Analysis of differentially expressed genes in early- and late-stage APPsw-transgenic and normal mice using cDNA microarray

The complexity of Alzheimer's disease (AD) has made it difficult to examine its underlying mechanism. A gene microarray offers a solution to the complexity through a parallel analysis of most of the genes expressed in the brains from AD-transgenic mice. In our previous study, a total of 52 differentially expressed genes were identified in 18-month-old APPsw-transgenic mice compared to age-matched normal mice. We extended our work to better understand the relevant gene profiles from both early- and late-stage transgenic and normal mice. To accomplish this, cDNA microarray was used with the large-scale screening of the brain mRNA from transgenic and normal mice of 1 and 18 months of age. We identified a total of 48 genes, 6 up-regulated and 42 down-regulated, differentially expressed with a significant degree of induction and reduction in the brains from moderate 18-month-old transgenic mice compared to 1-month-old transgenic mice. In parallel, a total of 40 differentially expressed genes, 6 up-regulated and 34 down-regulated, were also found in the brains from moderate 18-month-old normal mice compared to 1-month-old normal mice. Thus, differentially expressed genes upon APPsw overexpression and the aging process are useful targets through which investigators can choose genes of particular interest. In the future, it will be necessary to study the function of differentially expressed genes, which are targets for developing drugs, using pharmacoproteomics.     

D-半乳糖导致小鼠海马基因表达谱变化

本实验采用cDNA芯片研究D-半乳糖皮下注射小鼠海马的基因表达变化。小鼠皮下注射D-半乳糖[50m∥(kg．d)]60d造模，Morris水迷宫测试小鼠行为，分别提取模型组和对照组海马组织总RNA，掺入荧光分子Cy3和Cy5，经逆转录合成cDNA荧光探针与4000点小鼠cDNA基因芯片杂交。结果显示，在4000条待研究的基因中，两组小鼠海马间存在2倍表达差异的有76条，其中上调26条，下调50条。经分析，模型组基因表达谱与老年性痴呆(AD)相关基因表达谱在氧应激、能量代谢相关基因等方面有相似之处。提示D-半乳糖小鼠模型有可能作为拟AD病理模型。     

脂代谢相关三基因突变小鼠肝组织基因表达差异研究

目的研究3个脂代谢相关基因联合突变小鼠与野生型小鼠肝脏基因表达差异及其与血脂代谢紊乱和动脉粥样硬化病变的关系。方法应用BiostarM-40S型小鼠cDNA表达谱芯片检测不同基因型小鼠肝脏基因表达的差异，并观察不同年龄小鼠血浆总胆固醇和甘油三脂的浓度以及主动脉内膜形态变化。结果在被测的4000条基因中，与野生型小鼠比较，5周龄三基因突变小鼠肝脏基因表达上调92条，下调105条，脂代谢相关基因中与胆固醇合成相关的基因表达下调，与甘油三脂代谢相关的肝脂肪酶基因表达水平上调。糖代谢、细胞骨架蛋白和免疫等相关的基因表达也有明显差异。5周龄的三基因突变小鼠血浆总胆固醇和甘油三脂水平明显高于野生型小鼠，伴有主动脉内膜损伤，并随年龄增长而加重。结论三基因突变导致肝脏中与脂类、糖类以及免疫等相关的多种基因表达改变，可能共同参与了血脂代谢紊乱和动脉粥样硬化的发生发展。     

Characterization of the human ABC superfamily: isolation and mapping of 21 new genes using the expressed sequence tags database

As an approach to characterizing all human ATP-binding cassette (ABC) superfamily genes, a search of the human expressed sequence tag (EST) database was performed using sequences from known ABC genes. A total of 105 clones, containing sequences of potential ABC genes, were identified, representing 21 distinct genes. This brings the total number of characterized human ABC genes from 12 to 33. The new ABC genes were mapped by PCR on somatic cell and radiation hybrid panels and yeast artificial chromosomes (YACs). The genes are located on human chromosomes 1, 2, 3, 4, 6, 7, 10, 12, 13, 14, 16, 17 and X; at locations distinct from previously mapped members of the superfamily. The characterized genes display extensive diversity in sequence and expression pattern and this information was utilized to determine potential structural, functional and evolutionary relationships to previously characterized members of the ABC superfamily.      

Identification of candidate coding region single nucleotide polymorphisms in 165 human genes using assembled expressed sequence tags

Using assembled expressed sequence tags (ESTs) from 50 different cDNA libraries, we have identified contigs that represent the complete coding sequences of 850 known human genes, and have scanned these for high quality sequence substitutions. We report the identification and characteristics of 201 candidate single nucleotide polymorphisms found in the coding sequences (cSNPs) of 165 of these genes. Using a conservative calculation, coding region nucleotide diversity (the average number of differences between any pair of chromosomes) was found to be 3 per 10,000 bp based on this data. This analysis reveals that assembled ESTs from multiple libraries may provide a rich source of comparative sequences to search for cSNPs in the human genome.     

Global analysis of differentially expressed genes in early gestational decidua and chorionic villi using a 9600 human cDNA microarray

The global gene expression profiles of the decidua and chorionic villi of early human pregnancies were analysed by using cDNA microarray technology. Decidual and villous placental tissues were obtained from first trimester abortus and mRNA was extracted for cDNA microarray analysis. The human cDNA microarray [9600 clones, including known regulatory genes and expressed sequence tags (EST)] with colorimetric detection was used to identify differentially expressed genes between early gestational decidua and villi. According to cDNA microarray analysis, we have identified 641 genes with highly expressed mRNA in both decidua and villi, 49 genes with higher expressions in decidua, and 75 genes with higher expression in chorionic villi. These differentially expressed genes were further grouped into categories by their putative functions, including: cell growth-related factors, hormones/cytokines, cell adhesion molecules, signal transduction molecules, apoptosis-related factors, cytoskeleton/extracellular matrix proteins, and EST. Immunohistochemical stainings of cathepsin L, leukaemia inhibitory factor-receptor, and proliferative cell nuclear antigen showed results consistent with the microarray data. Identification of the differentially expressed genes between decidua and villi by microarray provide a global profiling of the gene expression pattern. This work adds to our understanding of placentation by reporting the gene expression profiles during first trimester human pregnancies using cDNA microarray.     

A novel PCR-based technique using expressed sequence tags and gene homology for murine genetic mapping: localization of the complement genes

The complement system is a cascade of serum proteins and receptors which forms a vital arm of innate immunity and enhances the adaptive immune response. This work establishes the chromosomal localization of four key genes of the murine complement system. Mapping was performed using a novel and rapid PCR restriction length polymorphism method which was developed to exploit the murine expressed sequence tag (EST) database. This technique circumvents the laborious cDNA or genomic cloning steps of other mapping methods by relying on EST data and the prediction of exon-intron boundaries. This method can be easily applied to the genes of other systems, ranging from the interests of the individual researcher to large-scale gene localization projects. Here the complement system, probably one of the most well-characterized areas of immunology, was used as a model system. It was shown that the C3a receptor C1r and C1s genes form an unexpected complement gene cluster towards the telomeric end of chromosome 6. The second mannose binding lectin-associated serine protease gene was mapped to the telomeric end of chromosome 4, which is distinct from other complement-activating serine proteases. These results provide new insights into the evolution of this group of proteins.     

Identification of genes expressed by zebrafish oligodendrocytes using a differential microarray screen

Myelination of central nervous system axons requires that oligodendrocytes extend multiple membrane processes that specifically recognize and wrap axons, which is followed by expression of proteins necessary for formation of myelin sheaths. To identify new genes that might be important for myelination, we used microarrays to analyze the expression profiles of cells sorted from transgenic zebrafish embryos and larvae under conditions that permitted or blocked oligodendrocyte development. Here, we describe eight genes that have not been previously implicated in oligodendrocyte development. Among the predicted functions of proteins encoded by these genes are lipid sensing, cell–cell junction formation, cytoskeleton regulation, and intracellular signaling. The predicted functions raise the possibility that these genes are involved in multiple cellular events during oligodendrocyte differentiation and myelin formation. Developmental Dynamics 239:2041–2047, 2010. © 2010 Wiley‐Liss, Inc.     

Identification of novel genes expressed during rhabdomyosarcoma differentiation using cDNA microarrays

Rhabdomyosarcomas (RMS) are highly aggressive tumors that are thought to arise as a consequence of the regulatory disruption of the growth and differentiation of skeletal muscle progenitor cells. Normal myogenesis is characterized by the expression of the myogenic regulatory factor gene family but, despite their expression in RMS, these tumor cells fail to complete the latter stages of myogenesis. The RMS cell line RD-A was treated with 12-O-tetradecanoylphorbol-13-acetate to induce differentiation and cultured for 10 days. RNA was extracted on days 1, 3, 6, 8 and 10. A human skeletal muscle cDNA microarray was developed and used to analyze the global gene expression of RMS tumors over the time-course of differentiation. As a comparison, the genes identified were subsequently examined during the differentiated primary human skeletal muscle cultures. Prothymosin alpha (PTMA), and translocase of inner mitochondrial membrane 10 (Tim10), two genes not previously implicated in RMS, showed reduced expression during differentiation. Marked differences in the expression of PTMA and Tim10 were observed during the differentiation of human primary skeletal muscle cells. These results identify several new genes with potential roles in the myogenic arrest present in rhabdomyosarcoma. PTMA expression in RMS biopsy samples might prove to be an effective diagnostic marker for this disease.     

Human cochlear expressed sequence tags provide insight into cochlear gene expression and identify candidate genes for deafness

To identify candidate genes for human hearing disorders and to understand better human hearing at the molecular level, we constructed a human cochlear cDNA library. An aliquot of the unsubtracted cochlear library was contributed to the IMAGE Consortium at Lawrence Livermore National Laboratory for the generation of expressed sequence tags (ESTs) by the Merck/WashU EST project. Over 4000 ESTs were developed from the cochlear cDNA library and deposited in the GenBank EST database. Sequence clustering shows that the majority of clones are in low copy numbers, demonstrating the high complexity of the library. The sequences of 1388 cochlear ESTs (33%) match 517 known human genes. Among these are genes previously shown to cause both syndromic and non- syndromic hearing loss. A number of the cochlear ESTs show high homology to non-human genes, suggesting new gene family members or human homologs of animal genes. We also report the chromosomal map positions of 437 cochlear ESTs. These provide positional candidate genes for 18 different non-syndromic hearing disorders. A Human Cochlear EST Database web site (http://www.bwh.partners. org/pathology ) has been created to provide access to the cochlear clone data for gene discovery investigations.      

大鼠小脑部分表达序列标签的鉴定

目的:为了获取大鼠小脑特异表达的cDNA序列,筛选新的EST基因片段,以便进一步获取有意义的cDNA全基因。方法:以大鼠大脑、脑干mRNA逆转录cDNA作为driver(驱动)cDNA,大鼠小脑mRNA逆转录cDNA作为tester(测试)cDNA,经消减杂交法,消除与大脑及脑干相同的cDNA,并富集低丰度基因,从而获得大鼠小脑特异表达基因片段,以及低表达基因片段,克隆制备成大鼠小脑特异表达cDNA文库。结果:共挑选出32个阳性克隆质粒,测序得到34个不同基因片段的序列。最后用反Northern杂交去除假阳性,筛选出8个有意义的差异表达cDNA基因片段。同时,将测序结果与Genbank进行同源性比较,发现13个新的EST序列,并申请获得基因序列号(AW288461-AW288474)。结论:抑制消减杂交法是一种筛选特异表达基因的有效方法。本结果可为研究脑功能的分子机制提供有益的资料。     

应用表达芯片筛选小鼠肝癌淋巴道转移相关基因

目的采用表达芯片比较高、低淋巴道转移力小鼠肝癌腹水型细胞株Hca—F和Hca—P的基因表达谱,以筛选出与肿瘤淋巴道转移相关的基因。方法分别提取Hca—F和Hca—P细胞的总RNA,反转录合成生物素标记的cRNA探针,并与Affy—metrix GeneChip MOE430A（包括22690个转录本,对应于约14500个小鼠已知基因和4371个EST）杂交,检测结果利用生物信息学进行分析。结果Hca—F和Hca—P相比,在14500个已知基因中,有901个（6．2％）表达上调幅度≥2倍;在4371个EST中,有129个（3％）上调幅度≥2倍。公布了差异表达≥8倍的37个基因并根据Gene Ontology（GO）分类和TreeView分析,按照其参与的生物学过程和具有的分子功能进行了功能分类。其中有19个基因参与了组织发生、细胞黏附、信号转导、细胞生长、分化及代谢等的生物学过程,29个基因分别具有转运、移动、蛋白激酶、蛋白结合及受体活性等分子功能,7个基因的生物学功能尚不清楚。结论表达芯片检测与肿瘤淋巴道转移模型相结合,为肿瘤转移研究提供新方法、新思路,一些过量表达的基因将为肿瘤转移机制的研究提供新线索。     

Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense

Trypanosoma congolense is one of the most economically important pathogens of livestock in Africa. Culture-derived parasites of each of the three main insect stages of the T. congolense life cycle, i.e., the procyclic, epimastigote and metacyclic stages, and bloodstream stage parasites isolated from infected mice, were used to construct stage-specific cDNA libraries and expressed sequence tags (ESTs or cDNA clones) in each library were sequenced. Thirteen EST clusters encoding different variant surface glycoproteins (VSGs) were detected in the metacyclic library and 26 VSG EST clusters were found in the bloodstream library, 6 of which are shared by the metacyclic library. Rare VSG ESTs are present in the epimastigote library, and none were detected in the procyclic library. ESTs encoding enzymes that catalyze oxidative phosphorylation and amino acid metabolism are about twice as abundant in the procyclic and epimastigote stages as in the metacyclic and bloodstream stages. In contrast, ESTs encoding enzymes involved in glycolysis, the citric acid cycle and nucleotide metabolism are about the same in all four developmental stages. Cysteine proteases, kinases and phosphatases are the most abundant enzyme groups represented by the ESTs. All four libraries contain T. congolense-specific expressed sequences not present in the Trypanosoma brucei and Trypanosoma cruzi genomes. Normalized cDNA libraries were constructed from the metacyclic and bloodstream stages, and found to be further enriched for T. congolense-specific ESTs. Given that cultured T. congolense offers an experimental advantage over other African trypanosome species, these ESTs provide a basis for further investigation of the molecular properties of these four developmental stages, especially the epimastigote and metacyclic stages for which it is difficult to obtain large quantities of organisms. The T. congolense EST databases are available at: http://www.sanger.ac.uk/Projects/T_congolense/EST_index.shtml.