Facile determination of DNA-binding nuclear factor-kappaB by chemiluminescence detection

A simple, rapid, and sensitive method for the assay of a sequence-specific DNA-binding protein, nuclear factor-kappaB (NF-kappaB), has been developed by using a DNA-detectable chemiluminogenic reagent and a centrifugal filter that distinguishes different molecular sizes. After the formation of a complex between NF-kappaB and DNA, the unbound DNA is separated from the complex by the centrifugal filter. The amount of the bound NF-kappaB is estimated by chemiluminescence detection of the bound DNA. This detection is performed within 2 min at room temperature by the use of a chemiluminogenic reagent, 3',4',5'-trimethoxyphenylglyoxal, which selectively recognizes guanine moiety in oligonucleotides or DNAs. This method does not require any labeled probes or antibodies and can determine a concentration as low as 5 nM of DNA-binding NF-kappaB. The sensitivity is nearly the same as that of other methods such as gel shift assay using fluorescence-labeled probes and enzyme-linked immunosorbent assay. Therefore, the current method provides a convenient tool for surveying various DNA-binding proteins.     

雾化吸入雷公藤内酯醇对哮喘大鼠气道平滑肌增生及NF-κB、Bcl-2表达的影响

目的：探讨雷公藤内酯醇对哮喘气道重构及核因子-kappaB（NF-κB）、Bcl-2表达的影响。方法：将40只SD大鼠随机分为5组（n=8）：正常对照组（A组）;哮喘4周组（B组）;哮喘6周组（C组）;治疗4周组（D组）;治疗6周组（E组）。测定气道反应性并观察气道壁嗜酸性粒细胞浸润;图像分析软件测定支气管壁厚度、支气管平滑肌厚度及支气管平滑肌细胞核数量;免疫组织化学染色、Western印迹法检测PCNA、NF-κB、Bcl-2蛋白的表达,逆转录聚合酶链式反应（RT-PCR）检测Bcl-2mRNA表达。结果：①B组、C组NF-κB的蛋白表达量显著高于A组（P均〈0.01）,E组上述指标较B组、C组、D组均显著降低（P〈0.01、P〈0.01、P〈0.05）;②B组、C组Bcl-2蛋白及mRNA表达水平显著高于A组（P〈0.01）;E组蛋白表达量较B组、C组、D周组均显著降低（依次为P〈0.05、P〈0.01、P〈0.01）,mRNA表达水平与上述各组比较亦均显著降低（P〈0.01）,E组蛋白及mRNA表达水平与A组相比仍较高（依次为P〈0.05、P〈0.01）;③B组、C组PCNA的蛋白表达量明显高于A组（P〈0.01）;④B组及C组支气管壁厚度、支气管壁平滑肌厚度、支气管壁平滑肌细胞核数量均较A组明显增加（P〈0.01）,而E组上述指标较B组、C组、D组均显著降低（P〈0.01）;⑤B组、C组的气道反应性均高于A组（P均〈0.01）,E组较B组、C组、D组均显著降低（P〈0.01、P〈0.01、P〈0.05）。结论：哮喘气道平滑肌增生与气道平滑肌细胞（ASMCs）凋亡不足相关。NF-κB可能通过抑制ASMCs凋亡,参与哮喘气道高反应性及气道重构过程。雷公藤内酯醇可能通过下调NF-κB而抑制Bcl-2的表达,从而促进ASMCs凋亡、抑制气道平滑肌增生。     

High expression of diffuse panbronchiolitis critical region 1 gene promotes cell proliferation,migration and invasion in pancreatic ductal adenocarcinoma

Diffuse panbronchiolitis critical region 1 (DPCR1) is located in the major histocompatibility complex (MHC) class I. It was reported to be downregulated in invasive pituitary adenoma compared with that in non-invasive tumors, but upregulated in the precursor of gastric carcinogenesis. However, the direct effect of DPCR1 on cancer cells has rarely been reported, and the role DPCR1 in pancreatic ductal adenocarcinoma (PDAC) remains unclear. The clinical sample validation and public data analysis of the present study demonstrated that DPCR1 was upregulated markedly in PDAC and this high expression was negatively correlated with the patient prognosis. Functionally, knocking down DPCR1 in PDAC cell lines inhibited cell proliferation, migration and invasion in vitro. Tumor xenograft experiments further showed that suppression of DPCR1 inhibited tumor growth in vivo. In addition, the results of RNA deep sequencing and qRT-PCR assay showed that DPCR1 participated in PADC progression by regulating nuclear factor-kappa B signaling pathway, suggesting that it might be a novel oncogene in tumor progression and a potential therapeutic target in PDAC as well.     

IL-4-induced upregulation of adenine nucleotide translocase 3 and its role in Th cell survival from apoptosis

We have identified mitochondrial adenine nucleotide translocase (ANT)3 as a novel target up-regulated by IL-4 in human T cells. The IL-4-induced ANT3 expression is dependent on tyrosine kinase, NF-kappaB, PI3K/Akt, and Erk pathways. In fact, IL-4 induced specific activation of NF-kappaB, Akt, and Erk in Jurkat T cells and partially rescued these cells from dexamethasone-induced apoptosis. The IL-4-mediated T cell survival was blocked by inhibitors of tyrosine kinase, NF-kappaB, PI3K/Akt, and Erk. During the IL-4-induced T cell rescue, there was a concomitant increase in ANT3, nuclear NF-kappaB, and Bcl-2 and a decrease in ANT1, I-kappaB, and mitochondrial Bax-alpha levels. Importantly, overexpression of ANT3 effectively protected T cells from dexamethasone-induced apoptosis, while forced expression of ANT1 caused apoptosis. In contrast, siRNA knock-out of ANT3 expression induced T cell apoptosis and blocked the IL-4-mediated cell survival. Together these results suggest that ANT3 has a potential role in Th cell survival and immune cell homeostasis.     

TNF-related weak inducer of apoptosis receptor,a TNF receptor superfamily member,activates NF-kappa B through TNF receptor-associated factors

TNF-related weak inducer of apoptosis (TWEAK) is a member of the TNF ligand family that induces angiogenesis in vivo. The TWEAK receptor (TweakR) is a recently identified member of the TNF receptor (TNFR) superfamily and is expressed on smooth muscle cells (SMCs) and endothelial cells (ECs). In this report we identify the TNF receptor-associated factor (TRAF) family of signal transducers as important components of TweakR-mediated NF-kappa B activation. Coimmunoprecipitation experiments suggested potential interactions between the cytoplasmic tail of TweakR with TRAFs 1, 2, 3, and 5. Dominant negative forms of TRAF2 and TRAF5 substantially inhibited TweakR-mediated NF-kappa B activation, suggesting a role of TRAFs in regulating smooth muscle and endothelial cell function. Using alanine-scanning analysis, we defined a TRAF-binding motif, PIEET, in TweakR that mediates TRAF binding and NF-kappa B activation. Furthermore, TweakR mutations within the TRAF-binding motif abolished TweakR-stimulated SMC migration, revealing a role for TRAFs in TweakR-induced activation events.     

Targeting nuclear factor-kappa B activation pathway by thymoquinone: role in suppression of antiapoptotic gene products and enhancement of apoptosis

Thymoquinone (TQ), derived from the medicinal plant Nigella sativa, exhibits antiinflammatory and anticancer activities through mechanism(s) that is not fully understood. Because numerous effects modulated by TQ can be linked to interference with the nuclear factor-kappaB (NF-kappa B) signaling, we investigated in detail the effect of this quinone on NF-kappa B pathway. As examined by DNA binding, we found that TQ suppressed tumor necrosis factor-induced NF-kappa B activation in a dose- and time-dependent manner and inhibited NF-kappaB activation induced by various carcinogens and inflammatory stimuli. The suppression of NF-kappaB activation correlated with sequential inhibition of the activation of I kappa B alpha kinase, I kappa B alpha phosphorylation, I kappa B alpha degradation, p65 phosphorylation, p65 nuclear translocation, and the NF-kappa B-dependent reporter gene expression. TQ specifically suppressed the direct binding of nuclear p65 and recombinant p65 to the DNA, and this binding was reversed by DTT. However, TQ did not inhibit p65 binding to DNA when cells were transfected with the p65 plasmid containing cysteine residue 38 mutated to serine. TQ also down-regulated the expression of NF-kappa B-regulated antiapoptotic (IAP1, IAP2, XIAP Bcl-2, Bcl-xL, and survivin), proliferative (cyclin D1, cyclooxygenase-2, and c-Myc), and angiogenic (matrix metalloproteinase-9 and vascular endothelial growth factor) gene products. This led to potentiation of apoptosis induced by tumor necrosis factor and chemotherapeutic agents. Overall, our results indicate that the anticancer and antiinflammatory activities previously assigned to TQ may be mediated in part through the suppression of the NF-kappa B activation pathway, as shown here, and thus may have potential in treatment of myeloid leukemia and other cancers.     

Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach

A computational geometry technique based on Delaunay tessellation of protein structure, represented by C(alpha) atoms, is used to study effects of single residue mutations on sequence-structure compatibility in HIV-1 protease. Profiles of residue scores derived from the four-body statistical potential are constructed for all 1881 mutants of the HIV-1 protease monomer and compared with the profile of the wild-type protein. The profiles for an isolated monomer of HIV-1 protease and the identical monomer in a dimeric state with an inhibitor are analyzed to elucidate changes to structural stability. Protease residues shown to undergo the greatest impact are those forming the dimer interface and flap region, as well as those known to be involved in inhibitor binding.     

A20 inhibits the release of inflammatory cytokines by suppressing the activation of the nuclear factor-kappa B pathway in osteoarthritic fibroblast-like synoviocytes

A growing number of studies suggest that synovitis plays an important role in the pathogenesis and progression of osteoarthritis (OA). As a negative mediator of the nuclear factor-kappa B (NF-κB) signaling pathway, the zinc finger protein A20 has significant anti-inflammatory properties. In this study, the differential expression of A20 was investigated at the mRNA and protein levels in human normal OA fibroblast-like synoviocytes (FLSs) and normal FLSs pretreated with TNF-α. We then measured the activation of the NF-κB pathway and expression of pro-inflammatory cytokines in the above three groups by western blotting, a human cytokine array and ELISA. We found that TNF-α activated the NF-κB pathway, increased the expression of the pro-inflammatory cytokines IL-6 and IL-8, and A20 expression in human normal FLSs. However, the role of A20 in FLSs was unclear. To clarify this, we investigated the effect of A20 overexpression in human normal FLSs. The results indicate that A20 inhibits the NF-κB signaling pathway activation and OA-associated pro-inflammatory cytokines release. The results of this study indicate that A20 has anti-inflammatory effects in FLSs, which makes it a potential target for OA synovitis treatment.     

Amyotrophic lateral sclerosis: a novel hypothesis involving a gained 'loss of function' in the JNK/SAPK pathway

Abstract

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease that mainly affects motor neurons. Despite intensive research efforts inspired by the mile-stone discovery linking the Cu/Zn superoxide dismutase 1 (SOD1) gene to a subset of familial cases, the mechanisms underlying disease pathogenesis are still largely unknown. Nonetheless, the recent finding of a second gene associated with familial form of the disease, ALS2, is likely to be of great help in elucidating the key pathways involved in motor neuron degeneration. Here, we provide evidence that the JNK/SAPK pathway plays a critical neuroprotective role in susceptible motor neurons in ALS. The involvement of the JNK/SAPK pathway integrates our knowledge about these two known genetic factors into a single pathogenic pathway involved in both sporadic and familial ALS.     

脑组织核因子-κB激活对实验性变态反应性脑脊髓炎的作用

为探讨脑组织核因子－κB（NF－κB）对实验性变态反应性脑脊髓炎（EAE）的作用,分别用凝胶电泳迁移分析和NF－κB p65免疫组化方法测定了CFA－GPSCH诱导大鼠EAE1、7、14和21d时脑组织NF－κB活性和蛋白表达的动态变化,并观察了这些变化与EAE症状之间的关系。结果表明;对照组大鼠脑组织仅有少量NF－κB蛋白表达,其活性也很低;诱导EAE后,伴随着大鼠EAE症状及脑组织病理损伤的出现和进行性加重,其NF－κB活性和蛋白表达量逐渐增高;在免疫后14d达到高峰,NF－κB阳性细胞主要位于脉络丛、穹隆下器、血管“套袖样”病灶的周围,与EAE病变部位一致,此时大鼠EAE发病率最高、病情最重、体重减轻最显著、脑组织病理改变也最明显;21h脑组织NF－κB活性和蛋白表达量逐渐下降,大鼠EAE症状也逐渐恢复。应用NF－κB特异性抑制剂PDTC以抑制脑内组织NF－κB活性和蛋白表达量逐渐下降,大鼠EAE症状也逐渐恢复。应用NF－κB特异性抑制剂PDTC以抑制脑内NF－κB蛋白表达后,大鼠EAE症状和脑组织损伤明显减轻,说明脑组织NF－κB的动态变化与EAE症状及脑组织损伤程度密切相关。结论：脑组织NF－κB的激活对EAE的发病起着关键的作用,应用NF－κB抑制剂可能是防治该病的有效方法之一。     

Application of a systems approach to study developmental gene regulation

All cells in a multicellular organism contain the same genome, yet different cell types express different sets of genes. Recent advances in high throughput genomic technologies have opened up new opportunities to understand the gene regulatory network in diverse cell types in a genome-wide manner. Here, I discuss recent advances in experimental and computational approaches for the study of gene regulation in embryonic development from a systems perspective. This review is written for computational biologists who have an interest in studying developmental gene regulation through integrative analysis of gene expression, chromatin landscape, and signaling pathways. I highlight the utility of publicly available data and tools, as well as some common analysis approaches.     

Reduction of chemokine IL-8 and RANTES expression in human bronchial epithelial cells by a sea-water derived saline through inhibited nuclear factor-kappaB activation

The NaCl content of airway surface fluid is believed to be of central importance in lung pathology. To test whether the Na+ concentration could influence the inflammatory response in human bronchial epithelial cells (BECs), we investigated the interleukin (IL)-8 and RANTES expression in BECs exposed to an isotonic sea-water derived low Na+ (ISW) saline compared to isotonic 0.9% NaCl saline. Exposure of BECs to ISW saline caused a significant decrease in IL-8 and RANTES gene expression and protein production as compared to that observed with 0.9% NaCl saline. Furthermore, we observed a concomitant reduction of phosphorylated IkappaBalpha associated with a marked inhibition of NF-kappaB-DNA binding activity in BECs exposed to ISW saline as compared to 0.9% NaCl saline. These findings support a new role for Na+ in the pathogenesis of airway inflammatory disorders. Therapies targeted at lowering Na+ level in airway epithelium may be beneficial in treating inflammatory lung diseases.