Differentially expressed genes in the liver of thioacetamide treated rats

Thioacetamide is a hepatotoxic and hepatocarcinogenic compound that affects liver metabolism, inhibits mRNA transport and induces enlargement of the nucleolus. To investigate the effect of thioacetamide at the molecular level, differential display RT-PCR was conducted. Analysis of nineteen differentially expressed genes demonstrated that ten cDNAs have their expression inhibited while the other nine were positively affected by thioacetamide. Two of the cDNAs were homologous to known genes-TAP and ankyrin-binding glycoprotein-1, two corresponded to repetitive sequences and seven were homologous to expressed sequence tags. The differential expression of some of the isolated cDNAs was confirmed by northern hybridization. It is proposed that since the product of TAP is involved in mRNA transport, thioacetamide inhibition of TAP expression might, at least partially, explain the thioacetamide-induced swelling of the nucleolus.     

Identification of age-dependently expressed genes in mouse liver by differential display–PCR analysis

The aim of this study was to identify genes expressed in an age-dependent manner in mouse (Mus musculus) liver. To search for age-dependently expressed genes, we used a fluorescence differential display–PCR (FDD–PCR) technique on total RNA extracted from mouse livers collected at seven different developmental stages. All differentially expressed cDNAs detected by FDD–PCR were reamplified, subcloned and sequenced, and six genes were confirmed to show age-dependent expression by quantitative real-time PCR analysis. Nucleotide sequence analyses showed that four of them had high homology with known genes (mitochondrial DNA, cytosolic aldehyde dehydrogenase, cell division cycle 2-like 5 and complement component 8 alpha polypeptide), and two with expressed sequence tags of unknown genes. The FDD–PCR technique was effective for detecting novel age-dependently expressed genes, and also for newly characterizing individual expression patterns of known genes. The age-dependent expression patterns of known genes revealed in this study may provide an opportunity to investigate the unknown physiological roles of the proteins they encode.     

Isolation of 10 differentially expressed cDNAs in differentiated Neuro2a cells induced through controlled expression of the GD3 synthase gene

Recently, we showed that transfection of GD3 synthase cDNA into Neuro2a cells, a mouse neuroblastoma cell line, causes cell differentiation with neurite sprouting. In a search for the genes involved in this ganglioside-induced Neuro2a differentiation, we used a tetracycline-regulated GD3 synthase cDNA expression system combined with differential display PCRs to identify mRNAs that were differentially expressed at four representative time points during the process. We report here the identification of 10 mRNAs that are expressed highly at the Neuro2a differentiated stage. These cDNAs were named GDAP1-GDAP10 for (ganglioside-induced differentiation-associated protein) cDNAs. It is interesting that in retinoic acid-induced neural differentiated mouse embryonic carcinoma P19 cells, GDAP mRNA expression levels were also up-regulated (except that of GDAP3), ranging from three to >10 times compared with nondifferentiated P19 cells. All the GDAP genes (except that of GDAP3) were developmentally regulated. The GDAP1, 2, 6, 8, and 10 mRNAs were expressed highly in the adult mouse brain, whereas all the other GDAP mRNAs were expressed in most tissues. Our results suggested that these GDAP genes might be involved in the signal transduction pathway that is triggered through the expression of a single sialyltransferase gene to induce neurite-like differentiation of Neuro2a cells.     

Isolation of diallyl trisulfide inducible differentially expressed genes in human gastric cancer cells by modified cDNA representational difference analysis

Extensive epidemiologic studies indicated protective effects of consumption of garlic on reducing human gastric cancer (HGC) incidence. Diallyl trisulfide (DATS), a critical organic allyl sulfur component of garlic, was reported to have chemopreventive effects in inhibiting tumor process. We used DATS to treat HGC cell line BGC823 cells, and showed that DATS induces G1/S arrest and apoptosis in BGC823 cells demonstrated by a flow cytometric analysis. To further isolate DATS inducible differentially expressed genes in BGC823 cells, we combined a highly specific subtractive hybridization of cDNA representational difference analysis (cDNA RDA) with a sensitive bidirectional radioactive detection of mRNA differential display (mRNA DD) to develop a subtractive hybridization differential display (SHDD) method. This modified method adopted a first round of bidirectional subtractive hybridization between two sample cDNAs and a second round of bidirectional subtractive hybridization between the two resultant first-round difference products. Bidirectional subtractive hybridizations magnified the differences between the two sample cDNAs and favored isolating mRNA species with very small expression differences. We employed the SHDD method to detect DATS inducible differentially expressed genes in BGC823 cells. A total of 14 cDNA fragments (11 upregulated and 3 downregulated by DATS treatment) were isolated and confirmed by reverse Northern blot analysis. Our data show that SHDD is a powerful technique for identifying differentially expressed mRNA species between two sample cDNAs and provide useful cellular and molecular information for understanding the effects of garlic against human gastric cancer.     

应用基因表达谱芯片研究黄药子对小鼠肝脏的毒性机制(简报)

黄药子为薯蓣科植物黄独(Dioscorea bulbifera L．)的块茎,临床常用于治疗甲状腺肿、抗肿瘤、抗炎、抗病毒等。近年来临床上关于黄药子的毒副作用,尤其是对肝、肾的不良反应屡有报道。当黄药子或其代谢物在肝细胞内累积时会直接干扰肝细     

In silico cloning of evolutionarily conserved mouse F-LANa]

Differentially expressed genes between normal liver and hepatocellular carcinomas were investigated using differential display. In previous study, human F-LANa was identified as a differentially expressed gene, up-regulated in hepatocellular carcinoma. In this study, we developed an in silico cloning approach to rapidly and accurately characterize the mouse ortholog of the human F-LANa. Mouse F-LANa encodes a 239 aa protein exhibiting 97.9% similarity to the human ortholog gene. Homology analysis was carried out in various species and showed that F-LANa was evolutionarily conserved from yeast to human. Based on the alignment results, phylogenetic tree was established here.     

进化上保守的小鼠FLANa基因的计算机克隆

EST(expressed sequence tag,表达序列标签)是对cDNA克隆进行测序时得到的序列,一般位于该克隆的一端,序列为单次测序所得到的。现在EST已成为一个非常大的数据库,并被广泛运用于基因家族新成员的寻找,也可作为人染色体上的标志来寻找多态性位点,还可以用来比较某基因在不同组织和病理状态中的表达模式。在EST数据库中,     

Cataloging altered gene expression in young and senescent cells using enhanced differential display.

Recently, a novel PCR-based technique, differential display (DD), has facilitated the study of differentially expressed genes at the mRNA level. We report here an improved version of DD, which we call Enhanced Differential Display (EDD). We have modified the technique to enhance reproducibility and to facilitate sequencing and cloning. Using EDD, we have generated and verified a catalog of genes that are differentially expressed between young and senescent human diploid fibroblasts (HDF). From 168 genetags that were identified initially, 84 could be sequenced directly from PCR amplified bands. These sequences represent 27 known genes and 37 novel genes. By Northern blot analysis we have confirmed the differential expression of a total of 23 genes (12 known, 11 novel), while 19 (seven known, 12 novel) did not show differential expression. Several of the known genes were previously observed by others to be differentially expressed between young and senescent fibroblasts, thereby validating the technique.     

Male specific genes from dioecious white campion identified by fluorescent differential display

Fluorescent differential display (FDD) has been used to screen for cDNAs that are differentially up-regulated in male flowers of the dioecious plant Silene latifolia in which an X/Y chromosome system of sex determination operates. To adapt FDD to the cloning of large numbers of differential cDNAs, a novel method of confirming the differential expression of these has been devised. FDD gels were Southern electro-blotted and probed with mixtures of individual cDNA clones derived from different FDD product ligation reactions. These Southern blots were then stripped and re-probed with further mixtures of individual cloned FDD products to identify the maximum number of recombinant clones carrying the true differential amplification products. Of 135 differential bands identified by FDD, 56 differential amplification products were confirmed; these represent 23 unique differentially expressed genes as determined by virtual Northern analysis and two genes expressed at or below the level of detection by virtual Northern analysis. These two low expressed genes show bands of hybridization on genomic Southern blots that are specific to male plants, indicating that they are derived from, or closely related to, Y chromosome genes.     

Estrogen-dependent and cell-specific regulation of gene expression in RUCA-I endometrial adenocarcinoma cells

Estrogens are believed to play a crucial role in growth regulation and differentiation of the normal endometrial tissue as well as in the carcinogenesis of the endometrium. Therefore, the influence of estrogens and antiestrogens on gene expression in the estrogen receptor-positive rat endometrial adenocarcinoma cell line RUCA-I was investigated. Differentially expressed genes were detected by differential display PCR of RNA of untreated, estradiol-treated and antiestrogen-treated RUCA-I cells. By means of the PCR technique, 14 differentially expressed fragments could be detected. Three of these 14 differentially expressed fragments were confirmed by Northern blotting. The steady state mRNA levels of the three gene fragments named AH41, AH42 and AH44 were downregulated by the antiestrogen ICI 164384. Further characterization revealed that the fragment AH41 is not expressed in stromal cells but in the human and rodent epithelial cell lines, BG-1 and RUCA-II. A comparison of the cDNA sequence of fragment AH41 with the EMBL database showed no high homology to known genes. Therefore, fragment AH41 has to be regarded as a fragment of a novel, estradiol-sensitive gene.     

Differential mRNA display analysis of two related but functionally distinct rat insulinoma (RIN) cell lines: identification of CD24 and its expression in the developing pancreas

To identify genes that might play a role in growth and differentiation of pancreatic beta-cells, we have applied the technique of differential mRNA display to the lineage-related, but functionally distinct rat insulinoma (RIN) cell lines RIN-5AH and RIN-A12. Direct comparison of PCR-generated RIN-5AH and RIN-A12 cDNAs on DNA sequencing gels revealed 31 differentially expressed bands. By Northern blot hybridization, authentic differential expression was confirmed for three cDNAs derived from RIN-5AH cells and four cDNAs from RIN-A12 cells. Nucleotide sequences were determined for these cDNAs and database searches identified one known gene that encoded heat stable antigen CD24. Of the remaining six genes, three matched with established sequence tags from fetal tissue, and three were potentially novel. By RT-PCR analysis, five of the seven genes were expressed in normal fetal and/or adult pancreas. In a detailed survey of CD24 protein expression in the pancreas using the CD24-specific monoclonal antibody J11d, CD24 was predominantly expressed in ductal epithelial cells (E13.5-15.5), developing endocrine (alpha, beta and delta) and exocrine cells (E15.5-20.5) and mature exocrine and peripheral islet delta-cells post E20.5. The retention of CD24 expression in a large proportion of delta-cells but only in a minority of alpha- and beta-cells leads us to hypothesize that CD24 may mark a pool of precursor endocrine cells within adult islets.     

PS-2基因的克隆及其在肝癌中的表达

利用荧光差异显示技术比较了正常肝、肝硬化和肝癌组织 m RNA的表达 ,1 4个有差异的条带通过 Northern blot分析表明其中 9个为阳性 .令人感兴趣的是一个～ 5 0 0 bp的 c DNA片段 ,它在正常肝和肝硬化中低表达 ,在肝癌组织中高表达 .通过测序 ,发现该片段与 PS- 2 ( presenilin- 2 )基因有 94 %的同源性 .PS- 2基因的突变与早发性阿尔茨海默氏症有关 ,但在肝癌发生中的作用未明 .也许 PS- 2基因的上调涉及到肝癌发生的分子机理