Reconstruction and analysis of the NF-kB pathway interactome: a systems biology approach

Background. One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as “inflammaging”, negatively correlated with longevity. A prominent mediator of inflammation is the transcription factor NF-kB, that acts as key transcriptional regulator of many genes coding for pro-inflammatory cytokines. Many different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory network characterized by high complexity. NF-kB signaling has been proposed to be responsible of inflammaging. Scope of this analysis is to provide a wider, systemic picture of such intricate signaling and interaction network: the NF-kB pathway interactome. Methods. The study has been carried out following a workflow for gathering information from literature as well as from several pathway and protein interactions databases, and for integrating and analyzing existing data and the relative reconstructed representations by using the available computational tools. Strong manual intervention has been necessarily used to integrate data from multiple sources into mathematically analyzable networks. The reconstruction of the NF-kB interactome pursued with this approach provides a starting point for a general view of the architecture and for a deeper analysis and understanding of this complex regulatory system. Results. A “core” and a “wider” NF-kB pathway interactome, consisting of 140 and 3146 proteins respectively, were reconstructed and analyzed through a mathematical, graph-theoretical approach. Among other interesting features, the topological characterization of the interactomes shows that a relevant number of interacting proteins are in turn products of genes that are controlled and regulated in their expression exactly by NF-kB transcription factors. These “feedback loops”, not always well-known, deserve deeper investigation since they may have a role in tuning the response and the output consequent to NF-kB pathway initiation, in regulating the intensity of the response, or its homeostasis and balance in order to make the functioning of such critical system more robust and reliable. This integrated view allows to shed light on the functional structure and on some of the crucial nodes of thet NF-kB transcription factors interactome. Conclusion. Framing structure and dynamics of the NF-kB interactome into a wider, systemic picture would be a significant step toward a better understanding of how NF-kB globally regulates diverse gene programs and phenotypes. This study represents a step towards a more complete and integrated view of the NF-kB signaling system.

Influência do exercício físico sobre o estresse oxidativo, as MAPK e o NF-kB no músculo sóleo de ratos com insuficiência cardíaca induzida por estenose aórtica

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Elafin prevents lipopolysaccharide-induced AP-1 and NF-kB activation via an effect on the ubiquitin-proteasome pathway

In this paper we follow on from our research into SLPI by assessing the immunomodulatory activity of elafin - an antiprotease related to SLPI and also present on the respiratory tract. We demonstrate for the first time that exogenously applied elafin inhibits lipopolysaccharide-induced activation of the NF-kappaB and AP-1 pathways in monocytes. I designed this project and supervised Marcus Butler during his MD thesis.

Clusterin facilitates COMMD1 and I-kB degradation to enhance NF-kB activity in prostate cancer cells

Secretory clusterin (sCLU) is a stress-activated, cytoprotective chaperone that confers broad-spectrum cancer treatment resistance, and its targeted inhibitor (OGX-011) is currently in phase II trials for prostate, lung, and breast cancer. However, the molecular mechanisms by which sCLU inhibits treatment-induced apoptosis in prostate cancer remain incompletely defined. We report that sCLU increases NF-κB nuclear translocation and transcriptional activity by serving as a ubiquitin-binding protein that enhances COMMD1 and I-κB proteasomal degradation by interacting with members of the SCF-βTrCP E3 ligase family. Knockdown of sCLU in prostate cancer cells stabilizes COMMD1 and I-κB, thereby sequestrating NF-κB in the cytoplasm and decreasing NF-κB transcriptional activity. Comparative microarray profiling of sCLU-overexpressing and sCLU-knockdown prostate cancer cells confirmed that the expression of many NF-κB–regulated genes positively correlates with sCLU levels. We propose that elevated levels of sCLU promote prostate cancer cell survival by facilitating degradation of COMMD1 and I-κB, thereby activating the canonical NF-κB pathway.

Ibuprofen supplementation and its effects on NF-KB activation in skeletal muscle following resistance exercise

Resistance exercise triggers a subclinical inflammatory response that plays a pivotal role in skeletal muscle regeneration. Nuclear factor‐κB (NF‐κB) is a stress signalling transcription factor that regulates acute and chronic states of inflammation. The classical NF‐κB pathway regulates the early activation of post‐exercise inflammation; however there remains scope for this complex transcription factor to play a more detailed role in post‐exercise muscle recovery. Sixteen volunteers completed a bout of lower body resistance exercise with the ingestion of three 400 mg doses of ibuprofen or a placebo control. Muscle biopsy samples were obtained prior to exercise and at 0, 3 and 24 h post‐exercise and analysed for key markers of NF‐κB activity. Phosphorylated p65 protein expression and p65 inflammatory target genes were elevated immediately post‐exercise independent of the two treatments. These changes did not translate to an increase in p65 DNA binding activity. NF‐κB p50 protein expression and NF‐κB p50 binding activity were lower than pre‐exercise at 0 and 3 h post‐exercise, but were elevated at 24 h post‐exercise. These findings provide novel evidence that two distinct NF‐κB pathways are active in skeletal muscle after resistance exercise. The initial wave of activity involving p65 resembles the classical pathway and is associated with the onset of an acute inflammatory response. The second wave of NF‐κB activity comprises the p50 subunit, which has been previously shown to resolve an acute inflammatory program. The current study showed no effect of the ibuprofen treatment on markers of the NF‐κB pathway, however examination of the within group effects of the exercise protocol suggests that this pathway warrants further research.

Étude de la régulation du facteur de transcription NF-kB dans l'infection par le RSV

L’infection par le Virus Respiratoire Syncytial cause des affections pulmonaires aiguës en pédiatrie caractérisée par une réponse inflammatoire excessive médiée par la production de cytokines par les cellules épithéliales des voies aériennes. Les gènes codant pour ces cytokines sont régulés par le facteur de transcription NF-κB (p50/p65) dont l’activation est classiquement induite par la phosphorylation de son inhibiteur IκBα, ce qui permet l’accumulation de l’hétérodimère au noyau. Par contre, nous avons récemment identifié la phosphorylation en sérine 536 de la sous-unité p65 comme une autre étape essentielle à son activation lors de l’infection des AEC par RSV. Le travail présenté dans ce mémoire a permis de démontrer que l’inhibition de l’expression de RIG-I, de Cardif ou de TRAF6, 3 protéines impliquées dans la reconnaissance cellulaire des virus, conduit à l’inhibition de cette phosphorylation en réponse à RSV. Nous avons également établi à l’aide d’inhibiteurs pharmacologiques et d’ARNi que, parmi les diverses kinases connues pour phosphoryler p65 en réponse à divers stimulus, IKKα/β sont essentielles à cette phosphorylation lors d’une stimulation par RSV. Puisque TRAF6 est bien connu dans la littérature pour activer le complexe IKK, nous proposons que TRAF6, après reconnaissance de l’ARN viral de RSV par RIG-I, active le complexe IKK qui induit la phosphorylation de la sousunité p65 de NF-κB, permettant l’expression de gènes cibles. D’autre part, nous avions précédemment démontré que Nox2, un isoforme de NADPH oxydase, contrôle l’activation de NF-κB en régulant les phosphorylations de IκBα et p65. Nous montrons ici que l’inhibition de Nox2 réduit fortement l’activité du complexe kinase IKK. De plus, la présence au niveau basal de Nox2 est critique pour le niveau d’ARN messager de Cardif. Nous proposons donc que la régulation de la phosphorylation de p65 en ser536 par Nox2 soit via son effet sur Cardif en permettant la fonctionnalité de la voie RIG-I.

Identification of the nuclear factor kappa-beta (NF-kB) in cortical of mice Wistar using Technovit 7200 VCR (R)

Objective: this study aimed to develop a nondecalcified bone sample processing technique enabling immunohistochemical labeling of proteins by kappa-beta nuclear factor (NF-kB) utilizing the Technovit 7200 VCR (R) in adult male Wistar rats. Study Method: A 1.8 mm diameter defect was performed 0.5mm from the femur proximal joint by means of a round bur. Experimental groups were divided according to fixing solution prior to histologic processing: Group 1- ethanol 70%; Group 2-10% buffered formalin; and Group 3- Glycerol diluted in 70% ethanol at a 70/30 ratio + 10% buffered formalin. The post-surgical periods ranged from 01 to 24 hours. Control groups included a nonsurgical procedure group (NSPG) and surgical procedures where bone exposure was performed (SPBE) without drilling. Prostate carcinoma was the positive control (PC) and samples subjected to incomplete immunohistochemistry protocol were the negative control (NC). Following euthanization, all samples were kept at 4 degrees C for 7 days, and were dehydrated in a series of alcohols at -20 degrees C. The polymer embedding procedure was performed at ethanol/polymer ratios of 70%-30%, 50%-50%, 30%-70%, 100%, and 100% for 72 hours at -20 degrees C. Polymerization followed the manufacturer`s recommendation. The samples were grounded and polished to 10-15 mu m thickness, and were deacrylated. The sections were rehydrated and were submitted to the primary polyclonal antibody anti-NF-kB on a 1:75 dilution for 12 hours at room temperature. Results: Microscopy showed that the Group 2 presented positive reaction to NF-kB, diffuse reactions for NSPG and SPBE, and no reaction for the NC group. Conclusion: The results obtained support the feasibility of the developed immunohistochemistry technique.

Modulação da proliferação, morte celular e expressão gênica de mediadores inflamatórios pela ativação de RAGE e TLR4 em células da resposta imune inata e adaptativa: papel das vias de sinalização p38 MAPK e NF-kB

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Identificazione di fattori trascrizionali associati al differenziamento neurale in cellule di sarcoma di Ewing: ruolo di NF-kB

Il sarcoma di Ewing (ES) è un tumore maligno pediatrico dell’apparato scheletrico; è associato a una traslocazione specifica codificante la proteina di fusione EWS-FLI1 e all’alta espressione di CD99, una glicoproteina di membrana fisiologicamente coinvolta in diversi processi biologici. EWS-FLI1 e CD99, sono riportati avere ruoli divergenti nella modulazione della malignità e del differenziamento di ES. CD99 inoltre è riportato modulare il pathway di MAPK, il quale interagendo con molteplici fattori di trascrizione partecipa a processi di proliferazione e differenziamento. In questo studio abbiamo investigato in due linee cellulari di ES silenziate per CD99 (TC-71shCD99 e IOR/CARshCD99) l’attività basale di diversi fattori trascrizionali quali: NF-kBp65, AP1, Elk-1, E2F e CREB. L’unico fattore trascrizionale statisticamente significativo è risultato essere NF-kBp65 e abbiamo valutato il suo ruolo nel differenziamento neurale di cellule di ES e la relazione con EWS-FLI1 e CD99. L’attività trascrizionale di NF-kB è stata valutata attraverso gene reporter assay in linee cellulari di ES a diversa espressione di CD99, EWS-FLI1 e NF-kB stesso. Il differenziamento neurale è stato valutato come espressione di βIII-Tubulin in immunofluorescenza. Il silenziamento di CD99 induce una down-modulazione dell’attività trascrizionale di NF-kB, mentre il knockdown di EWS-FLI1 ne induce un’aumento. Inoltre, il silenziamento di EWS-FLI1 non è in grado di contrastare la riduzione dell’attività di NF-kB osservata dopo silenziamento di CD99, suggerendo un ruolo dominante del CD99 nel signaling di NF-kB. Cellule deprivate di CD99 ma non di EWS-FLI1, mostrano un fenotipo differenziato in senso neurale, fenotipo che viene perso quando le cellule sono indotte a sovraesprimere NF-kB. Inoltre, in cellule CD99 positive, il silenziamento di NF-kB induce un leggero differenziamento neurale. In conclusione, questi dati hanno evidenziato il ruolo di NF-kB nel differenziamento di cellule di ES e che potrebbe essere un potenziale target nel ridurre la progressione di questo tumore.

Vertical Inhibition of the PI3K/Akt/mTOR Pathway for the Treatment of Osteoarthritis

Osteoarthritis is characterized by degenerative alterations of articular cartilage including both the degradation of extracellular matrix and the death of chondrocytes. The PI3K/Akt pathway has been demonstrated to involve in both processes. Inhibition of its downstream target NF-kB reduces the degradation of extracellular matrix via decreased production of matrix metalloproteinases while inhibition of mTOR increased autophagy to reduce chondrocyte death. However, mTOR feedback inhibits the activity of the PI3K/Akt pathway and inhibition of mTOR could result in increased activity of the PI3K/Akt/NF-kB pathway. We proposed that the use of dual inhibitors of PI3K and mTOR could be a promising approach to more efficiently inhibit the PI3K/Akt pathway than rapamycin or PI3K inhibitor alone and produce better treatment outcome.

Nuclear Import Mechanisms of STAT and NF-kB Transcription Factors

The eukaryotic cell nucleoplasm is separated from the cytoplasm by the nuclear envelope. This compartmentation of eukaryotic cells requires that all nuclear proteins must be transported from the cytoplasm into the nucleus. Transport of macromolecules between the nucleus and the cytoplasm occurs through nuclear pore complexes (NPCs). Proteins to be targeted into the nucleus by the classical nuclear import system contain nuclear localization signals (NLSs), which are recognized by importin alpha, the NLS receptor. Importin alpha binds to importin beta, which docks the importin-cargo complex on the cytoplasmic side of the NPC and mediates the movement of the complex into the nucleus. Presently six human importin alpha isoforms have been identified. Transcription factors are among the most important regulators of gene expression in eukaryotic organisms. Transcription factors bind to specific DNA sequences on target genes and modulate the activity of the target gene. Many transcription factors, including signal transducers and activators of transcription (STAT) and nuclear factor kB (NF-kB), reside in the cytoplasm in an inactive form, and upon activation they are rapidly transported into the nucleus. In the nucleus STATs and NF-kB regulate the activity of genes whose products are critical in controlling numerous cellular and organismal processes, such as inflammatory and immune responses, cell growth, differentiation and survival. The aim of this study was to investigate the nuclear import mechanisms of STAT and NF-kB transcription factors. This work shows that STAT1 homodimers and STAT1/STAT2 heterodimers bind specifically and directly to importin alpha5 molecule via unconventional dimer-specific NLSs. Importin alpha molecules have two regions, which have been shown to directly interact with the amino acids in the NLS of the cargo molecule. The Arm repeats 2-4 comprise the N-terminal NLS binding site and Arm repeats 7-8 the C-terminal NLS binding site. In this work it is shown that the binding site for STAT1 homodimers and STAT1/STAT2 heterodimers is composed of Arm repeats 8 and 9 of importin alpha5 molecule. This work demonstrates that all NF-kB proteins are transported into the nucleus by importin alpha molecules. In addition, NLS was identified in RelB protein. The interactions between NF-kB proteins and importin alpha molecules were found to be directly mediated by the NLSs of NF-kB proteins. Moreover, we found that p50 binds to the N-terminal and p65 to the C-terminal NLS binding site of importin alpha3. The results from this thesis work identify previously uncharacterized mechanisms in nuclear import of STAT and NF-kB. These findings provide new insights into the molecular mechanisms regulating the signalling cascades of these important transcription factors from the cytoplasm into the nucleus to the target genes.

NF-KB Activation and Severity of Gastritis in Helicobacter pylori-Infected Children and Adults.

In contrast to adults, Helicobacter pylori gastritis in children is reported as milder and ulcer disease as uncommon, but unequivocal data are lacking.