Effect of p53 genotype on gene expression profiles in murine liver

The tumor suppressor protein p53 is a key regulatory element in the cell and is regarded as the “guardian of the genome”. Much of the present knowledge of p53 function has come from studies of transgenic mice in which the p53 gene has undergone a targeted deletion. In order to provide additional insight into the impact on the cellular regulatory networks associated with the loss of this gene, microarray technology was utilized to assess gene expression in tissues from both the p53^−/− and p53^+/− mice. Six male mice from each genotype (p53^+/+, p53^+/−, and p53^−/−) were humanely killed and the tissues processed for microarray analysis. The initial studies have been performed in the liver for which the Dunnett test revealed 1406 genes to be differentially expressed between p53^+/+ and p53^+/− or between p53^+/+ and p53^−/− at the level of p ≤ 0.05. Both genes with increased expression and decreased expression were identified in p53^+/− and in p53^−/− mice. Most notable in the gene list derived from the p53^+/− mice was the significant reduction in p53 mRNA. In the p53^−/− mice, not only was there reduced expression of the p53 genes on the array, but genes associated with DNA repair, apoptosis, and cell proliferation were differentially expressed, as expected. However, altered expression was noted for many genes in the Cdc42-GTPase pathways that influence cell proliferation. This may indicate that alternate pathways are brought into play in the unperturbed liver when loss or reduction in p53 levels occurs.     

Microarray analysis of gene expression profile in the corpus cavernosum of hypercholesterolemic rats after chronic treatment with PDE5 inhibitor

Gene expression changes in the corpus cavernosum of hypercholesterolemic rats were not fully assessed, which were not previously known to be associated with hypercholesterolemia-related erectile dysfunction (ED). To provide molecular insight into pathophysiology of hypercholesterolemia-related ED and to investigate the effects of Udenafil, a phosphodiesterase type 5 (PDE5) inhibitor, on gene expression, we performed microarray gene expression analysis via gene discovery methods using GenoCheck platinum cDNA chip (Ansan, S. Korea). Sixteen male Sprague-Dawley rats were fed 2% cholesterol diet for 5 months. Half of them were orally treated with Udenafil (20 mg/kg/day) simultaneously. Eight age-matched rats fed normal diet were served as normal control. RNA was extracted from corpus cavernosum and microarray analysis was performed. Decreased erectile responses and hypercholesterolemia were observed in hypercholesterolemic control group. In microarray analysis, 122 candidate genes were noted to be altered based on the magnitude of expression changes, which includes 44 down-regulated and 78 up-regulated genes compared with the age-matched normal controls. These changes were, however, significantly attenuated by treatment with Udenafil. Out of the 78 up-regulated genes, 8 genes were significantly decreased by the chronic treatment with Udenafil. The altered genes were cytochrome oxidase biogenesis protein OXA1, skeletal muscle myosin heavy chain, lipophilin, fast skeletal muscle isoforms beta/alpha, myosin light chain 3, cytochrome c oxidase, adipocyte fatty acid binding protein and one EST gene. In contrast, among the 44 down-regulated genes, Kruppel-like factor 5 and cyclin D1 genes were increased after the Udenafil treatment. These results provide the molecular basis for understanding the pathogenesis of hypercholesterolemia-related ED and offer clues on determining the underlying action mechanism of a PDE5 inhibitor.     

芹菜NHL-like蛋白基因克隆与表达分析

植物生长发育过程中会遭遇各种病原物的攻击,植物为了应对这些危害并适应外界的生存竞争,逐渐演化出了复杂的防御机制。NHL基因家族庞大,部分NHL基因受病原物诱导后会过量表达,增强植物对多种病原菌的抗性,是与植物防御机制密切相关的蛋白。本研究以津南实芹和美国西芹2个芹菜品种为试验材料,分别克隆出NHL-like蛋白基因AgNHL。序列分析表明,上述2种芹菜的AgNHL基因序列均含636 bp的开放阅读框,编码211个氨基酸。2种芹菜碱基序列,只有第36位不同,津南实芹为T,美国西芹为C,2种碱基序列相似性高达99.84%,编码的氨基酸序列相同。进化分析显示,2种芹菜的NHL-like蛋白与葡萄、大豆等植物的相似度较高,在第80~185氨基酸间含一个LEA-2蛋白保守结构域。荧光定量PCR结果表明,AgNHL基因主要在芹菜茎中表达,根中表达量最低,有明显组织特异性,品种差异也很显著。对2种芹菜分别进行4℃低温、38℃高温、20%PEG处理、0.2 mol/L NaCl处理2 h表达分析显示,低温、盐处理下该基因表达量明显上升。     

Microarray analysis of gene expression profiles in the bovine mammary gland during lactation

Mammary glands undergo functional and metabolic changes during virgin, lactation and dry periods. A total of 122 genes were identified as differentially expressed, including 79 up-regulated and 43 down-regulated genes during lactation compared with virgin and dry periods. Gene ontology analysis showed the functional classification of the up-regulated genes in lactation, including transport, biosynthetic process, signal transduction, catalytic activity, immune system process, cell death, and positive regulation of the developmental process. Microarray data clarified molecular events in bovine mammary gland lactation.     

Microarray analysis of piceatannol-induced changes in gene expression in human gastric cancer cells

Piceatannol, isolated from the roots of Rheum undulatum, prevented oxygen radical formation and inhibited lipid peroxidation; the effective concentrations were 25 M for a radical scavenging assay and 2.1 M for a microsome assay. Using cDNA microarray analysis to determine which genes were modulated by piceatannol, 33 genes were up-regulated while 157 genes were down-regulated in the human gastric cancer cell line.     

Microarray analysis revealed different gene expression patterns in HepG2 cells treated with low and high concentrations of the extracts of Anacardium occidentale shoots

In this study, the effects of low and high concentrations of the Anacardium occidentale shoot extracts on gene expression in liver HepG2 cells were investigated. From MTT assays, the concentration of the shoot extracts that maintained 50% cell viability (IC₅₀) was 1.7 mg/ml. Cell viability was kept above 90% at both 0.4 mg/ml and 0.6 mg/ml of the extracts. The three concentrations were subsequently used for the gene expression analysis using Affymetrix Human Genome 1.0 S.T arrays. The microarray data were validated using real-time qRT–PCR. A total of 246, 696 and 4503 genes were significantly regulated (P < 0.01) by at least 1.5-fold in response to 0.4, 0.6 and 1.7 mg/ml of the extracts, respectively. Mutually regulated genes in response to the three concentrations included CDKN3, LOC100289612, DHFR, VRK1, CDC6, AURKB and GABRE. Genes like CYP24A1, BRCA1, AURKA, CDC2, CDK2, CDK4 and INSR were significantly regulated at 0.6 mg/ml and 1.7 mg but not at 0.4 mg/ml. However, the expression of genes including LGR5, IGFBP3, RB1, IDE, LDLR, MTTP, APOB, MTIX, SOD2 and SOD3 were exclusively regulated at the IC₅₀ concentration. In conclusion, low concentrations of the extracts were able to significantly regulate a sizable number of genes. The type of genes that were expressed was highly dependent on the concentration of the extracts used.     

Role of MyD88 in TLR agonist-induced functional alterations of human adipose tissue-derived mesenchymal stem cells

In this study, we established an in vitro model of osteogenic-inductive differentiation of rat bone marrow mesenchymal stem cells (BMSCs) to determine the mechanisms and relative gene function underlying BMSCs osteogenesis. Osteoplastic differentiation of the third generation BMSCs was induced with the α-minimal essential medium containing β-glyceraldehyde-3-phosphate, l-ascorbic acid, dexamethasone and 1,25–2(OH)₂ vitamin D₃ prior to applying gene chip technology (also called microarray technology) for global gene expression screening. Real-time quantitative PCR (Real-time PCR) was used to determine the temporal profile of mRNA expression of regulated genes during osteogenic differentiation of BMSCs. A bioinformatic analysis was utilized to determine the functional significance of the identified osteogenic-related genes. Purkinje cell protein 4 (Pcp4) mRNA expression was identified by the gene chip screening as being up-regulated during osteoplastic differentiation of BMSCs. Real-time PCR analysis confirmed the increased expression of Pcp4 mRNA expression during osteoplastic differentiation of BMSCs with an upward trend that peaked at day 14. The bioinformatic analysis identified Pcp4 as a gene involved in the deposition of calcium and the modulation of CaM-dependent protein kinase. Thus, we hypothesize that Pcp4 osteoplastic differentiation of BMSCs is mediated in part via Pcp4-induced calcium deposition to form mineral nodules and modulation of certain signal transduction pathways of BMPs.     

嗜热四膜虫金属硫蛋白基因MMT2和MTT4的表达规律比较与进化模式分析

多个金属硫蛋白基因异构型已在四膜虫中被鉴定,这些异构型可分为7a和7b两个亚家族。该文利用实时荧光定量PCR技术检测了嗜热四膜虫金属硫蛋白基因MTT2和MTT4在Hg、Cu、Cd、Zn、H2O2暴露下的表达水平,结果显示两者表达规律相似,均为:Cu暴露下上调最高(>200倍),Hg次之,Cd、Zn上调倍数不大,H2O2有下调趋势。此表达规律明显有别于7a亚家族,具有7b亚家族的表达特征。同种诱导物暴露下MTT4的上调表达幅度比MTT2高出数倍,结合生物信息学分析结果,推测可能与MTT2和MTT4上游调控元件(如AP-1、MRE等)的数量差异有关。基于MTT2和MTT4在结构和功能上的高度相似性,推测两者可能是经近期基因复制事件产生,并遵循基因剂量模型进化而来。     

Effects of maturation on RNA transcription and protein expression of four MRP genes in human placenta and in BeWo cells

The placenta is a multifunctional organ that protects the fetus from toxic compounds and the MRPs contribute to this function. The expression of MRP1, MRP2, MRP3, and MRP5 was compared in human placental tissue and in BeWo cells by real-time RT-PCR analysis; protein expression was assessed by Western blot. MRP1 and MRP3 were the most abundantly expressed genes in placenta but only MRP1 was highly expressed in the BeWo cells. Expression of MRP1 increased 4-fold in the third as compared with first trimester placental samples, and increased 20-fold with polarization of BeWo cells. MRP2, MRP3, and MRP5 were weakly expressed both in placenta and BeWo cells. Protein expression followed mRNA quantification for MRP1 and MRP5 but not for MRP2 and MRP3. These data indicated that MRP1 and MRP5 increase with trophoblast maturation, suggesting a particular role for these proteins in the organ functional development.     

内参基因在昆虫实时荧光定量PCR中的研究进展

作为一种高效的定量PCR技术,实时荧光定量PCR(qRT-PCR)因其灵敏度高、特异性强、定量准确等优点,已被广泛运用于昆虫基因表达和转录分析。然而,为了控制样本RNA在质量和逆转录效率上存在差异,必须筛选表达稳定的"看家基因"作为内参基因,对目的基因表达量进行校正和标准化。许多学者研究表明,昆虫种类和实验条件的不同,导致选择的内参基因也不尽相同。因此,本文综述了前人有关昆虫内参基因的研究及其稳定性评价,为其它昆虫内参基因的研究提供理论参考依据。     

痢疾杆菌侵袭HeLa细胞基因表达谱的研究

采用cDNA微阵列技术检测了HeLa细胞被痢疾杆菌侵袭1h和3h后的基因表达变化,共发现2倍以上差异表达基因752个,上调基因有509个,下调基因有306个,并初步推测HeLa细胞通过激活某些信号通路,诱导表达多个基因,产生整体的细胞效应,以对抗痢疾杆菌的侵袭。对显著差异表达的两个基因TNFR 1B和ERBB2,在痢疾杆菌侵袭HeLa细胞1h和3h后的表达量经荧光实时定量PCR验证,确定这两个基因的确在痢疾杆菌侵袭期间高表达,它们在细胞对痢疾杆菌2457T侵袭反应中起重要的作用。这些结果促进了对痢疾杆菌分子致病机理的认识,也为形成预防和治疗痢疾的策略提供了理论基础。     

Differential responses of normal human coronary artery endothelial cells against multiple cytokines comparatively assessed by gene expression profiles

Endothelial cells play an important role in terms of biological functions by responding to a variety of stimuli in the blood. However, little is known about the molecular mechanism involved in rendering the variety in the cellular response. To investigate the variety of the cellular responses against exogenous stimuli at the gene expression level, we attempted to describe the cellular responses with comprehensive gene expression profiles, dissect them into multiple response patterns, and characterize the response patterns according to the information accumulated so far on the genes included in the patterns. We comparatively analyzed in parallel the gene expression profiles obtained with DNA microarrays from normal human coronary artery endothelial cells (HCAECs) stimulated with multiple cytokines, interleukin-1β, tumor necrosis factor-, interferon-β, interferon-γ, and oncostatin M, which are profoundly involved in various functional responses of endothelial cells. These analyses revealed that the cellular responses of HCAECs against these cytokines included at least 15 response patterns specific to a single cytokine or common to multiple cytokines. Moreover, we statistically extracted genes contained within the individual response patterns and characterized the response patterns with the genes referring to the previously accumulated findings including the biological process defined by the Gene Ontology Consortium (GO). Out of the 15 response patterns in which at least one gene was successfully extracted through the statistical approach, 11 response patterns were differentially characterized by representing the number of genes contained in individual criteria of the biological process in the GO only. The approach to dissect cellular responses into response patterns and to characterize the pattern at the gene expression level may contribute to the gaining of insight for untangling the diversity of cellular functions.