Reporter gene analysis showed that expression of CBP potentiated IFN-gamma and tumor necrosis factor (TNFalpha)-induced promoter activity and that the CBP-mediated synergy depended upon STAT1- and NF-kappaB-binding sites in the promoter. Experiments with CBP mutants indicated that the N-terminal and C-terminal regions were necessary for the transcriptional synergy, although the histone acetyltransferase activity of CBP was dispensable. A co-immunoprecipitation assay demonstrated that STAT1 and NF-kappaB RelA (p65) simultaneously associated with CBP in vivo. Furthermore, chromatin immunoprecipitation revealed that, although costimulation with IFN-gamma and TNFalpha did not cooperatively enhance the levels of acetylated histones, it did result in increased recruitment of STAT1, CBP, and RNA polymerase II at the promoter region of the CXCL 9 gene. Together, these results demonstrate that the STAT1/NF-kappaB-dependent transcriptional synergy could result from the enhanced recruitment of RNA polymerase II complex to the promoter via simultaneous interaction of CBP with STAT1 and NF-kappaB.

Substance P enhances the production of interferon-induced protein of 10 kDa by human keratinocytes in synergy with interferon-gamma

A neuropeptide substance P is related to skin inflammation. Interferon-induced protein of 10 kDa (IP-10) chemoattracts T helper 1 cells, and interferon-induced protein of 10 kDa production by keratinocytes is enhanced in inflammatory skin diseases such as psoriasis. We examined the in vitro effects of substance P on interferon-induced protein of 10 kDa production by human keratinocytes. Though substance P alone did not induce interferon-induced protein of 10 kDa production, it enhanced interferon-induced protein of 10 kDa secretion, mRNA expression, and promoter activity induced by suboptimal concentrations of interferon-gamma. Interferon-stimulated response element and two nuclear factor-kappaB sites on interferon-induced protein of 10 kDa promoter were responsible for the enhancement by substance P. Substance P alone enhanced transcriptional activity and transcription factor binding through the two nuclear factor-kappaB sites, whereas it did not alter interferon-gamma-induced transcriptional activity and transcription factor binding through interferon-stimulated response element. The effects of substance P on interferon-induced protein of 10 kDa production and nuclear factor-kappaB activation were inhibited by neurokinin-1 receptor antagonist, phospholipase C inhibitor, intracellular Ca2+ chelator, and anti-oxidant. These results suggest that substance P may induce nuclear factor-kappaB activation and interferon-induced protein of 10 kDa production in synergy with interferon-gamma via neurokinin-1 receptor on keratinocytes. These effects of substance P may be mediated via phospholipase C activation, intra-cellular Ca2+ signal, and reactive oxygen intermediates.

Nuclear transcription factors in the hippocampus

In the mammalian hippocampus, there is a trisynaptic loop that has been often referred to in studies on learning and memory mechanisms and their physiological correlate, the long-term potentiation (LTP). The three sets of synapses are formed by the fibers of perforant pathway terminating on granule cells and by the mossy fibers and Schaeffer collaterals making connections with the pyramidal cells. Each of the three types of synapses can develop LTP. LTP is accompanied by changes in gene expression and it is the nuclear transcription, involving specific transcription factors, that is the starting point for the series of biological amplifications and consolidations both necessary for such sustained changes. The transcription factors are proteins that control gene expression, development and functional formation in every eukaryotic cell. Two categories of transcription factors have been defined to date: general factors that comprise at least 20 proteins to form multiple preinitiation complex at the TATA box (TATA rich sequence) or regulatory factors that bind to promoter or enhancer regions at specific sites on the DNA close to, or distant from, the TATA box. Transcription factors have been divided into five different major classes according to unique protein motifs. These include basic domain, zinc-finger, helix-turn-helix, beta-Scaffold factors with minor groove contacts and other transcription factors not specifically classified. Much evidence has been accumulating in favor of the participation of several transcription factors in the consolidation of memory in the mammalian hippocampus following a spatial memory task. It is, therefore, of great importance that the involvement of transcription factors in de novo protein synthesis relevant to the synaptic mechanisms that mediate the formation of long-term memory should be summarized and discussed. No specific correlation between transduction of extracellular signals and expression of nuclear transcription factors, however, has been demonstrated to date.

Regulation of the expression of mouse TAP-associated glycoprotein (tapasin) by cytokines

The expression of antigen presenting MHC class I molecules can be enhanced through cytokines, e.g. upon infection with bacteria or viruses, either directly by enhancing class I gene transcription or by increasing the amounts of accessory proteins of the loading complex. Tapasin plays a significant role in the peptide loading of class I molecules. Here, we describe recognition motifs of cytokine inducible transcription factors in the promoter region of the mouse tapasin gene, most of them clustered within the 140 base pairs upstream of the start codon. Tapasin mRNA was strongly induced in vivo after infection with the facultatively intracellular bacterium Listeria monocytogenes in an IFN-gamma-dependent fashion. Accordingly, both tapasin mRNA and protein were strongly induced in a time and dose dependent manner in embryonic fibroblasts treated with the cytokines IFN-gamma and IFN-beta, and weakly induced after treatment with TNF-alpha. Co-stimulation of tapasin by TNF-alpha and IFN-gamma resulted in a weak synergistic effect. Using fibroblasts either lacking IRF-1 or inhibited in protein synthesis we show that secondary transcription factors are necessary for a maximal stimulation of tapasin expression upon IFN-gamma stimulation. The sequential induction of TAP1, LMP2, and tapasin before the stimulated expression of class I heavy chain is discussed.

Endothelial injury: cause and effect of alloimmune inflammation

This review discusses the concept that endothelial cells may facilitate inflammation, but are also targets of the inflammatory response. Endothelial cells express several molecules that promote leukocyte recruitment, and other molecules, such as MHC class I that enable endothelial injury. Circulating alloantibodies produced following transplantation may also target the endothelium for injury. It has been shown that the expression of select protective genes within endothelial cells, including anti-apoptotic genes, may provide resistance to immune-mediated injury. Thus, an understanding of the mechanisms by which endothelial cells are injured and by which endothelial cells are protected is important for our understanding of allograft rejection.

Transcription factor NF-IL6 (C/EBPbeta) activates the expression of the mouse MHC class I H2-Kb gene in response to TNF-alpha via the intragenic downstream regulatory element

The 5'-enhancer-deleted genomic construct of the H2-K(b) gene, stably integrated into the genome of L(tk-) fibroblasts, retains full competence to be induced by tumor necrosis factor-alpha (TNF-alpha) treatment. The only defined regulatory region in this construct is the intragenic downstream regulatory element (H2DRE). Computational inspection uncovered two potential NF-IL6 (C/EBPbeta) binding motifs within the H2DRE. Chloramphenicol acetyltransferase (CAT) reporter gene assay revealed that NF-IL6 is able to elevate transcription from H2DRE. Moreover, transient transfection of an NF-IL6 expression vector increased both constitutive and TNF-alpha-induced mRNA levels of endogenous H2 class I genes, and transfection of an NF-IL6 dominant negative construct decreased the expression of endogenous H2 class I genes in a dose-dependent manner. Using the electrophoretic mobility shift assay (EMSA) and antibody supershift assay, we were able to qualify the two computationally identified NF-IL6 binding motifs as one high-affinity and one low-affinity binding site. We conclude that the H2-K(b) gene belongs to target genes of the NF-IL6 (C/EBPbeta) in the course of the cellular response to TNF-alpha, and we discuss some consequences of this conclusion in a general framework of inducible expression of the H2-K(b) gene.

Critical role of tumor necrosis factor-alpha and NF-kappa B in interferon-gamma -induced CD40 expression in microglia/macrophages

CD40 is a member of the tumor necrosis factor (TNF) receptor superfamily. CD40 expression on antigen-presenting cells (including macrophages and microglia) is crucial for T-cell activation. Aberrant expression of CD40 has been associated with autoimmune inflammatory diseases such as multiple sclerosis and rheumatoid arthritis. We have recently shown that the cytokine interferon (IFN)-gamma is the most potent inducer of CD40 expression in macrophages and microglia, and this induction is mediated by the IFN-gamma-activated transcription factor STAT-1alpha and constitutively expressed PU.1 and/or Spi-B. In this study, we have discovered that a major component of IFN-gamma-induced CD40 expression involves the endogenous production of the cytokine TNF-alpha. The inclusion of anti-TNF-alpha-neutralizing antibody significantly inhibits IFN-gamma-induced CD40 mRNA and CD40 promoter activity. IFN-gamma-induced CD40 protein expression is attenuated in TNF-alpha-deficient microglia and can be restored with exogenous TNF-alpha. Site-directed mutagenesis studies demonstrate that three of the four NF-kappaB elements in the CD40 promoter are required for IFN-gamma-induced CD40 promoter activity. IFN-gamma treatment leads to the activation of NF-kappaB in a time-dependent manner, which is inhibited in the presence of anti-TNF-alpha-neutralizing antibody. These results indicate that IFN-gamma-induced TNF-alpha production and subsequent NF-kappaB activation are integral parts of the mechanism of IFN-gamma-induced CD40 expression.

Activation of signal transducer and activator of transcription 1 (STAT1) is not sufficient for the induction of STAT1-dependent genes in endothelial cells. Comparison of interferon-gamma and oncostatin M

We compared human endothelial cell (EC) responses to interferon-gamma (IFN gamma) and oncostatin M (OnM), cytokines that utilize Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling. Both cytokines cause phosphorylation of Tyr residue 701 and Ser residue 727 of STAT1, as shown by immunoblotting. Both activate DNA binding of STAT1 homodimers, shown by electrophoretic mobility shift assay. However, only IFN gamma increases expression of three STAT1-dependent gene products examined, namely transporter associated with antigen processing-1 (TAP1), interferon regulatory factor-1 (IRF1), and class I major histocompatibility complex (MHC) protein, as demonstrated by immunoblotting. Only IFN gamma increases TAP1 transcription assessed by reporter gene assay. OnM pretreatment or co-treatment does not inhibit IFN gamma responses. Interestingly, IFN gamma activation of STAT1 is considerably more long-lived than that produced by OnM. To determine whether duration is functionally significant, we transduced EC with a chimeric receptor containing extracellular domains of platelet-derived growth factor receptor beta and intracellular regions of gp130, the signaling subunit of the OnM receptor, mutated to prevent binding of the tyrosine phosphatase SHP-2. Addition of platelet-derived growth factor to such transduced cells produces STAT1 activation that is comparable in magnitude and duration to that caused by IFN gamma, but still fails to induce TAP1, IRF1, or class I MHC molecules. OnM also activates STAT1 but not transcription of STAT1-dependent genes in HepG2 cells. Transient transfection of HepG2 cells with a STAT-defective mouse IFN gamma receptor failed to complement the OnM STAT signal. We conclude that STAT1 activation is necessary but not sufficient for induction of transcription of IFN gamma-responsive genes. However, signals provided by IFN gamma other than STAT1 activation cannot be provided in trans to complement the response to OnM.

IRF and tuberculosis

Tuberculosis is the most prevalent infectious disease and causes more deaths than any other, yet only 5%-10% of people infected by the causative agent, Mycobacterium tuberculosis, will develop the disease. Thus, natural resistance among humans is the norm. Fundamental immune responses to M. tuberculosis are being elucidated, including induction of interferon regulatory factor-1 (IRF-1). Moreover, IRF-1 has been found necessary for normal resistance to infection by mycobacteria in mice. Roles for IRF-1 in a plethora of immune system functions have been described. This review considers molecular responses to infection by M. tuberculosis that might account for induction of IRF-1 and highlights putative connections between immunomodulatory functions of IRF-1 and immune responses relevant to infection by M. tuberculosis. However, the complexity inherent in pleiotropy and redundancy limits the ability to draw firm conclusions. In many cases, it remains to be demonstrated that a particular function of IRF-1 is the basis for a known response to infection. For example, although IRF-1 is required for a Th1 cell-mediated, adaptive immune response in some circumstances, it is not known if the Th1 response to infection by M. tuberculosis requires IRF-1. Conversely, some known contributions by IRF-1 to fundamental aspects of the immune system are not yet proven relevant in the host response to infection. For example, it is not known if control of T cell subset development by IRF-1 is significant for host defense against M. tuberculosis. Functions of other IRF that overlap with or are distinct from the functions of IRF-1 also could be important for the immune response to M. tuberculosis.

Regulation of apoptotic cell death by cytokines in a human salivary gland cell line: distinct and synergistic mechanisms in apoptosis induced by tumor necrosis factor alpha and interferon gamma

We examined the mechanisms of apoptosis in a human salivary gland (HSG) cell line induced by tumor necrosis factor (TNF) alpha and interferon (IFN) gamma. DNA fragmentation and the activation of caspase-3 were determined in HSG cells cultured with TNF-alpha or IFN-gamma. Mitochondrial dysfunction also appeared to be involved in the process because a disruption of mitochondrial transmembrane potential with the activation of caspase-9 was demonstrated in TNF-alpha- and IFN-gamma-stimulated HSG cells. Activation of caspase-8 was thought to be essential in TNF-alpha--induced apoptosis of HSG cells; however, the activation of caspase-8 was not involved in IFN-gamma-induced apoptosis of HSG cells. In contrast, Bcl-2 appeared to be an indispensable regulatory molecule in IFN-gamma-induced, but not in TNF-alpha-induced, apoptosis of HSG cells because its expression was inhibited in IFN-gamma-stimulated, but not in TNF-alpha-stimulated, cells. The inhibitory effect of IFN-gamma in Bcl-2 expression was enhanced by coadministration of TNF-alpha and, interestingly, apoptosis of HSG cells, as assessed by DNA fragmentation and the activation of caspase-9 and caspase-3, and disruption of mitochondrial transmembrane potential was also synergistically augmented by TNF-alpha and IFN-gamma. Our results suggest that cytokines expressed in the salivary glands of patients with Sjögren syndrome play an important role in regulating apoptosis of acinar-ductal epithelial cells through distinct and synergistic mechanisms, thereby modulating salivary gland function in patients with Sjögren syndrome.

Analysis of gene expression using high-density and IFN-gamma-specific low-density cDNA arrays

The combination of high and low density cDNA filter array technology potentially permits both the identification of subsets of induced genes and convenient and rapid multisample expression profiling of such subsets under a variety of conditions. The JAK/STAT1 pathway for IFN-gamma signaling in human cells has been well characterized, but the extent and importance of additional pathways remain to be established. Here, using high-density filter arrays of the RZPD UniGene set, we identified 18 novel IFN-gamma-inducible genes. Expression profiling was carried out using low-density arrays representing both novel and known IFN-gamma-inducible genes. Initial experiments failed to detect evidence for any novel non-JAK-dependent pathways in cells expressing a kinase-dead JAK2. The data, however, validated the potential of the combined methods in establishing rapid and convenient expression profiling of several hundred genes in response to any ligand of choice.

Organization and functional analysis of the mouse transporter associated with antigen processing 2 promoter

In accordance with the key role of MHC class I molecules in the adaptive immune response against viruses, they are expressed by most cells, and their expression can be enhanced by cytokines. The assembly and cell surface expression of class I complexes depend on a continuous peptide supply. The peptides are generated mainly by the proteasome and are transported to the endoplasmic reticulum by a peptide transport pump consisting of two subunits, TAP1 and TAP2. The proteasome low molecular weight polypeptide (2 and 7), as well as TAP (1 and 2) genes, are coordinately regulated and are induced by IFNs. Despite this coordinate regulation, examination of tumors shows that these genes can be discordantly down-regulated. In pursuing a molecular explanation for these observations, we have characterized the mouse TAP2 promoter region and 5'-flanking sequence. We show that the 5' untranslated regions of TAP2 genes have a characteristic genomic organization that is conserved in both the mouse and the human. The mouse TAP2 promoter belongs to a class of promoters that lack TATA boxes but contain a MED1 (multiple start site element downstream) sequence. Accordingly, transcription is initiated from multiple sites within a 100-nucleotide window. An IFN regulatory factor 1 (IRF1)/IRF2 binding site is located in this region and is involved in both basal and IRF1-induced TAP2 promoter activity. The implication of the extensive differences found among the promoters of class I heavy chain, low molecular weight polypeptide, and TAP genes, all encoding proteins involved in Ag presentation, is discussed.

Induction of endothelial-leukocyte interaction by interferon-gamma requires coactivation of nuclear factor-kappaB

To determine whether nuclear factor (NF)-kappaB is necessary to confer endothelial cell responsiveness to interferon (INF)-gamma in terms of vascular cell adhesion molecule (VCAM)-1 expression and leukocyte adhesion, human endothelial cells were treated with IFN-gamma in the presence of low concentrations (LCs) of interleukin (IL)-1alpha (</=100 pg/mL), which activates NF-kappaB but does not induce VCAM-1 expression. Although IFN-gamma induced major histocompatibility complex class II antigen expression and although a high concentration of IL-1alpha (10 ng/mL) induced leukocyte adhesion and VCAM-1 expression, neither IFN-gamma nor LC IL-1alpha was able to induce VCAM-1 expression or leukocyte adhesion. However, the combination of IFN-gamma and LC IL-1alpha induced VCAM-1 expression and increased leukocyte adhesion (67% and 49% of high-concentration IL-1alpha, respectively). Electrophoretic mobility shift assays and immunoblotting of nuclear extracts showed that IFN-gamma activated signal transducers and activators of transcription (STAT)-1alpha and interferon regulatory factor (IRF)-1 but not NF-kappaB, whereas LC IL-1alpha activated NF-kappaB but not STAT-1alpha or IRF-1. Nuclear run-on studies showed that LC IL-1alpha is necessary but not sufficient for inducing VCAM-1 gene transcription and that the combination of IFN-gamma and LC IL-1alpha is required for full VCAM-1 gene transcription. These findings suggest that factors that activate NF-kappaB can synergize with IFN-gamma in promoting endothelial-leukocyte interaction.

MHC class I gene expression and regulation

Major histocompatibility complex (MHC) is a conglomerate of genes that play an important role in recognition of self and nonself. These genes are under tight control. In this review we have discussed the transcription processes regulating MHC gene expression. Various biological or chemical modulators can modulate MHC gene expression. The promoter region of class I genes can be activated through several pathways. Hence, these genes are not typical "domestic" genes. Extensive studies on regulation of MHC class I expression, using transfection techniques and transgenic animal models, have resulted in identification of various cis-acting sequences involved in positive and negative regulation of class I genes. Work is in progress to identify the transacting proteins that bind to these sites and to delineate the mechanisms that regulate constitutive and inducible expression of class I genes in normal and diseased cells. It has been seen that various biological molecules (IFN, GM-CSF, IL-2) and other chemicals up-regulate the MHC expression. If the exact mechanisms are known by which the expression of class I genes is up regulated, the efforts can be made to balance the beneficial and toxic effects of biological molecules with one another, which may facilitate the use of combination of these molecules in subpharmacological doses (to eliminate toxicity) for early and better management of neoplastic diseases, as it is well-known that during malignancy MHC gene expression is down-regulated. In the future, the use of transgenic and knockout mice will be useful in acquiring a better understanding, which may further help in cancer therapy.

Immune response in Stat2 knockout mice

Type I IFNs induce gene expression through Stat1 and Stat2, which can in turn associate either to form Stat1 homodimers or the transcription factor ISGF-3. Stat1 homodimers also transduce signals for IFN-gamma. To explore the unique properties of Stat2 and ISGF-3 in type I IFN signaling, its gene was targeted for deletion. Stat2 null mice exhibit a number of defects in immune response. This includes an increased susceptibility to viral infection and the loss of a type I IFN autocrine/ paracrine loop, which in turn regulates several aspects of immune response. Intriguingly, Stat2-deficient fibroblasts exhibit a more significant defect in their response to type I IFNs than macrophages, highlighting tissue-specific differences in the response to this family of ligands.