Age-Correlated Gene Expression in Normal and Neurodegenerative Human Brain Tissues

Background

Human brain aging has received special attention in part because of the elevated risks of neurodegenerative disorders such as Alzheimer''s disease in seniors. Recent technological advances enable us to investigate whether similar mechanisms underlie aging and neurodegeneration, by quantifying the similarities and differences in their genome-wide gene expression profiles.

Principal Findings

We have developed a computational method for assessing an individual''s “physiological brain age” by comparing global mRNA expression datasets across a range of normal human brain samples. Application of this method to brains samples from select regions in two diseases – Alzheimer''s disease (AD, superior frontal gyrus), frontotemporal lobar degeneration (FTLD, in rostral aspect of frontal cortex ∼BA10) – showed that while control cohorts exhibited no significant difference between physiological and chronological ages, FTLD and AD exhibited prematurely aged expression profiles.

Conclusions

This study establishes a quantitative scale for measuring premature aging in neurodegenerative disease cohorts, and it identifies specific physiological mechanisms common to aging and some forms of neurodegeneration. In addition, accelerated expression profiles associated with AD and FTLD suggest some common mechanisms underlying the risk of developing these diseases.     

Investigating microRNA-Target Interaction-Supported Tissues in Human Cancer Tissues Based on miRNA and Target Gene Expression Profiling

Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data. In this study, we propose a method to investigate miRNA-target interaction-supported tissues, which is based on experimentally validated miRNA-target interactions. The tissue specificity results by our method are in accordance with the experimental results in the literature.

Availability and Implementation

Our analysis results are available at http://tsmti.mbc.nctu.edu.tw/ and http://www.stat.nctu.edu.tw/hwang/tsmti.html.     

Expression of Human BMP-2 Gene in Different Tissues of Tobacco Plants

The bone morphogenetic proteins (BMPs) are a family of growth factors that regulate the development of bone. BMP-2 is the most effective in the induction of bone tissue. A large amount of BMP-2 is needed for both bone tissue engineering research and clinical application. Thus, an effective way is necessary to produce sufficient BMP-2 protein. With the advance in plant biotechnology, transgenic plants have been targeted as a bioreactor to produce desired recombinant proteins. Here, the expression of recombinant human bmp-2 gene (rhbmp-2) was studied in tobacco plants using gus as a reporter gene. The difference of expression levels in root, stem and leaf tissues was analyzed by GUS activity assay, semi-quantitive RT-PCR and western blotting. The results indicated that the expression levels of fusion protein in root and stem tissues were significantly higher than those in leaf tissue. For the protein compositions in root and stem tissues were simpler than those in leaf tissue, this suggested that the purification process with root and stem tissues would potentially be easier.     

重组人BMP-2在烟草不同组织中的表达

骨形态发生蛋白（BMPs）是一类调节骨组织发育的生长因子。BMP-2是BMP家族中诱骨活性最强的。在骨组织工程研究和临床应用中需要大量的BMP-2。因此,研究出一种能够有效地大量生产BMP-2的方法是十分必要的。随着植物分子生物学的进展,转基因植物被用作一种生物反应器来生产目的蛋白。以gus作为报告基因,研究了重组人bmp-2基因在烟草中的表达。通过GUS活性检测、半定量PCR和Western blotting分析了根、茎、叶组织中基因表达的水平,结果显示融合蛋白在根和茎组织中表达量显著高于叶组织。由于根和茎组织中蛋白组成与叶组织相比相对简单,提示其更易于进行目的蛋白的纯化。     

The Effect of Statins on Blood Gene Expression in COPD

BackgroundCOPD is currently the fourth leading cause of death worldwide. Statins are lipid lowering agents with documented cardiovascular benefits. Observational studies have shown that statins may have a beneficial role in COPD. The impact of statins on blood gene expression from COPD patients is largely unknown.ObjectiveIdentify blood gene signature associated with statin use in COPD patients, and the pathways underpinning this signature that could explain any potential benefits in COPD.MethodsWhole blood gene expression was measured on 168 statin users and 451 non-users from the ECLIPSE study using the Affymetrix Human Gene 1.1 ST microarray chips. Factor Analysis for Robust Microarray Summarization (FARMS) was used to process the expression data. Differential gene expression analysis was undertaken using the Linear Models for Microarray data (Limma) package adjusting for propensity score and surrogate variables. Similarity of the expression signal with published gene expression profiles was performed in ProfileChaser.Results25 genes were differentially expressed between statin users and non-users at an FDR of 10%, including LDLR, CXCR2, SC4MOL, FAM108A1, IFI35, FRYL, ABCG1, MYLIP, and DHCR24. The 25 genes were significantly enriched in cholesterol homeostasis and metabolism pathways. The resulting gene signature showed correlation with Huntington’s disease, Parkinson’s disease and acute myeloid leukemia gene signatures.ConclusionThe blood gene signature of statins’ use in COPD patients was enriched in cholesterol homeostasis pathways. Further studies are needed to delineate the role of these pathways in lung biology.     

UBC9在人肺癌组织中高表达及其临床意义(英文)

目的:由于Ubc9在肿瘤的发生于恶化中发挥巨大作用,本研究目的是对泛素结合酶(Ubc9)mRNA和Ubc9蛋白在非小细胞肺癌组织中表达进行检测,评估Ubc9在肺癌预后中的指导意义。方法:通过荧光定量PCR、免疫组织化学法、Western-blot检测100例非小细胞肺癌病人中Ubc9 mRNA、蛋白水平的表达进一步研究Ubc9的表达与肺癌临床特征的关系。结果:实验结果显示在肺癌细胞中Ubc9阳性表达显示为黄棕色颗粒,与癌旁组织比较,Ubc9 mRNA、蛋白在肺癌组织中高表达,并且与肺癌的临床分型(分期、淋巴结转移、吸烟、分化)有关。Ubc9 mRNA、蛋白在肺癌中的表达癌组织高于癌旁、有淋巴结转移的高于无转移、吸烟高于不吸烟者、低分化组织高于高分化组织。结论:由此可见Ubc9 mRNA、蛋白水平的高表达可能对肺癌临床特征的评估,以及预测术后生存率都有重要指导意义。     

Gene Expression Profiling in Human Lung Development: An Abundant Resource for Lung Adenocarcinoma Prognosis

A tumor can be viewed as a special “organ” that undergoes aberrant and poorly regulated organogenesis. Progress in cancer prognosis and therapy might be facilitated by re-examining distinctive processes that operate during normal development, to elucidate the intrinsic features of cancer that are significantly obscured by its heterogeneity. The global gene expression signatures of 44 human lung tissues at four development stages from Asian descent and 69 lung adenocarcinoma (ADC) tissue samples from ethnic Chinese patients were profiled using microarrays. All of the genes were classified into 27 distinct groups based on their expression patterns (named as PTN1 to PTN27) during the developmental process. In lung ADC, genes whose expression levels decreased steadily during lung development (genes in PTN1) generally had their expression reactivated, while those with uniformly increasing expression levels (genes in PTN27) had their expression suppressed. The genes in PTN1 contain many n-gene signatures that are of prognostic value for lung ADC. The prognostic relevance of a 12-gene demonstrator for patient survival was characterized in five cohorts of healthy and ADC patients [ADC_CICAMS (n = 69, p = 0.007), ADC_PNAS (n = 125, p = 0.0063), ADC_GSE13213 (n = 117, p = 0.0027), ADC_GSE8894 (n = 62, p = 0.01), and ADC_NCI (n = 282, p = 0.045)] and in four groups of stage I patients [ADC_CICAMS (n = 22, p = 0.017), ADC_PNAS (n = 76, p = 0.018), ADC_GSE13213 (n = 79, p = 0.02), and ADC_qPCR (n = 62, p = 0.006)]. In conclusion, by comparison of gene expression profiles during human lung developmental process and lung ADC progression, we revealed that the genes with a uniformly decreasing expression pattern during lung development are of enormous prognostic value for lung ADC.     

用cDNA微阵列研究内毒素休克小鼠肺组织基因表达谱的改变

利用cDNA微阵列检测了小鼠内毒素休克2 h及20 h肺组织基因表达谱的改变.发现内毒素休克2 h有128个基因表达上调,3个基因下调;内毒素休克20 h有51个基因表达上调,21个下调.并用RT-PCR进一步验证了结果的可靠性.初步分析了基因表达谱改变的意义.有助于从基因组水平阐明内毒素休克的分子机制.     

人肺癌细胞CPP32基因的克隆及表达

蛋白酶尤其是ＩＣＥ家族的蛋白酶是细胞死亡机制的核心成分．ＩＣＥ蛋白酶家族中,ＣＰＰ３２（又称Ｙａｍａ,ａｐｏｐａｉｎ）在不同形式的凋亡途径中起核心作用．为深入研究ＣＰＰ３２的结构与功能,克隆了ＣＰＰ３２基因,并在大肠杆菌中进行了表达．采用ＲＴ－ＰＣＲ技术从人肺癌细胞株中获得了ＣＰＰ３２蛋白酶基因．ＤＮＡ序列分析表明,该基因由已报道的编码ＣＰＰ３２αｐ２０亚单位和ＣＰＰ３２βｐ１０亚单位的核苷酸组成,提示ＩＣＥ家族蛋白酶寡聚化可能受ＤＮＡ水平调控．将获得的ＣＰＰ３２基因分别重组到ｐＢＶ３２１和ｐＥＸ３１Ｂ载体上,并分别转化到大肠杆菌中,均获得了ＣＰＰ３２基因的较高表达,表达产物主要以包涵体形式存在．     

SEGEL: A Web Server for Visualization of Smoking Effects on Human Lung Gene Expression

Cigarette smoking is a major cause of death worldwide resulting in over six million deaths per year. Cigarette smoke contains complex mixtures of chemicals that are harmful to nearly all organs of the human body, especially the lungs. Cigarette smoking is considered the major risk factor for many lung diseases, particularly chronic obstructive pulmonary diseases (COPD) and lung cancer. However, the underlying molecular mechanisms of smoking-induced lung injury associated with these lung diseases still remain largely unknown. Expression microarray techniques have been widely applied to detect the effects of smoking on gene expression in different human cells in the lungs. These projects have provided a lot of useful information for researchers to understand the potential molecular mechanism(s) of smoke-induced pathogenesis. However, a user-friendly web server that would allow scientists to fast query these data sets and compare the smoking effects on gene expression across different cells had not yet been established. For that reason, we have integrated eight public expression microarray data sets from trachea epithelial cells, large airway epithelial cells, small airway epithelial cells, and alveolar macrophage into an online web server called SEGEL (Smoking Effects on Gene Expression of Lung). Users can query gene expression patterns across these cells from smokers and nonsmokers by gene symbols, and find the effects of smoking on the gene expression of lungs from this web server. Sex difference in response to smoking is also shown. The relationship between the gene expression and cigarette smoking consumption were calculated and are shown in the server. The current version of SEGEL web server contains 42,400 annotated gene probe sets represented on the Affymetrix Human Genome U133 Plus 2.0 platform. SEGEL will be an invaluable resource for researchers interested in the effects of smoking on gene expression in the lungs. The server also provides useful information for drug development against smoking-related diseases. The SEGEL web server is available online at http://www.chengfeng.info/smoking_database.html.     

Transient Gene Expression in Intact and Organized Rice Tissues

Regulated gene expression of chimeric genes has been studied extensively in electroporated protoplasts. The applicability of these assays is limited, however, because protoplasts are not always physiologically identical to the cells from which they are derived. We have developed a procedure to electroporate DNA into intact and organized leaf structures of rice. Optimization of the new gene delivery system mainly involved eliminating explant-released nucleases, prolonging the DNA/explant incubation time, and expanding the pulse time. Using a [beta]-glucuronidase gene under the control of constitutive promoters, we demonstrated that all cell types within a leaf base were susceptible to electroporation-mediated DNA uptake. Although the technique was initially developed for leaf bases of young etiolated rice seedlings, we proved that it was equally applicable both to other monocotyledons, including wheat, maize, and barley, and to other explants, such as etiolated and green sheath and lamina tissues from rice. Transient gene expression assays with electroporated leaf bases showed that the promoter from a pea light-harvesting chlorophyll a/b-binding protein gene displayed both light- and chloroplast-dependent expression in rice, and that the promoter from the Arabidopsis S-adenosylmethionine synthetase gene was, as in transgenic Arabidopsis and tobacco, preferentially expressed in cells surrounding the vascular bundles.     

一种新的抑癌候选基因——NDR2在人类正常组织及相应肿瘤中的表达

为观察NDR2基因在人类正常组织及相应肿瘤组织中的表达分布特点,收集人脑与胶质瘤、肺与肺癌、胃与胃癌、结肠与结肠癌组织标本,分别进行组织石蜡切片和总RNA提取,应用免疫组化方法和RT-PCR技术检测NDR2蛋白质及mRNA表达水平,并通过DNA测序验证PCR产物的正确性.免疫组化结果表明,在上述各组织均有NDR2蛋白不同程度的表达.RT-PCR结果显示,在人脑和胶质瘤组织、肺与肺癌组织、胃与胃癌组织、结肠与结肠癌组织中均有NDR2 mRNA表达,其表达水平以脑组织为最高.NDR2 mRNA在正常脑和肺组织的表达水平分别显著高于胶质瘤与肺癌组织,而结肠与结肠癌组织,胃与胃癌组织NDR2 mRNA表达水平则无显著差别.以上结果表明,NDR2基因可能广泛表达于人体正常组织内,而在胶质瘤与肺癌中的表达较相应正常组织减低,提示该基因可能与神经系统及呼吸系统肿瘤的发生发展有关,为进一步探讨该基因功能提供了线索.