小鼠脑组织及培养神经元Neuro-2a 在内质网应激反应时的基因表达谱分析

内质网是真核细胞的重要细胞器。某些细胞内外因素如病原体感染等能引起从内质网到胞浆和胞核的信号传导途径活化,即内质网应激反应。但是,目前国内外尚无针对内质网应激反应的基因表达谱分析报道。本研究中,用3种已报道的内质网应激反应诱导剂,包括蛋白质糖基化抑制剂衣霉素(tunicamycin)、内质网Ca ²⁺-ATPases抑制剂毒胡萝卜素（thapsigargin）和乙脑病毒(Japanese encephalitis virus, JEV),分别处理小鼠颅腔和小鼠脑神经瘤细胞（Neuro-2a）,试剂处理组与未处理组的第二代RNA测序分析发现,衣霉素、毒胡萝卜素和乙脑病毒在体外和体内均引起分子伴侣基因Hsp70表达上调,诱导内质网应激反应。衣霉素、毒胡萝卜素和乙脑病毒体外处理诱导的内质网应激反应信号通路中,基因差异表达相似性高于体内处理组。乙脑病毒和糖基化抑制剂衣霉素体内外处理,主要诱导内质网应激反应的非折叠蛋白质反应信号通路,引起相关基因Atf4、Bip、Edem和Perk等表达上调。内质网Ca ²⁺-ATPases抑制剂毒胡萝卜素主要诱导内质网超负荷反应,激活NF-κB信号通路。乙脑病毒诱导的内质网应激反应相关差异表达基因数量最多,体外与体内合计有40种。乙脑病毒体内外处理上调的基因包括Bax、Casp12、Atf4、Bip、Edem和Perk等,下调的基因包括Sec23/24、Nef、Svip和Jnk等。糖基化抑制剂衣霉素体内外处理上调基因包括Gadd34、Atf4、Ermani和Bip等,下调基因包括Grp94、Atf6、Sec23/24和Nef等。内质网Ca ^-2+-ATPases抑制剂毒胡萝卜素体内外处理上调的基因包括Sec61、Trap和Ask1等。衣霉素、毒胡萝卜素和乙脑病毒体内外处理也通过内质网应激反应,调控与炎症或凋亡相关的MAPK信号通路和P53信号通路。本研究首次通过使用3种内质网应激反应诱导剂分别处理小鼠和细胞,揭示了体内外内质网应激反应引起的基因表达谱变化,为内质网应激反应相关疾病的治疗提供了新思路。     

Extracting gene networks for low-dose radiation using graph theoretical algorithms

Genes with common functions often exhibit correlated expression levels, which can be used to identify sets of interacting genes from microarray data. Microarrays typically measure expression across genomic space, creating a massive matrix of co-expression that must be mined to extract only the most relevant gene interactions. We describe a graph theoretical approach to extracting co-expressed sets of genes, based on the computation of cliques. Unlike the results of traditional clustering algorithms, cliques are not disjoint and allow genes to be assigned to multiple sets of interacting partners, consistent with biological reality. A graph is created by thresholding the correlation matrix to include only the correlations most likely to signify functional relationships. Cliques computed from the graph correspond to sets of genes for which significant edges are present between all members of the set, representing potential members of common or interacting pathways. Clique membership can be used to infer function about poorly annotated genes, based on the known functions of better-annotated genes with which they share clique membership (i.e., “guilt-by-association”). We illustrate our method by applying it to microarray data collected from the spleens of mice exposed to low-dose ionizing radiation. Differential analysis is used to identify sets of genes whose interactions are impacted by radiation exposure. The correlation graph is also queried independently of clique to extract edges that are impacted by radiation. We present several examples of multiple gene interactions that are altered by radiation exposure and thus represent potential molecular pathways that mediate the radiation response.     

ATF4在内质网应激调控成骨分化中的作用

为避免内质网中未折叠蛋白质的过度累积,真核细胞能激活一系列信号通路来维持内质网稳态,这个过程称为内质网应激。在骨生长发育中,适宜的内质网应激有助于成骨细胞、破骨细胞和软骨细胞的生长,可以促进骨髓间充质干细胞向成骨细胞分化。而过度的内质网应激会抑制成骨分化,严重的甚至导致骨质疏松、成骨不全等相关骨病的发生。内质网应激时可激活未折叠蛋白质反应,其主要是通过PERK/eIF2α/ATF4信号通路,上调转录激活因子4(ATF4)的表达。ATF4位于许多成骨分化调节因子的下游,是促进成骨分化的关键因子,在内质网应激对成骨分化的调节中发挥重要作用。在成骨分化过程中,适宜的内质网应激能通过激活PERK信号通路,诱导ATF4表达增加,进而上调骨钙素、骨涎蛋白等成骨所必需基因的表达,促进成骨分化。过度的内质网应激会激活ATF4/CHOP促凋亡途径,并导致Bax、胱天蛋白酶等凋亡信号分子的大量产生,进而导致细胞凋亡,抑制成骨分化。由于ATF4在ERS和成骨分化中的重要作用,ATF4在骨质疏松、成骨不全等骨相关疾病的治疗中具有重要意义。本文通过综述ATF4在内质网应激调控成骨分化中的作用机制,为相关骨性疾病治疗提供理论依据。     

Anticipating endoplasmic reticulum stress. A novel early response before pathogenesis-related gene induction

When it is attacked by a pathogen, a plant produces a range of defense-related proteins. Many of these are synthesized by the rough endoplasmic reticulum (RER) to be secreted from the cell or deposited in vacuoles. Genes encoding endoplasmic reticulum (ER)-resident chaperones, such as the lumenal binding protein (BiP), are also induced under these conditions. Here, we show that BiP induction occurs systemically throughout the plant. Furthermore, this induction occurs rapidly and precedes expression of genes encoding pathogenesis-related (PR) proteins. The underlying signal transduction pathway was shown to be independent of the signaling molecule salicylic acid and the unfolded protein response pathway. In addition, BiP induction was independent of PR gene induction. Overproduction of BiP alone was not sufficient to cause induction of PR gene expression; however, limiting the amount of BiP in the ER lumen via superimposed ER stress inhibited the induction of PR gene expression. We propose that the induction of BiP expression during plant-pathogen interactions is required as an early response to support PR protein synthesis on the RER and that a novel signal transduction pathway exists to trigger this rapid response.     

Down-regulation of PERK enhances resistance to ionizing radiation

Although, ionizing radiation (IR) has been implicated to cause stress in endoplasmic reticulum (ER), how ER stress signaling and major ER stress sensors modulate cellular response to IR is unclear. Protein kinase RNA-like endoplasmic reticulum kinase (PERK) is an ER transmembrane protein which initiates unfolded protein response (UPR) or ER stress signaling when ER homeostasis is disturbed. Here, we report that down-regulation of PERK resulted in increased clonogenic survival, enhanced DNA repair and reduced apoptosis in irradiated cancer cells. Our study demonstrated that PERK has a role in sensitizing cancer cells to IR.     

ATF4在内质网应激调控成骨分化中的作用

为避免内质网中未折叠蛋白质的过度累积,真核细胞能激活一系列信号通路来维持内质网稳态,这个过程称为内质网应激。在骨生长发育中,适宜的内质网应激有助于成骨细胞、破骨细胞和软骨细胞的生长,可以促进骨髓间充质干细胞向成骨细胞分化。而过度的内质网应激会抑制成骨分化,严重的甚至导致骨质疏松、成骨不全等相关骨病的发生。内质网应激时可激活未折叠蛋白质反应,其主要是通过PERK/eIF2α/ATF4信号通路,上调转录激活因子4(ATF4)的表达。ATF4位于许多成骨分化调节因子的下游,是促进成骨分化的关键因子,在内质网应激对成骨分化的调节中发挥重要作用。在成骨分化过程中,适宜的内质网应激能通过激活PERK信号通路,诱导ATF4表达增加,进而上调骨钙素、骨涎蛋白等成骨所必需基因的表达,促进成骨分化。过度的内质网应激会激活ATF4/CHOP促凋亡途径,并导致Bax、胱天蛋白酶等凋亡信号分子的大量产生,进而导致细胞凋亡,抑制成骨分化。由于ATF4在ERS和成骨分化中的重要作用,ATF4在骨质疏松、成骨不全等骨相关疾病的治疗中具有重要意义。本文通过综述ATF4在内质网应激调控成骨分化中的作用机制,为相关骨性疾病治疗提供理论依据。     

Expression of CETP and of splice variants induces the same level of ER stress despite secretion efficiency differences

The cholesteryl ester transfer protein (CETP) gene has been associated with a variety of phenotypes, including HDL-cholesterol levels and, more sporadically, with cardiovascular disease, obesity, and extreme longevity. Alterations of CETP activity levels can be caused by single-base polymorphisms as well as by alternative splicing. In addition to the previously characterized alternative splicing that skips exon 9, we found additional minor variants and characterized the activity of the resultant proteins. The novel variants skipped exon 9 sequences and inserted one of two in-frame exons from Alu-derived intronic sequences. None of the alternatively spliced variants are efficiently secreted, and coexpression of them inhibits wild-type CETP secretion. Expression of the alternative spliced variants causes an induction of genes linked to the endoplasmic reticulum (ER) stress response, including the neighboring HERPUD1 (homocysteine- and ER stress-inducible protein, ubiquitin-like domain-containing) gene. Unexpectedly, even though wild-type CETP is secreted much more efficiently than spliced variants, it induces the same degree of stress response as spliced variants, whereas a control secreted protein does not. CETP plays a complex role in modulating ER stress, with its expression inducing the response and its cholesteryl ester transfer activity and differential splicing modulating the response in other ways.     

Cytoprotection by pre-emptive conditional phosphorylation of translation initiation factor 2

Transient phosphorylation of the alpha-subunit of translation initiation factor 2 (eIF2alpha) represses translation and activates select gene expression under diverse stressful conditions. Defects in the eIF2alpha phosphorylation-dependent integrated stress response impair resistance to accumulation of malfolded proteins in the endoplasmic reticulum (ER stress), to oxidative stress and to nutrient deprivations. To study the hypothesized protective role of eIF2alpha phosphorylation in isolation of parallel stress signaling pathways, we fused the kinase domain of pancreatic endoplasmic reticulum kinase (PERK), an ER stress-inducible eIF2alpha kinase that is normally activated by dimerization, to a protein module that binds a small dimerizer molecule. The activity of this artificial eIF2alpha kinase, Fv2E-PERK, is subordinate to the dimerizer and is uncoupled from upstream stress signaling. Fv2E-PERK activation enhanced the expression of numerous stress-induced genes and protected cells from the lethal effects of oxidants, peroxynitrite donors and ER stress. Our findings indicate that eIF2alpha phosphorylation can initiate signaling in a cytoprotective gene expression pathway independently of other parallel stress-induced signals and that activation of this pathway can single-handedly promote a stress-resistant preconditioned state.     

Effect of glutamine or glucose deprivation on the expression of cyclin and cyclin-dependent kinase genes in glioma cell line U87 and its subline with suppressed activity of signaling enzyme of endoplasmic reticulum-nuclei-1

Ischemia has been shown to induce a set of complex intracellular signaling events known as the unfolded protein response, which is mediated by endoplasmic reticulum-nuclei-1 sensing enzyme. We have studied the expression of several cyclin and cyclin-dependent kinase genes which participate in the control of cell cycle and proliferation under ischemic conditions (glucose or glutamine deprivation) in endoplasmic reticulum-nuclei-1-deficient glioma cells. It was shown that blockade of endoplasmic reticulum-nuclei signaling enzyme-1, the key endoplasmic reticulum stress sensor, leads to an increase of the expression levels of cyclin-dependent kinase-2 and cyclin A2, D3, E2 and G2 genes but suppresses cyclin D1. Moreover, the expression level of cyclin-dependent kinase-2 as well as cyclin A2, D3 and E2 mRNAs is significantly decreased under glucose or glutamine deprivation conditions both in control and endoplasmic reticulum-nuclei-1-deficient glioma cells. However, cyclin-dependent kinase-4 and -5 mRNA expressions is increased, but in glucose deprivation conditions only. Results of this study have shown that the expression of most tested genes of encoded cyclins and cyclin-dependent kinases is dependent on endoplasmic reticulum-nuclei-1 signaling enzyme function both in normal and glutamine and glucose deprivation conditions and possibly participates in cell adaptive response to endoplasmic reticulum stress associated with ischemia.     

酿酒酵母细胞中内质网应激与未折叠蛋白反应的研究进展

内质网应激激活的未折叠蛋白反应(Unfolded protein response,UPR)途径在酿酒酵母和哺乳动物细胞中是非常保守的。内质网(Endoplasmic reticulum,ER)是蛋白质合成、折叠和修饰的细胞器,也是贮存钙的主要场所之一。酵母细胞内质网钙平衡与UPR的作用是相互的;两个MAPK途径——HOG途径和CWI途径都是细胞应答内质网应激压力时生存所必需的;重金属镉离子能够激活UPR途径,它通过激活钙离子通道Cch1/Mid1进入细胞影响钙离子的功能。本文结合最新研究进展对酿酒酵母细胞中的两个MAPK途径、镉离子和钙离子稳态与内质网应激激活的UPR途径之间相互关系进行综述。     

Stress-Induced Neuroprotective Effects of Epiregulin and Amphiregulin

Members of the epidermal growth factor family play important roles in the regulation of cell growth, proliferation, and survival. However, the specific roles of each epidermal growth factor family member with respect to brain injury are not well understood. Gene chip assay screens have revealed drastic increases in the expression of the epidermal growth factor family members amphiregulin and epiregulin following lipopolysaccharide stimulation, which activates an immune response. Both immune activity and endoplasmic reticulum stress are activated during cerebral ischemia. We found that the expression levels of amphiregulin and epiregulin were significantly increased under conditions of cerebral ischemia. Because endoplasmic reticulum stress increased the expression of amphiregulin and epiregulin in glial cells, endoplasmic reticulum stress may be a key mediatory factor of pathophysiological activity. Recombinant epiregulin and amphiregulin proteins effectively inhibited endoplasmic reticulum stress and the subsequent induction of neuronal cell death. Therefore, the upregulation of the epidermal growth factor family members epiregulin and amphiregulin may play a critical role in preventing endoplasmic reticulum stress-induced cell death, thus providing a potential therapy for brain injury.     

Translation regulation by eukaryotic initiation factor-2 kinases in the development of latent cysts in Toxoplasma gondii

A key problem in the treatment of numerous pathogenic eukaryotes centers on their development into latent forms during stress. For example, the opportunistic protist Toxoplasma gondii converts to latent cysts (bradyzoites) responsible for recrudescence of disease. We report that Toxoplasma eukaryotic initiation factor-2alpha (TgIF2alpha) is phosphorylated during stress and establish that protozoan parasites utilize translation control to modulate gene expression during development. Importantly, TgIF2alpha remains phosphorylated in bradyzoites, explaining how these cells maintain their quiescent state. Furthermore, we have characterized novel eIF2 kinases; one in the endoplasmic reticulum and a likely regulator of the unfolded protein response (TgIF2K-A) and another that is a probable responder to cytoplasmic stresses (TgIF2K-B). Significantly, our data suggest that 1) the regulation of protein translation through eIF2 kinases is associated with development, 2) eIF2alpha phosphorylation is employed by cells to maintain a latent state, and 3) endoplasmic reticulum and cytoplasmic stress responses evolved in eukaryotic cells before the early diverging Apicomplexa. Given its importance to pathogenesis, eIF2 kinase-mediated stress responses may provide opportunities for novel therapeutics.     

Exposure to nickel, chromium, or cadmium causes distinct changes in the gene expression patterns of a rat liver derived cell line

Many heavy metals, including nickel (Ni), cadmium (Cd), and chromium (Cr) are toxic industrial chemicals with an exposure risk in both occupational and environmental settings that may cause harmful outcomes. While these substances are known to produce adverse health effects leading to disease or health problems, the detailed mechanisms remain unclear. To elucidate the processes involved in the toxicity of nickel, cadmium, and chromium at the molecular level and to perform a comparative analysis, H4-II-E-C3 rat liver-derived cell lines were treated with soluble salts of each metal using concentrations derived from viability assays, and gene expression patterns were determined with DNA microarrays. We identified both common and unique biological responses to exposure to the three metals. Nickel, cadmium, chromium all induced oxidative stress with both similar and unique genes and pathways responding to this stress. Although all three metals are known to be genotoxic, evidence for DNA damage in our study only exists in response to chromium. Nickel induced a hypoxic response as well as inducing genes involved in chromatin structure, perhaps by replacing iron in key proteins. Cadmium distinctly perturbed genes related to endoplasmic reticulum stress and invoked the unfolded protein response leading to apoptosis. With these studies, we have completed the first gene expression comparative analysis of nickel, cadmium, and chromium in H4-II-E-C3 cells.