Identification and characterization of differentially expressed genes in the early response phase during liver regeneration

The role of Tec kinase signaling pathways in the development of Mallory Denk Bodies in balloon cells in alcoholic hepatitis

Several research strategies have been used to study the pathogenesis of alcoholic hepatitis (AH). These strategies have shown that various signaling pathways are the target of alcohol in liver cells. However, few have provided specific mechanisms associated with Mallory-Denk Bodies (MDBs) formed in Balloon cells in AH. The formation of MDBs in these hepatocytes is an indication that the mechanisms of protein quality control have failed. The MDB is the result of aggregation and accumulation of proteins in the cytoplasm of balloon degenerated liver cells. To understand the mechanisms that failed to degrade and remove proteins in the hepatocyte from patients suffering from alcoholic hepatitis, we investigated the pathways that showed significant up regulation in the AH liver biopsies compared to normal control livers (Liu et al., 2015). Analysis of genomic profiles of AH liver biopsies and control livers by RNA-seq revealed different pathways that were up regulated significantly. In this study, the focus was on Tec kinase signaling pathways and the genes that significantly interrupt this pathway. Quantitative PCR and immunofluorescence staining results, indicated that several genes and proteins are significantly over expressed in the livers of AH patients that affect the Tec kinase signaling to PI3K which leads to activation of Akt and its downstream effectors.

Aberrant expression of the p53-inducible antiproliferative gene BTG2 in hepatocellular carcinoma is associated with overexpression of the cell cycle-related proteins

We previously reported that the abnormal BTG2 expression was related to genesis/development of hepatocellular carcinoma (HCC). The aim of this study was to evaluate the BTG2 expression in HCC compared with p53, cyclin D1, and cyclin E. For this purpose, modified diethylnitrosamine (DEN)-induced primary HCC rat model was established. Target proteins and mRNAs were measured by western blot and RT-PCR/northern blot, respectively. In rat liver, expression of BTG2 and other proteins was determined by western blot, and BTG2 mRNA in HCC/normal tissues was detected by high-flux tissue microarray (TMA) and in situ hybridization (ISH). BTG2 mRNA/protein expression was increased in fetal liver, 7701, and LO2 cell lines but decreased in HepG2 cells. BTG2/p53 were expressed early after DEN treatment, peaked at 5 weeks and decreased gradually thereafter. Cyclin-D1/Cyclin-E expression increased significantly with the tumor progression. BTG2 mRNA was expressed in 71.19% HCC by ISH and correlated with differentiation. Expression of p53/cyclin D1/cyclin E was positive in 82.35/94.12/76.47% BTG2 mRNA-negative tissues, respectively. BTG2 protein expression was lost in 32.2% (19/59) HCC tissues, and the mRNA/protein expression correlated significantly with the increasing tumor grade (P < 0.05). In conclusion, BTG2 expression is commonly impaired in HCC which may be a factor involved in deregulation of cyclin-D1/cyclin-E expression during hepatocarcinogenesis.

TEC protein tyrosine kinase is involved in the Erk signaling pathway induced by HGF

BACKGROUND/AIMS

TEC, a member of the TEC family of non-receptor type protein tyrosine kinases, has recently been suggested to play a role in hepatocyte proliferation and liver regeneration. This study aims to investigate the putative mechanisms of TEC kinase regulation of hepatocyte differentiation, i.e. to explore which signaling pathway TEC is involved in, and how TEC is activated in hepatocyte after hepatectomy and hepatocyte growth factor (HGF) stimulation.

METHODS

We performed immunoprecipitation (IP) and immunoblotting (IB) to examine TEC tyrosine phosphorylation after partial hepatectomy in mice and HGF stimulation in WB F-344 hepatic cells. The TEC kinase activity was determined by in vitro kinase assay. Reporter gene assay, antisense oligonucleotide and TEC dominant negative mutant (TEC(KM)) were used to examine the possible signaling pathways in which TEC is involved. The cell proliferation rate was evaluated by (3)H-TdR incorporation.

RESULTS

TEC phosphorylation and kinase activity were increased in 1 h after hepatectomy or HGF treatment. TEC enhanced the activity of Elk and serum response element (SRE). Inhibition of MEK1 suppressed TEC phosphorylation. Blocking TEC activity dramatically decreased the activation of Erk. Reduced TEC kinase activity also suppressed the proliferation of WB F-344 cells. These results suggest TEC is involved in the Ras-MAPK pathway and acts between MEK1 and Erk.

CONCLUSIONS

TEC promotes hepatocyte proliferation and regeneration and is involved in HGF-induced Erk signaling pathway.

Omic analyses unravels global molecular changes in the brain and liver of a rat model for chronic Sake (Japanese alcoholic beverage) intake

The effects of chronic administration of Sake (Japanese alcoholic beverage, Nihonshu) on brain and liver of female F334 (Fisher) rats were surveyed via global omic analyses using DNA microarray, 2-DE, and proton nuclear magnetic resonance. Rats weaned at 4 wk of age were given free access to Sake (15% alcohol), instead of water. At 13 months of age, and 24 h after withdrawal of Sake supply, rats were sacrificed, and the whole brain and liver tissues dissected for analyses. In general, molecular changes in brain were found to be less than those in liver. Transcriptomics data revealed 36 and 9, and 80 and 62 up- and down-regulated genes, in the brain and liver, respectively, with binding and catalytic activity gene categories the most prominently changed. Results suggested Sake-induced fragility of brain and liver toxicity/damage, though no significant abnormalities in growth were seen. At protein level, a striking decrease was found in the expression of NADH dehydrogenase (ubiquinone) Fe-S protein 1 in brain, suggesting attenuation of mitochondrial metabolism. In liver, results again suggested an attenuation of mitochondrial function and, in addition, glycoproteins with unknown function were induced at protein and gene levels, suggesting possible changes in glycoprotein binding in that organ. Metabolomic analysis of brain revealed significant increases in valine, arginine/ornithine, alanine, glutamine, and choline with decreases in isoleucine, N-acetyl aspartate, taurine, glutamate, and gamma aminobutyric acid. Our results provide a detailed inventory of molecular components of both brain and liver after Sake intake, and may help to better understand effects of chronic Sake drinking.

Identification of differentially expressed genes during proliferative response of the liver induced by follistatin

The liver mass is controlled strictly and maintained constant in normal and pathological situations. An exception is observed after an administration of follistatin, which induces proliferation in intact liver. In the present study, we identified genes differentially expressed in proliferating liver caused by overexpression of follistatin-288. Adenovirus vector encoding follistatin-288 (Ad-FS) or green fluorescent protein was injected intraperitoneally in rats. Changes in the liver weight, expression of follistatin and nuclear bromodeoxyuridine labeling were measured. Samples taken on day 5 and day 7 were used to prepare RNA for microarray analysis. The expression of the genes was confirmed by quantitative reverse transcriptase PCR. After the injection of Ad-FS follistatin mRNA peaked on day 3, which was followed by progressive increase in the protein expression. A peak in bromodeoxyuridine labeling was observed on day 7. Microarray data from day 5 and day 7 samples showed that follistatin modified the expression of 907 genes, of which 575 were overexpressed and 332 were downregulated taking into consideration a two fold change reference compared to control rats. In particular, significant increases and time related changes in gene expression after the Ad-FS injection were found in nine genes including growth differentiation factor 15 and fibroblast growth factor 21. This study confirmed that follistatin induced proliferation in intact liver, and identified candidate genes involved in follistatin-induced liver cell growth.

Involvement of Egr-1 in HGF-induced elevation of the human 5alpha-R1 gene in human hepatocellular carcinoma cells

Steroid 5alpha-reductase 1 (5alpha-R1), a key enzyme in the conversion of steroids into their respective 5alpha-reduced derivatives, plays a key role in some hormone-dependent tumours and is abundant in the liver, although it is also widely distributed throughout the body. HGF (hepatocyte growth factor) is a pleiotropic cytokine/growth factor involved in the progression of hepatocellular carcinoma. In the present paper, we report the stimulatory effect of HGF on human 5alpha-R1 transcription in hepatocellular carcinoma cells. Pre-treatment with actinomycin D or cycloheximide blocked the up-regulation of 5alpha-R1 mRNA expression by HGF, indicating that the increased level of 5alpha-R1 mRNA expression is regulated by transcriptional activation and was dependent on de novo protein synthesis. Functional analysis of the 5'-flanking region of the 5alpha-R1 gene by transfection analysis showed that the -79 to -50 region functioned as the HGF-responsive region. Mutagenesis and electrophoretic mobility-shift assays demonstrated that induction of 5a-R1 by HGF is mediated by an Egr-1 (early growth-response gene 1)-binding site at -60/-54. In addition, overexpression of Egr-1 was sufficient to transactivate 5alpha-R1 promoter activity, and knockdown of Egr-1 with gene-specific small interfering RNA resulted in inhibition of HGF-induced up-regulation of endogenous 5alpha-R1 expression. These data provide the first evidence that HGF stimulates 5alpha-R1 expression through up-regulation of the transcription factor Egr-1, thus suggesting the possibility that regulation of steroid metabolism by HGF represents a mechanism for high risk of hepatocellular carcinogenesis in males.

Analysis on the protein structure and function of retinoic acid induced 16

AIM: To analyze the protein structure and function of Homo sapiens retinoic acid induced 16 (RAI16) cDNA nucleotides sequence.

METHODS: Using some related computer software and database, RAI16 cDNA sequence and the deduced amino acid (AA) sequence were analyzed and compared with those of other species, and the secondary structure and hydrophobicity of the protein were determined and predicted.

RESULTS: RAI16 cDNA sequence consisted of 2863 nucleotides encoding a 759-AA protein. RAI16 protein included a 31-AA signal peptide. The protein had no transmembrane domain, and its subcellular localization was in endoplasmic reticulum. The secondary structure contained several kinds of conformations. RAI16 protein appeared as a compact and globular domain, and was a secretory and hydrophilicity protein (grand average of hydropathicity: -0.136). The protein was also unstable (the unstable coefficient: 53.11), with many phosphorylation and proteinase sites.

CONCLUSION: As a new signal protein, RAI16 may be involved in the signal transduction and transcription of hepatoma cell differentiation by interacting with Tec protein.

Proteomic analysis of the transition from quiescent to proliferating stages in rat liver hepatectomy model

The 70% (or 2/3) partial hepatectomy (PHx) rat liver model provides an effective medium for study of the transition and regulation of hepatocytes from quiescent to proliferating phase. Although the gene expression pattern has come under intense scrutiny, a differential proteomic study could help to reveal the mechanism of how the process is initiated and regulated. The proteomic changes were analyzed in two groups, 7 h after 70% PHx test group and sham-operation control group, by two-dimensional gel electrophoresis with 907 +/- 33 and 910 +/- 64 spots on gels, respectively. Twelve down-regulated spots and twenty-six up-regulated spots were recognized using ImageMaster software and were identified by matrix-assisted laser desorption/ionization-mass spectrometry-quadrupole time of flight mass spectrometry and/or tandem mass spectrometry reconfirmation. Some of the differential proteins were associated with stress defense, lipid metabolism, and macromolecular biosynthesis while the others were shown to be involved in regulating transcript factors associated with liver regeneration. A "proteomic model" for liver regeneration was suggested based on our data and related scientific literature to interpret the differential proteome pattern that reflected the transition of cells from quiescent to proliferating state, including but not limited to the rat liver after 70% PHx.

Tissue distribution and signal transduction of Tec tyrosine kinase in rats

AIM: To detect the tissue distribution of Tec tyrosine kinase in rats, and to investigate the possible signal transduction pathways in which Tec is involved.

METHODS: The total RNA was extracted from the tissues of rat heart, liver, spleen, lung, brain, thymus gland and muscle. Northern blot was used to detect the expression of Tec RNA. Reporting gene plasmids and Tec expression vector were co-transfected into WBF-344 cells, and post-transfection cells were stimulated by hepatic growth factor (HGF). Then cells were lysed and the luciferace activity was measured.

RESULTS: Northern blot suggested that Tec tyrosine kinase was highly expressed in the tissues of rat liver and kidney. Report gene assay showed the Elk luciferase activity was increased about 2-3 folds in comparison with that of the controls, while other signaling pathways had no obviously changes.

CONCLUSION: Tec tyrosine kinase is involved in Erk/mitogen-activated protein kinase signal pathway mediated by HGF. Tec probably plays an important role in the proliferation of liver cells.

A liver specific gene that is expressed in growth hormone transgenic mice and in normal female mice as a function of age

Growth hormone (GH) acts on various organs to exert its growth and metabolic effects. GH induces transcription of a number of genes in different organs including liver. By performing subtractive hybridization analysis on liver cDNAs of GH transgenic and non-transgenic mice, differentially expressed cDNAs were obtained. This paper describes the isolation and characterization of a liver cDNA, termed cDNA #5, that contains 1897 bp and is predicted to encode a protein (P5) of 512 aa residues. P5 has five immunoglobulin related domains thus allowing it to be classified as a member of the immunoglobulin super family (IGSF). Also, P5 shows significant similarity to both rat and human alpha-1-B glycoprotein which is an acidic serum protein of unknown function. mRNA #5 was detected in the liver hepatocytes of male and female GH transgenic mice and in the liver of female, but not of male, non-transgenic mice. mRNA #5 was not present in dwarf mice including the Ames dwarf, those that express a GH antagonist and those with the GH receptor and binding protein gene disrupted. These findings suggest that induction of mRNA #5 in the liver requires a continuous pattern of GH secretion and an intact GH-GH receptor-signaling complex. mRNA #5 levels in female non-transgenic mice were observed to vary with age implying that gender-specific age-dependent factor(s) may be involved in the induction of mRNA #5. The appearance of mRNA #5 in post-hepatectomized liver that coincides with the proliferative phase of liver regeneration suggests that it may be involved in hepatocyte proliferation. Together these data suggest that expression of cDNA #5 is liver-specific, sexually dimorphic, age-dependent, and may be involved in hepatocyte hyperplasia and liver enlargement.

Rapid induction and activation of Tec tyrosine kinase in liver regeneration

BACKGROUND

Previous studies have indicated that Tec tyrosine kinase is differentially expressed in the regenerating liver. The purpose of the present study was to further investigate the potential involvement of Tec tyrosine kinase in hepatocyte proliferation and liver regeneration.

METHODS

Tec kinase gene expression after partial (two-thirds) hepatectomy was examined by representational difference analysis. Tissue distribution and potential involvement of Tec kinase in liver regeneration and hepatocyte proliferation were then determined by northern blotting, reverse transcription-polymerase chain reaction (RT-PCR), and western blotting. Full-length rat Tec cDNA was cloned.

RESULTS

Using this cDNA as the probe, northern blotting showed that Tec was specifically expressed in liver and kidney, the highest expression of Tec being detected in embryonic day 15-19 fetal livers. In contrast, the expression level of Tec in adult and neonatal rat livers was significantly decreased. Similar results were obtained from western blotting analyzes. It was thus hypothesized that Tec might be involved in hepatocyte proliferation. To test this hypothesis, Tec expression was examined in regenerating rat livers. An increase in Tec expression and activation of Tec kinase were observed within 1 h after partial hepatectomy. Moreover, it has been shown that hepatocyte growth factor (HGF) dramatically induces Tec expression in primary rat hepatocytes. Additionally, it was observed that Tec gene expression in serum-starved liver tumor cell line HepG2 was substantially decreased. Stimulation with 10% fetal bovine serum and insulin but not epidermal growth factor resulted in dramatic elevation of Tec expression in these cells.

CONCLUSION

Tec is an inducible early response gene that might enhance hepatocyte proliferation and liver regeneration.

Pooling samples within microarray studies: a comparative analysis of rat liver transcription response to prototypical toxicants

Combining or pooling individual samples when carrying out transcript profiling using microarrays is a fairly common means to reduce both the cost and complexity of data analysis. However, pooling does not allow for statistical comparison of changes between samples and can result in a loss of information. Because a rigorous comparison of the identified expression changes from the two approaches has not been reported, we compared the results for hepatic transcript profiles from pooled vs. individual samples. Hepatic transcript profiles from a single-dose time-course rat study in response to the prototypical toxicants clofibrate, diethylhexylphthalate, and valproic acid were evaluated. Approximately 50% more transcript expression changes were observed in the individual (statistical) analysis compared with the pooled analysis. While the majority of these changes were less than twofold in magnitude ( approximately 80%), a substantial number were greater than twofold (approximately 20%). Transcript changes unique to the individual analysis were confirmed by quantitative RT-PCR, while all the changes unique to the pooled analysis did not confirm. The individual analysis identified more hits per biological pathway than the pooled approach. Many of the transcripts identified by the individual analysis were novel findings and may contribute to a better understanding of molecular mechanisms of these compounds. Furthermore, having individual animal data provided the opportunity to correlate changes in transcript expression to phenotypes (i.e., histology) observed in toxicology studies. The two approaches were similar when clustering methods were used despite the large difference in the absolute number of transcripts changed. In summary, pooling reduced resource requirements substantially, but the individual approach enabled statistical analysis that identified more gene expression changes to evaluate mechanisms of toxicity. An individual animal approach becomes more valuable when the overall expression response is subtle and/or when associating expression data to variable phenotypic responses.

Activation of TEC and STAT3 after partial hepatectomy or hepatocytic growth factor stimulation

AIM: To study the activation of TEC and STAT3 in the hepatocyte after partial hepatectomy (PH) or hepatocytic growth factor (HGF) stimulation in the mice.

METHODS: Mice of SPF degree and WB F-344 cell (liver stem cell line) were used in this study. In vivo and in vitro experimental models of PH and HGF stimulation were established respectively. Immunoprecipitation (IP) and immunoblotting (IB) were used to observe the phosphorylation level and time of TEC and STAT3. On the other hand, electrophoretic mobility shift assay (EMSA) was used to detect the binding ability of STAT3 DNA.

RESULTS: TEC and STAT3 were both inducibly phosphorylated in one hour after PH or HGF stimulation. Ten to twenty minutes after PH, levels of TEC and STAT3 reached the peak. About 10 min after HGF stimulation, TEC phosphorylation level reached maximum value and about 30 min STAT3 phosphorylation level reached peak value. Meanwhlie, STAT3 DNA binding activity was enhanced both In vivo and in vitro experiments.

CONCLUSION: After PH or HGF-stimulation, both TEC and STAT3 are quickly phosphorylated in one hour, and they synergically affect the early proliferation of hepatocytes.

Apoptosis signals in lymphoblasts induced by focused ultrasound

We investigated the effects of focused ultrasound (FUS) on specific molecular signaling and cellular response in three closely related human Tk6 lymphoblast cell lines that differed only in their p53 status. The applied ultrasound parameters fell between the physical dose range, which is safely used in medical diagnostics (peak pressure<0.1 MPa) and that used for high-energy FUS thermal ablation therapy (peak pressure>10 MPa). Based on cDNA microarrays and protein analysis, we found that FUS at the intermediate peak pressure of 1.5 MPa induced a complex signaling cascade with upregulation of proapoptotic genes [e.g., p53, p21, Thy1 (CD 90)]. Simultaneously, FUS downregulated cellular survival components (e.g., bcl-2, SOD). The p53 status was important for the reaction of the cells to ultrasound. Apoptosis and G1 arrest were induced primarily in p53+ cells, while p53- cells showed less apoptosis but exhibited G2 arrest. Likewise, the proliferation of lymphoblasts was much more strongly inhibited in p53+ than in p53- cells. Microarray analysis further demonstrated an upregulation of genes involved in oxidative stress (e.g., ferritin), suggesting that indirect sonochemical effects via reactive oxygen species play a causative role in the interaction of ultrasound with lymphoblasts. An important characteristic of FUS in therapeutic ultrasound applications is its ability to be administered to the human body in a targeted manner while sparing intermediate tissues. Therefore, our data indicate that this noninvasive, mechanical wave transmission, which is free of ionizing radiation, has the potential to specifically induce localized cell signals and apoptosis.

Screening and identification of genes transactivated by human augmenter of liver regeneration by microarray assay

AIM: Augmenter of liver regeneration (ALR) is a protein that plays a role in liver regeneration. In order to clarify the effect of the expression of ALR on profile of the hepatocytic gene expression, we analyzed difference between the HepG2 cells transfected with ALR and controls by using gene chip technology.

METHODS: Total RNA was extracted from HepG2 cells,and RT-PCR was performed to amplify the coding region of ALR. The expression of ALR in the transfected HepG2 cells was confirmed by Western blot. Total mRNA was isolated from the transfected HepG2 cells with pcDNA3.1(-) and pcDNA3-ALR, respectively. cDNA was prepared by reverse transcription. Microarray assay was conducted for screening of up-and down-regulated genes in both HepG2 cells.

RESULTS: The expressive vector of pcDNA3(-)-ALR was constructed and confirmed by restriction enzyme digestion and DNA sequencing. The expression of ALR was confirmed by Western blot. After screening with cDNA microarray, we found 2 genes were up-regulated, and 24 genes including TNFRSF1A-associated via death domain, tissue inhibitor of metalloproteinase 1, epididymal androgen-related protein, down-regulated.

CONCLUSION: ALR is a cell growth factor, which has some influences on gene expression profile of hepatocytes; Microarray technology is a method to analyze gene expression spectra of trans-regulation of a protein and conducive to understand the regulative effect of ALR on hepatocytes and other biological function.

Identification of Taxreb107 as a lactogenic hormone responsive gene in mammary epithelial cells

Mammary gland development and differentiation is regulated by a number of growth factors and hormones. Milk protein gene expression represents a hallmark of functional mammary epithelial differentiation and is coordinated by the lactogenic hormone prolactin and glucocorticoids. To date, few 'early-response' genes transcriptionally activated by lactogenic hormones have been described. We have used representational difference analysis (RDA) to search for lactogenic-responsive genes in SCp2 mouse mammary epithelial cells. One of the cDNAs identified encoded the DNA-binding protein Taxreb107, originally identified as a HTLV-I Tax responsive element binding protein. Increased Taxreb107 expression was confirmed following prolactin and dexamethasone-induced differentiation of SCp2 and HC11 mammary epithelial cells. Taxreb107 RNA levels were developmentally regulated in the mouse mammary gland, where levels increased substantially during mid- and late pregnancy and persisted during lactation. Overexpression of an antisense Taxreb107 cDNA construct or antisense oligonucleotide in HC11 mammary epithelial cells attenuated milk protein gene expression following prolactin and dexamethasone treatment. These findings indicate a role for Taxreb107 as a lactogenic hormone-responsive gene during differentiation of the mammary gland.

Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations

Methapyrilene (MP) exposure of animals can result in an array of adverse pathological responses including hepatotoxicity. This study investigates gene expression and histopathological alterations in response to MP treatment in order to 1) utilize computational approaches to classify samples derived from livers of MP treated rats based on severity of toxicity incurred in the corresponding tissue, 2) to phenotypically anchor gene expression pattems, and 3) to gain insight into mechanism(s) of methapyrilene hepatotoxicity. Large-scale differential gene expression levels associated with the exposure of male Sprague-Dawley rats to the rodent hepatic carcinogen MP for 1, 3, or 7 days after daily dosage with 10 or 100 mg/kg/day were monitored. Hierarchical clustering and principal component analysis were successful in classifying samples in agreement with microscopic observations and revealed low-dose effects that were not observed histopathologically. Data from cDNA microarray analysis corroborated observed histopathological alterations such as hepatocellular necrosis, bile duct hyperplasia, microvesicular vacuolization, and portal inflammation observed in the livers of MP exposed rats and provided insight into the role of specific genes in the studied toxicological processes.

Cloning of mouse genomic ribosomal protein L6 gene and analysis of its promoter

Ribosomal protein (Rp) L6 is also defined as Taxreb107 (Tax responsive element binding protein 107) for its binding activity to the long terminal repeats of human T cell leukemia virus (HTLV)-I. We cloned the genomic gene of mouse RpL6/Taxreb107 and analyzed its exon/intron structures. The promoter of RpL6/Taxreb107 contains recognition sites for multiple transcription factors including nuclear factor (NF)-kappa B. Luciferase reporter assay showed that the RpL6/Taxreb107 promoter has a constitutive activity in transfected cells, and the constitutive activity depends on the intact promoter. Expression of HTLV-I viral protein Tax mildly but reproducibly induced RpL6/Taxreb107 mRNA and promoter activity. We provide evidence suggesting that induction of RpL6/Taxreb107 by Tax is at least partially mediated by the NF-kappa B site in the promoter of RpL6/Taxreb107. Taken together, Tax up-regulates RpL6/Taxreb107 and this may provide a feedback mechanism to facilitate proliferation of HTLV-I-infected cells and production of viral particles.

Applying a highly specific and reproducible cDNA RDA method to clone garlic up-regulated genes in human gastric cancer cells

AIM: To develop and optimize cDNA representational difference analysis (cDNA RDA) method and to identify and clone garlic up-regulated genes in human gastric cancer (HGC) cells.

METHODS: We performed cDNA RDA method by using abundant double-stranded cDNA messages provided by two self-constructed cDNA libraries (Allitridi-treated and paternal HGC cell line BGC823 cells cDNA libraries respectively). BamH I and Xho I restriction sites harbored in the library vector were used to select representations. Northern and Slot blots analyses were employed to identify the obtained difference products.

RESULTS: Fragments released from the cDNA library vector after restriction endonuclease digestion acted as good marker indicating the appropriate digestion degree for library DNA. Two novel expressed sequence tags (ESTs) and a recombinant gene were obtained. Slot blots result showed a 8-fold increase of glia-derived nexin/protease nexin 1 (GDN/PN1) gene expression level and 4-fold increase of hepatitis B virus x-interacting protein (XIP) mRNA level in BGC823 cells after Allitridi treatment for 72 h.

CONCLUSION: Elevated levels of GDN/PN1 and XIP mRNAs induced by Allitridi provide valuable molecular evidence for elucidating the garlic's efficacies against neurodegenerative and inflammatory diseases. Isolation of a recombinant gene and two novel ESTs further show cDNA RDA based on cDNA libraries to be a powerful method with high specificity and reproducibility in cloning differentially expressed genes.

Nerve growth factor selectively regulates expression of transcripts encoding ribosomal proteins

BACKGROUND

NGF exerts a variety of actions including promotion of neuronal differentiation and survival. The PC12 rat pheochromocytoma cell line has proved valuable for studying how NGF works and has revealed that the NGF mechanism includes regulation of gene expression. Accordingly, we used SAGE (Serial Analysis of Gene Expression) to compare levels of specific transcripts in PC12 cells before and after long-term NGF exposure. Of the approximately 22,000 transcripts detected and quantified, 4% are NGF-regulated by 6-fold or more. Here, we used database information to identify transcripts in our SAGE libraries that encode ribosomal proteins and have compared the effect of NGF on their relative levels of expression.

RESULTS

Among the transcripts detected in our SAGE analysis, 74 were identified as encoding ribosomal proteins. Ribosomal protein transcripts were among the most abundantly expressed and, for naive and NGF-treated PC12 cells, represented 5.2% and 3.5%, respectively, of total transcripts analyzed. Surprisingly, nearly half of ribosomal protein transcripts underwent statistically significant NGF-promoted alterations in relative abundance, with changes of up to 5-fold. Of the changes, approximately 2/3 represented decreases. A time course revealed that the relative abundance of transcripts encoding RPL9 increases within 1 hr of NGF treatment and is maximally elevated by 8 hr.

CONCLUSIONS

These data establish that NGF selectively changes expression of ribosomal protein transcripts. These findings raise potential roles for regulation of ribosomal protein transcripts in NGF-promoted withdrawal from the cell cycle and neuronal differentiation and indicate that regulation of individual ribosomal protein transcripts is cell- and stimulus-specific.

Isolation and characterization of chicken TaxREB107, a putative DNA binding protein abundantly expressed in muscle

Myogenic regulatory factors (MRFs) are vital transcription factors that act at multiple points during development to establish the skeletal muscle phenotype. This class of muscle-restricted, basic helix-loop-helix (bHLH) proteins acts in concert with additional transcriptional modulators to precisely control muscle gene expression. We have isolated the chicken homologue of Tax responsive element binding protein 107 (TaxREB107). The cDNA is 83% homologous at the amino acid level to human and mouse TaxREB107 and contains a centrally located leucine zipper motif. Northern analysis demonstrated that the gene is expressed in multiple tissues including skeletal muscle. Immunofluorescent staining revealed that the cTaxREB107 protein is located in both the nuclear and cytoplasmic compartments. Distinct localization to the nucleoli supports the evidence that TaxREB107 is a ribosomal protein. Because TaxREB proteins also are implicated in transcriptional regulation, we overexpressed cTaxREB107 in embryonic myoblasts. cTaxREB107 increased troponin I reporter gene activity as well as MRF-directed transcription from a multimerized skeletal muscle E-box reporter gene (4Rtk-luc). However, cotransfection of expression plasmids coding for MyoD and cTaxREB107 did not produce an increase in 4Rtk-luc suggesting that cTaxREB107 enhances myogenic gene transcription through a means independent of a physical association with MyoD. In conclusion, our results define a role for cTaxREB107 during avian myogenesis as a positive modulator of skeletal muscle gene expression.