Alterations of gene expression profiles induced by sulfur dioxide in rat lungs

Sulfur dioxide (SO2) is a ubiquitous air pollutant presents in low concentrations in urban air and in higher concentrations in working environment.Few data are avail-able on the effects of being exposed to this pollutant on the molecular mechanism,although some biochemical changes in lipid metabolism,intermediary metabolism and oxidative stress have been detected.The present investigation aimed at analyzing the gene expression profiles of the lungs of Wistar rats short-term (20 ppm,6 h/day,for seven days) and long.term (5 ppm,1 h/day,for 30 days) exposed to SO2 by Affymetrix GeneChip (RAE230A) analysis.It was found that 31 genes,containing 18 known genes and 13 novel genes were up-regulated,and 31 genes,containing 20 known genes and 11 novel genes,were down-regulated in rats short-term exposed to SO2 compared with control rats.While there were 176 genes,containing 82 known genes and 94 novel genes were up-regulated,and 85 genes,containing 46 known genes and 39 novel genes,were down-regulated in rats long-term exposed to SO2 compared with control rats.It is suggested that:(1) SO2 exerts its effects by different mechanisms in vivo at high-dose short-term inhalation and at low-dose long-term inhalation;(2) a notable feature of the gene expression profile was the decreased expression of genes related to oxidative phosphorylation in lungs of rats short-term exposed to SO2,which shows high-dose short-term exposed to SO2 may cause the deterioration of mitochondrial functions;(3)discriminating genes in lungs of rats long-term exposed to SO2 included those involved in fatty acid metabolism,immune,inflammatory,oxidative stress,oncogene,tumor suppresser and extracellular matrix.The mechanism of low-dose long-term exposed to SO2 is more complex.     

用基因芯片研究高苯丙氨酸诱导神经元基因表达谱的改变

为深入了解苯丙酮尿症患者高苯丙氨酸损伤神经元的可能机制,我们将体外培养3d的胚鼠神经元随机分为两组：高苯丙氨酸组和对照组。高苯丙氨酸组加入0．9mmol/L苯丙氨酸诱导12h,对照组加入等体积的培养液,抽提RNA,与大鼠神经生物学芯片U34杂交,检测胚鼠原代神经元高苯丙氨酸作用下表达谱的改变,并用实时荧光定量聚合酶链式反应方法验证基因芯片的结果。发现芯片上1323条总探针组合数中有167条基因表达增加(12．6％),表达下调的已知基因数为7条,占总探针组合数的0.5％。按基因功能,表达上升的基因可分为信号转导相关基因、神经元相关基因、细胞骨架基因、代谢相关基因、离子通道基因、转录相关基因、细胞因子基因、凋亡相关基因等。研究结果证实了以前的报道,如Na^ 、K^ -ATP酶、凋亡、氧化应激、NMDA受体、Ca^2 参与了高苯丙氨酸对神经元的损伤过程。结果还显示,在高苯丙氨酸环境下,CaMKⅡ、Ras、P38、钙通道基因表达上升,部分与囊泡形成、神经递质释放有关的基因表达增强,与神经递质谷氨酸有关的受体和转运体基因表达上升。我们推测高苯丙氨酸可能激活轴NMDR Ca^2 -CaMKⅡ-Ras-P38,引起神经元突起异常;高苯丙氨酸环境下,神经递质释放可能异常：兴奋性神经递质谷氨酸可能参与了高苯丙氨酸引起的神经元损伤。高苯丙氨酸对神经元的损伤是多因素作用。     

Expression of arabidopsis cytosolic ascorbate peroxidase gene in response to ozone or sulfur dioxide

The effects of ozone or sulfur dioxide on antioxidant enzymes were investigated in Arabidopsis thaliana. Plants were fumigated with 0.1–0.15 ppm ozone or sulfur dioxide up to about 1 week in an environment-controlled chamber. Both pollutants increased the activities of ascorbate peroxidase and guaiacol per-oxidase in leaves, but had little effect on the activities of superoxide dismutase, catalase, monodehydroascorbate reductase, dehydroascorbate reductase or glutathione reductase. Ozone was more effective than sulfur dioxide in increasing the activities of the peroxidases. Ascorbate peroxidase activity increased 1.8-fold without a lag period during fumigation with 0.1 ppm ozone, while guaiacol peroxidase activity increased 4.4-fold with a 1-day lag. Expression of the APX1 gene encoding cytosolic ascorbate peroxidase was further investigated. Its protein levels in leaves exposed to 0.1 ppm ozone for 4 or 8 days were 1.5-fold higher than in controls. Both ozone and sulfur dioxide elevated APX1 mRNA levels in leaves at 4 and 7 days, whereas at 1 day only ozone was effective. The induction of APX1 mRNA levels by ozone (3.4- to 4.1-fold) was more prominent than that by sulfur dioxide (1.6-to 2.6-fold). The APX1 mRNA level increased by day and decreased by night. Exposure of plants to 0.1 ppm ozone enhanced the APX1 mRNA level within 3 h, which showed a diurnal rhythm similar to that of the control. These results demonstrate that near-ambient concentrations of ozone as well as similar concentrations of sulfur dioxide can induce APX1 gene expression in A. thaliana.Environmental Biology Division     

Large-scale analysis of gene expression profiles

The accumulation of DNA microarray data has now made it possible to use gene expression profiles to analyse expression data. A gene expression profile contains the expression data for a given gene over various samples, and can be contrasted with an expression signature, which contains the expression data for a single sample. Gene expression profiles are most revealing when samples are grouped appropriately, either by standard clinical or pathological categories or by categories discovered through cluster analysis techniques. Expression profiles can exist at various levels of abstraction, yielding information across various tissues or across diseases within a particular tissue. Hypothesis tests may be applied to expression profiles on a large scale to identify candidate genes of interest.     

Alterations of A549 lung cell gene expression in response to biochemical toxins

Health risks associated with the inhalation of potentially toxic materials have been a topic of great public concern. In vitro cellular analyses can provide mechanistic information on the molecular-level responses of lung-derived cell lines to a variety of these hazards. This understanding may be used to develop methods to reduce the damage from such toxins or to detect early stages of their effects. Here we describe an evaluation of the alterations in gene expression of an immortalized lung cell line (A549, human type II epithelia) to a variety of inhalation health hazards including etoposide, gliotoxin, streptolysin O, methyl methansesulfonate (MMS), and Triton X-100. The A549 cells display a dose–response relationship to each toxin with initial responses including alterations in metabolic activity, increases in membrane permeability, and initiation of response genes. In general, membrane-damaging agents (streptolysin O and Triton X-100) induce production of new ion channel proteins, structural proteins, and metabolic enzymes. Gliotoxin impacted the metabolic machinery, but also altered ion channels. Etoposide and MMS caused alterations in the cell cycle, induced DNA repair enzymes, and initiated apoptotic pathways, but MMS also induced immune response cascades. The mechanism of cell response to each toxin is supported by physiological analyses that indicated a fairly slow initiation of cell response to all compounds tested, except for Triton, which caused rapid decline in cell function due to solubilization of the cell membrane. However, Triton does induce production of a number of cell membrane-associated proteins and so its effects at low concentrations are likely translated throughout the cell. Together these results indicate a broader array of cellular responses to each of the test toxins than have previously been reported.     

Tumor-specific gene expression patterns with gene expression profiles

Gene expression profiles of 14 common tumors and their counterpart normal tissues were analyzed with machine learning methods to address the problem of selection of tumor-specific genes and analysis of their differential expressions in tumor tissues. First, a variation of the Relief algorithm, “RFE_Relief algorithm” was proposed to learn the relations between genes and tissue types. Then, a support vector machine was employed to find the gene subset with the best classification performance for distinguishing cancerous tissues and their counterparts. After tissue-specific genes were removed, cross validation experiments were employed to demonstrate the common deregulated expressions of the selected gene in tumor tissues. The results indicate the existence of a specific expression fingerprint of these genes that is shared in different tumor tissues, and the hallmarks of the expression patterns of these genes in cancerous tissues are summarized at the end of this paper.     

Endogenous generation of sulfur dioxide in rat tissues

While sulfur dioxide (SO₂) has been previously known for its toxicological effects, it is now known to be produced endogenously in mammals from sulfur-containing amino acid l-cysteine. l-cysteine is catalyzed by cysteine dioxygenase (CDO) to l-cysteinesulfinate, which converts to β-sulfinylpyruvate through transamination by aspartate aminotransferase (AAT), and finally spontaneously decomposes to pyruvate and SO₂. The present study explored endogenous SO₂ production, and AAT and CDO distribution in different rat tissue. SO₂ content was highest in stomach, followed by tissues in the right ventricle, left ventricle, cerebral gray matter, pancreas, lung, cerebral white matter, renal medulla, spleen, renal cortex and liver. AAT activity and AAT1 mRNA expression were highest in the left ventricle, while AAT1 protein expression was highest in the right ventricle. AAT2 and CDO mRNA expressions were both highest in liver tissue. AAT2 protein expression was highest in the renal medulla, but CDO protein expression was highest in liver tissue. In all tissues, AAT1 and AAT2 were mainly distributed in the cytoplasm rather than the nucleus. These observed differences among tissues endogenously generating SO₂ and associated enzymes are important in implicating the discovery of SO₂ as a novel endogenous signaling molecule.     

Altered gene expression profiles of NIH3T3 cells regulated by human lung cancer associated gene CT120

CT120, a novel membrane-associated gene implicated in lung carcinogenesis, was previously identified from chromosome 17pl 3.3 locus, a hot mutation spot involved in human malignancies. In the present study, we further determined that CT120 ectopic expression could promote cell proliferation activity of NIH3T3 cells using MTS assay, and monitored the downstream effects of CT120 in NIH3T3 cells with Atlas mouse cDNA expression arrays. Among 588 known genes, 133 genes were found to be upregulated or downregulated by CT120. Two major signaling pathways involved in cell proliferation, cell survival and anti-apoptosis were overexpressed and activated in response to CT120:One is the Raf/MEK/Erk signal cascades and the other is the PI3K/Akt signal cascades, suggesting that CT120 might contribute, at least in part, to the constitutively activation of Erk and Akt in human lung caner cells. In addition, some tumor metastasis associated genes cathepsin B, cathepsin D, cathepsin L, MMP-2/TIMP-2 were also upregulated by CT120, upon which CT120 might be involved in tumor invasiveness and metastasis. In addition, CT120 might play an important role in tumor progression through modulating the expression of some candidate “Lung Tumor Progression”genes including B-Raf, Rab-2, BAX, BAG-1, YB-1, and Cdc42.     

大鼠不同心肌肥厚模型左心室基因表达谱变化的比较

为了解心肌肥厚时基因表达谱的变化规律,本实验复制了三种大鼠心肌肥厚模型：肾上腹主动脉缩窄(suprarenal abdominal aortic stenosis,SRS)、动静脉瘘(arterial-vein fistula,AVF)和去甲。肾上腺素持续静脉输注(jugular vein infusion of norepinephrine,NEi),并应用组织化学方法和超声心动术检测大鼠心脏结构和功能指标,应用cDNA基因芯片技术检测心脏基因表达水平的变化。SRS和NEi引起大鼠向心性心肌肥厚,AVF引起大鼠离心性心肌肥厚,其中NEi大鼠心肌纤维化明显。对不同心肌肥厚模型间大鼠左心室基因表达谱的变化进行两两比较。结果显示,有部分基因在不同模型中表达水平均发生变化,其中多数基因在两种模型中表达水平改变的方向相同,也有少部分基因在两种模型中表达水平改变方向相反。综合比较三种心肌肥厚模型的基因表达谱,各种模型都有特异的基因表达变化,但是有19个基因在三种心肌肥厚模型中表达水平均发生改变。研究结果有可能成为心肌肥厚的标志性基因或治疗靶点,为心肌肥厚发生机制的深入研究提供了新的线索。     

二氧化硫生物学研究进展:从毒理学到生理学

本文以作者20余年的系列研究为基础,对二氧化硫(SO2)生物学研究进展进行了综述.首先,总结近年来SO2的毒理学作用及其机制的研究;其次,评述SO2作为一种新型气体信号分子的生理学作用及SO2供体方面的最新研究进展;最后介绍SO2的病理生理学作用的研究进展.     

基因芯片技术与基因表达谱研究

基因芯片技术是近年来出现的分子生物学与微电子技术相结合的最新DNA分析检测技术,该技术将成为信息科学与生命科学之间的联系纽带,为后基因组时代基因功能的分析提供一种最重要的技术手段,目前基因芯片技术已在基因表达谱等研究中得到广泛应用。     

根据基因表达谱筛选间接互作蛋白质进行蛋白质功能预测

利用基因表达谱数据,通过计算互作蛋白质的表达相关系数,来筛选、优化蛋白质互作网络。结果显示,利用经过筛选的互作数据,根据邻居计数法和卡方法进行功能预测的预测效果明显提高,距离待测蛋白质较远的邻居也包含着与待测蛋白质功能一致的信息。     

Alterations in the rat electrocardiogram induced by stationary magnetic fields

A field strength dependent increase in the amplitude of the T-wave signal in the rat electrocardiogram (ECG) was observed during exposure to homogeneous, stationary magnetic fields. For 24 adult Sprague-Dawley and Buffalo rats of both sexes, the T-wave amplitude was found to increase by an average of 408% in a 2.0 Tesla (1 Tesla = 10⁴ Gauss) field. No significant magnetically induced changes were observed in other components of the ECG record, including the P wave and the QRS complex. The minimum field level at which augmentation of the T wave could be detected was 0.3 Tesla. The magnetically induced increase in T-wave amplitude occurred instantaneously, and was immediately reversible after exposure to fields as high as 2.0 Tesla. No abnormalities in any component of the ECG record, including the T wave, were noted during a period of 3 weeks following cessation of a continuous 5-h exposure of rats to a 1.5-Tesla field. The heart rate and breathing rate of adult rats were not altered during, or subsequent to, application of fields up to 2.0 Tesla. The effect of animal orientation within the field was tested using juvenile rats 3–14 days old. The maximum increase in T-wave amplitude was observed when subjects were placed with the long axis of the body perpendicular to the lines of magnetic induction. These experimental observations, as well as theoretical considerations, suggest that augmentation of the signal amplitude in the T-wave segment of the ECG may result from a superimposed electrical potential generated by aortic blood flow in the presence of a stationary magnetic field.     

Regulation of adenosine 5'-phosphosulfate sulfotransferase by sulfur dioxide in primary leaves of beans (Phaseolus vulgaris)

SO₂ inhibited the light-induced increase of extractable adenosine 5′-phosphosulfate sulfotransferase in greening primary leaves of bean seedlings (Phaseolus vulgaris L. cv. Saxa (Radio) Stamm Vatter). In green primary leaves containing appreciable extractable adenosine 5′-phosphosulfate sulfotransferase activity, SO₂ treatment for 20 h decreased the activity of the enzyme to between 10 and 20% of the initial level. After removal of SO₂ from the air, the extractable adenosine 5′-phosphosulfate sulfotransferase activity increased after a lag, both in green and greening primary leaves, and was back to the control level after about 48 h. The sulfate concentration was increased about fourfold during SO₂ treatment. An increase in sulfate sulfur accompanied by a decrease in adenosine 5′-phosphosulfate sulfotransferase was also observed when bean seedlings, after excision of the roots, were transferred to nutrient solutions containing high sulfate concentrations, suggesting that sulfate is involved in the regulation of the enzyme.     

Biological and functional analysis of statistically significant pathways deregulated in colon cancer by using gene expression profiles

Gene expression profiling offers a great opportunity for studying multi-factor diseases and for understanding the key role of genes in mechanisms which drive a normal cell to a cancer state. Single gene analysis is insufficient to describe the complex perturbations responsible for cancer onset, progression and invasion. A deeper understanding of the mechanisms of tumorigenesis can be reached focusing on deregulation of gene sets or pathways rather than on individual genes. We apply two known and statistically well founded methods for finding pathways and biological processes deregulated in pathological conditions by analyzing gene expression profiles. In particular, we measure the amount of deregulation and assess the statistical significance of predefined pathways belonging to a curated collection (Molecular Signature Database) in a colon cancer data set. We find that pathways strongly involved in different tumors are strictly connected with colon cancer. Moreover, our experimental results show that the study of complex diseases through pathway analysis is able to highlight genes weakly connected to the phenotype which may be difficult to detect by using classical univariate statistics. Our study shows the importance of using gene sets rather than single genes for understanding the main biological processes and pathways involved in colorectal cancer. Our analysis evidences that many of the genes involved in these pathways are strongly associated to colorectal tumorigenesis. In this new perspective, the focus shifts from finding differentially expressed genes to identifying biological processes, cellular functions and pathways perturbed in the phenotypic conditions by analyzing genes co-expressed in a given pathway as a whole, taking into account the possible interactions among them and, more importantly, the correlation of their expression with the phenotypical conditions.     

Influence of 0.5 ppm nitrogen dioxide exposure of mice on macrophage congregation in the lungs

Summary The lungs of 12 mice, half of which were exposed to continuous 0.5 ppm nitrogen dioxide for 3 weeks, were explanted in culture, and the instances of macrophage congregation were quantitated according to numbers of target cells involved, categories of congregation from three to 11 or more, numbers of macrophages participating in each category for the total cultures, and the influence of delaying explantation for 24 and 96 hr. A total of 9042 macrophages and 2140 epithelial and spindle target cells were counted in the outgrowths from 306 explants. The incidence of macrophage congregation (or numbers of target cells) was greater for the cultures from the NO₂-exposed animals, both with respect to total incidences between groups (p→0), and the 0-hr (p<0.001) and 24-hr (p<0.01) culture subgroups. In addition, the values for T₃ to T₆ macrophage congregation were individually and consistently greater for the exposed animal group. Postmortem interval stress at 96 hr appeared to result in large colonies, but they were reduced greatly in number. Also the incidence of macrophage congregation fell by 28% as compared to 0-hr and 24-hr subgroups. Supported by Grants NHLI No. HL 17412 and EPA No. R. 800881.     

Alterations in metabolism and gene expression in brain regions during cuprizone-induced demyelination and remyelination

Exposure of mice to the copper chelator, cuprizone, results in CNS demyelination. There is remyelination after removal of the metabolic insult. We present brain regional studies identifying corpus callosum as particularly severely affected; 65% of cerebroside is lost after 6 weeks of exposure. We examined recovery of cerebroside and ability to synthesize cerebroside and cholesterol following removal of the toxicant. The temporal pattern for concentration of myelin basic protein resembled that of cerebroside. We applied Affymetrix GeneChip technology to corpus callosum to identify temporal changes in levels of mRNAs during demyelination and remyelination. Genes coding for myelin structural components were greatly down-regulated during demyelination and up-regulated during remyelination. Genes related to microglia/macrophages appeared in a time-course (peaking at 6 weeks) correlating with phagocytosis of myelin and repair of lesions. mRNAs coding for many cytokines had peak expression at 4 weeks, compatible with intercellular signaling roles. Of interest were other genes with temporal patterns correlating with one of the three above patterns, but of function not obviously related to demyelination/remyelination. The ability to correlate gene expression with known pathophysiological events should help in elucidating further function of such genes as related to demyelination/remyelination.