Open questions in the NF-κB field.

A variety of stress signals leads to activation of the inducible transcription factor NF-κB, one of the master regulators of the innate immune response. Despite a wealth of information available on the NF-κB core components and its control by different activation pathways and negative feedback loops, several levels of complexity hamper our understanding of the system. This has also contributed to the limited success of NF-κB inhibitors in the clinic and explains some of their unexpected effects. Here we consider the molecular and cellular events generating this complexity at all levels and point to a number of unresolved questions in the field. We also discuss potential future experimental and computational strategies to provide a deeper understanding of NF-κB and its coregulatory signaling networks.

Understanding and Therapeutic Targeting of the p53 Network.

Signaling networks function as highly intertwined regulatory hubs rather than linear cascades with a single endpoint [...].

Phosphorylation of the PA subunit of influenza polymerase at Y393 prevents binding of the 5'-termini of RNA and polymerase function.

The influenza A virus (IAV) polymerase is a multifunctional machine that can adopt alternative configurations to perform transcription and replication of the viral RNA genome in a temporally ordered manner. Although the structure of polymerase is well understood, our knowledge of its regulation by phosphorylation is still incomplete. The heterotrimeric polymerase can be regulated by posttranslational modifications, but the endogenously occurring phosphorylations at the PA and PB2 subunits of the IAV polymerase have not been studied. Mutation of phosphosites in PB2 and PA subunits revealed that PA mutants resembling constitutive phosphorylation have a partial (S395) or complete (Y393) defect in the ability to synthesize mRNA and cRNA. As PA phosphorylation at Y393 prevents binding of the 5' promoter of the genomic RNA, recombinant viruses harboring such a mutation could not be rescued. These data show the functional relevance of PA phosphorylations to control the activity of viral polymerase during the influenza infectious cycle.

TRAF6 Phosphorylation Prevents Its Autophagic Degradation and Re-Shapes LPS-Triggered Signaling Networks.

The ubiquitin E3 ligase TNF Receptor Associated Factor 6 (TRAF6) participates in a large number of different biological processes including innate immunity, differentiation and cell survival, raising the need to specify and shape the signaling output. Here, we identify a lipopolysaccharide (LPS)-dependent increase in TRAF6 association with the kinase IKKε (inhibitor of NF-κB kinase subunit ε) and IKKε-mediated TRAF6 phosphorylation at five residues. The reconstitution of TRAF6-deficient cells, with TRAF6 mutants representing phosphorylation-defective or phospho-mimetic TRAF6 variants, showed that the phospho-mimetic TRAF6 variant was largely protected from basal ubiquitin/proteasome-mediated degradation, and also from autophagy-mediated decay in autolysosomes induced by metabolic perturbation. In addition, phosphorylation of TRAF6 and its E3 ligase function differentially shape basal and LPS-triggered signaling networks, as revealed by phosphoproteome analysis. Changes in LPS-triggered phosphorylation networks of cells that had experienced autophagy are partially dependent on TRAF6 and its phosphorylation status, suggesting an involvement of this E3 ligase in the interplay between metabolic and inflammatory circuits.

MEKK1-Dependent Activation of the CRL4 Complex Is Important for DNA Damage-Induced Degradation of p21 and DDB2 and Cell Survival.

Cullin-4 ubiquitin ligase (CRL4) complexes are differentially composed and highly dynamic protein assemblies that control many biological processes, including the global genome nucleotide excision repair (GG-NER) pathway. Here, we identified the kinase mitogen-activated protein kinase kinase kinase 1 (MEKK1) as a novel constitutive interactor of a cytosolic CRL4 complex that disassembles after DNA damage due to the caspase-mediated cleavage of MEKK1. The kinase activity of MEKK1 was important to trigger autoubiquitination of the CRL4 complex by K48- and K63-linked ubiquitin chains. MEKK1 knockdown prohibited DNA damage-induced degradation of the CRL4 component DNA-damage binding protein 2 (DDB2) and the CRL4 substrate p21 and also cell recovery and survival. A ubiquitin replacement strategy revealed a contribution of K63-branched ubiquitin chains for DNA damage-induced DDB2/p21 decay, cell cycle regulation, and cell survival. These data might also have implications for cancer, as frequently occurring mutations of MEKK1 might have an impact on genome stability and the therapeutic efficacy of CRL4-dependent immunomodulatory drugs such as thalidomide derivatives.

Regulation of Transcription Factor NF-κB in Its Natural Habitat: The Nucleus.

Activation of the transcription factor NF-κB elicits an individually tailored transcriptional response in order to meet the particular requirements of specific cell types, tissues, or organs. Control of the induction kinetics, amplitude, and termination of gene expression involves multiple layers of NF-κB regulation in the nucleus. Here we discuss some recent advances in our understanding of the mutual relations between NF-κB and chromatin regulators also in the context of different levels of genome organization. Changes in the 3D folding of the genome, as they occur during senescence or in cancer cells, can causally contribute to sustained increases in NF-κB activity. We also highlight the participation of NF-κB in the formation of hierarchically organized super enhancers, which enable the coordinated expression of co-regulated sets of NF-κB target genes. The identification of mechanisms allowing the specific regulation of NF-κB target gene clusters could potentially enable targeted therapeutic interventions, allowing selective interference with subsets of the NF-κB response without a complete inactivation of this key signaling system.

Chromatin Targeting of HIPK2 Leads to Acetylation-Dependent Chromatin Decondensation.

The protein kinase homeodomain-interacting protein kinase 2 (HIPK2) plays an important role in development and in the response to external cues. The kinase associates with an exceptionally large number of different transcription factors and chromatin regulatory proteins to direct distinct gene expression programs. In order to investigate the function of HIPK2 for chromatin compaction, HIPK2 was fused to the DNA-binding domains of Gal4 or LacI, thus allowing its specific targeting to binding sites for these transcription factors that were integrated in specific chromosome loci. Tethering of HIPK2 resulted in strong decompaction of euchromatic and heterochromatic areas. HIPK2-mediated heterochromatin decondensation started already 4 h after its chromatin association and required the functionality of its SUMO-interacting motif. This process was paralleled by disappearance of the repressive H3K27me3 chromatin mark, recruitment of the acetyltransferases CBP and p300 and increased histone acetylation at H3K18 and H4K5. HIPK2-mediated chromatin decompaction was strongly inhibited in the presence of a CBP/p300 inhibitor and completely blocked by the BET inhibitor JQ1, consistent with a causative role of acetylations for this process. Chromatin tethering of HIPK2 had only a minor effect on basal transcription, while it strongly boosted estrogen-triggered gene expression by acting as a transcriptional cofactor.

Sixty Years of Placebo-Controlled Antipsychotic Drug Trials in Acute Schizophrenia: Systematic Review, Bayesian Meta-Analysis, and Meta-Regression of Efficacy Predictors.

OBJECTIVE: Antipsychotic drug efficacy may have decreased over recent decades. The authors present a meta-analysis of all placebo-controlled trials in patients with acute exacerbations of schizophrenia, and they investigate which trial characteristics have changed over the years and which are moderators of drug-placebo efficacy differences. METHOD: The search included multiple electronic databases. The outcomes were overall efficacy (primary outcome); responder and dropout rates; positive, negative, and depressive symptoms; quality of life; functioning; and major side effects. Potential moderators of efficacy were analyzed by meta-regression. RESULTS: The analysis included 167 double-blind randomized controlled trials with 28,102 mainly chronic participants. The standardized mean difference (SMD) for overall efficacy was 0.47 (95% credible interval 0.42, 0.51), but accounting for small-trial effects and publication bias reduced the SMD to 0.38. At least a "minimal" response occurred in 51% of the antipsychotic group versus 30% in the placebo group, and 23% versus 14% had a "good" response. Positive symptoms (SMD 0.45) improved more than negative symptoms (SMD 0.35) and depression (SMD 0.27). Quality of life (SMD 0.35) and functioning (SMD 0.34) improved even in the short term. Antipsychotics differed substantially in side effects. Of the response predictors analyzed, 16 trial characteristics changed over the decades. However, in a multivariable meta-regression, only industry sponsorship and increasing placebo response were significant moderators of effect sizes. Drug response remained stable over time. CONCLUSIONS: Approximately twice as many patients improved with antipsychotics as with placebo, but only a minority experienced a good response. Effect sizes were reduced by industry sponsorship and increasing placebo response, not decreasing drug response. Drug development may benefit from smaller samples but better-selected patients.

NF-kappaB inhibitors for the treatment of inflammatory diseases and cancer.

The NF-kappaB/Rel signaling system is a paradigm for gene activation in response to inflammatory and menacing stimuli. Given the growing body of evidence showing an important involvement of NF-kappaB for the onset of autoimmune diseases and different types of cancer, NF-kappaB is an important drug target for the adjuvant therapy of these diseases. Great efforts have been made for the development of highly specific NF-kappaB inhibitors, some of them being currently tested in phase II clinical trials. Here we discuss recent progress in the identification of druggable components of the NF-kappaB signaling system and the development and potential use of novel NF-kappaB inhibitors.

Inhibition of NF-kappaB activation and expression of inflammatory mediators by polyacetylene spiroketals from Plagius flosculosus.

Transcription factor NF-kappaB plays a key role for the inducible expression of genes mediating proinflammatory effects and is thus an important target for the development of antiinflammatory drugs. Here, we show that extracts from the plant Plagius flosculosus (L.) Alavi and Heyw. can inhibit the induction of NF-kappaB activity, and we describe the identification of three spiroketal compounds. Of those, only compound 1 could inhibit the phosphorylation and proteasomal degradation of IkappaB, thus preventing the nuclear import and DNA binding of NF-kappaB. Accordingly, compound 1, which is also found in the widely used medicinal herb chamomile, interfered with the LPS-induced production of IL-1, IL-6, TNF, and PGE2 in primary human monocytes.

The NF-kappaB pathway as a potential target for autoimmune disease therapy.

A battery of proinflammatory agents triggers the activation of NF-kappaB. This inducible transcription factor participates in the expression of an exceptionally large number of target genes, many of them contributing to the regulation of innate and adaptive immunity. Since some target genes also function as NF-kappaB activators, activation of this transcription factor allows the establishment of a signal amplification loop. Dysregulation of the NF-kappaB system and hyperactivated expression of inflammatory mediators are often found in association with some autoimmune diseases, which occur upon mounting of the adaptive immune response against self-antigens. In this review we summarize the relevance of aberrant NF-kappaB signaling for the development and perpetuation of some autoimmune diseases such as rheumatoid arthritis, diabetes mellitus type 1 and Crohn's disease. The assets and drawbacks of systemic or cell-type specific NF-kappaB inhibitors and their potential use in therapy of autoimmune diseases are critically discussed.

NF-kappaB activation pathways induced by T cell costimulation.

Analysis of knockout mice and of T cells deficient for individual signaling proteins allowed the identification of novel members of the costimulation-induced NF-kappaB activation pathway while biochemical approaches started to unveil their functional mechanisms. These results show that NF-kappaB activation depends on an early wave of tyrosine phosphorylation that allows the inducible formation of multiprotein complexes containing several proteins required for NF-kappaB activation: adaptor proteins including Src homology 2 domain-containing leukocyte phosphoprotein 76 (SLP-76) and proteins with enzymatic activity, such as phospholipase C (PLC) gamma and the exchange factor Vav1. While Vav1 contributes to Rac-dependent reorganization of the actin cytoskeleton, activated PLCgamma1 generates the protein kinase C (PKC) activator diacylglycerol. In T cells, the novel PKC isoform PKCtheta is indispensable for NF-kappaB activation and its enzymatic activity depends on recruitment to the immunological synapse. Downstream from PKCtheta, the caspase recruitment domain (CARD) proteins CARD11/CARMA1 and Bcl10 relay T cell receptor-derived signals to the IkappaB kinase (IKK) complex. Many members of the NF-kappaB activation cascade, including the IKKs, are either constitutively or inducibly translocated to the lipid raft fraction, showing a highly organized spatial distribution of these NF-kappaB activating proteins.

Lipoteichoic acid selectively induces the ERK signaling pathway in the cornea.

PURPOSE: To identify signal transduction pathways and gene expression induced by the bacterial cell wall component lipoteichoic acid (LTA) in human corneal keratocytes. METHODS: Human corneal keratocytes were cultured in the presence of 6.25 to 50 microg/ml LTA from Staphylococcus aureus. Induced DNA-binding of NF-kappaB was determined by electrophoretic mobility shift assays (EMSAs). Activation of MAP-kinase signaling pathways (p38, JNK-1/2, ERK-1/2, Elk 1, MEK-1/2, c-Raf) was evaluated by Western blotting using phospho-specific antibodies. To investigate the effect of LTA signaling on gene expression, keratocytes were transfected with a luciferase reporter gene under the control of serum response elements (SREs). LTA-induced gene expression was quantified using luciferase assays. RESULTS: Exposure of various concentrations of LTA up to 24 hours did not lead to activation of NF-kappaB, whereas TNF-alpha potently induced this transcription factor. A systematic analysis of LTA-activated MAPK pathways revealed no significant effects on JNK and p38, but a dose- and time-dependent phosphorylation of members of the ERK pathway. Analysis of the ERK-activating signaling cascade showed LTA-induced phosphorylation of ERK-1, MEK1/2, and c-Raf. ERK activity resulted in an enhanced transcription of an SRE-controlled reporter gene. CONCLUSIONS: LTA induces SRE-enhanced gene transcription in corneal keratocytes that is selectively mediated by the ERK pathway. Therefore, it seems possible that components of the bacterial cell wall such as LTA can alter the transcriptional program within the corneal stroma and thereby trigger an inflammatory response.

Prohibitin and prohibitone are contained in high-molecular weight complexes and interact with alpha-actinin and annexin A2.

The closely related proteins prohibitin (p32) and prohibitone (p37) are evolutionarily conserved with homologues found from cyanobacteria to man. They are thought to be exclusively mitochondrial and have been assigned many-rather different-functions, ranging from a role in lifespan, in mitochondrial inheritance and as chaperones of mitochondrial proteases in yeast. Evidence for a localisation outside of mitochondria has been brought forward in mammalian cells, where they influence cell-cycle progression and are found in association with cell surface receptors. We have employed a yeast two-hybrid screen to identify other interacting proteins and have identified alpha-actinin and annexin A2 as binding partners for prohibitin and prohibitone. Coprecipitation experiments supported the putative binding between prohibitin and prohibitone on the one hand and annexin A2 or alpha-actinin on the other hand in intact cells. Surface plasmon resonance analysis was used to determine relative affinities between prohibitin and alpha-actinin and between prohibitone and annexin A2 and alpha-actinin, respectively. We further show that prohibitin and prohibitone can also form homomeric (preferentially tetrameric) and heteromultimeric complexes, with significant affinities.