Differential Display Method Research Articles

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.

Expression and regulation of the transcriptional repressor ZNF43 in Ewing sarcoma cells.

In vitro, cells derived from Ewing sarcoma (ES) with the characteristic somatic rearrangement between the genes EWS and FLII can be induced to differentiate toward a neuronal phenotype by exposure to agents such as dibutyryl cyclic AMP (db cAMP) or retinoic acid. Therefore, expression of the chimeric Ews-Flil protein does not irreversibly block the capacity of Ewing cells to engage in the neuronal differentiation program initiated by these agents. To identify genes that might be involved in the maintenance of Ewing cells in their undifferentiated state, a PCR-based differential display method was used to compare gene expression patterns in Ewing cell lines with those induced to differentiate toward a neuronal phenotype. A cDNA was expressed at high levels in proliferating Ewing-derived EW-1 cells and downregulated in EW-1 cells induced to differentiate, which corresponds to ZNF43, a multi-zinc finger protein containing the Krüppel-associated box (KRAB) transcriptional repression domain. Treatment of EW-1 cells with antisense oligonucleotides complementary to ZNF43 mRNA induces morphological differentiation and growth arrest. These findings suggest a role for ZNF43 in the maintenance of ES cells in an undifferentiated state, and that ZNF43 could be a primary target for differentiation stimuli in Ewing cells.

Human Secreted Frizzled-Related Protein Is Down-regulated and Induces Apoptosis in Human Cervical Cancer

To identify genes involved in cervical carcinogenesis, the mRNA differential display method was used. A 220-bp cDNA fragment called CA11 was present in normal cervical tissue but not in primary cervical cancer tissue or cervical cancer cell lines. CA11 exhibited 98% homology with the recorded human secreted frizzled-related protein (hsFRP) sequence. A dominant hsFRP mRNA transcript of approximately 4.6 kb was present in three normal cervical tissues examined. Expression of the transcript was nearly absent from three cervical cancer tissues and from five human cervical cancer-derived cell lines. Results from in situ hybridization showed that the hsFRP transcript was confined to the normal cervical epithelial layer. When hsFRP-transfected HeLa and CUMC-6 cervical cancer cells were cultured in serum-free medium, most of the cells died within 8 days. This effect is associated with the apoptotic process. The caspase-3 inhibitor 1, Ac-DEVD-CHO, blocked hsFRP-induced apoptotic cell death. Additionally, cleavage of poly (ADP-ribose) polymerase in hsFRP-transfected cells was confirmed by colorimetric assay. These results indicate that the hsFRP gene probably functions as a tumor suppressor in normal cervical epithelium and down-regulation of hsFRP contributes to development of cervical cancer.

The polyketide synthase gene pks4 from Gibberella fujikuroi encodes a key enzyme in the biosynthesis of the red pigment bikaverin

The ascomycete Gibberella fujikuroi mating population C (MP-C) is well known for the production of gibberellins, but also produces many other secondary metabolites, including the red polyketide pigment bikaverin. Here, we used a differential display method to clone a polyketide synthase gene pks4 responsible for the first step of bikaverin biosynthesis. Sequence analysis indicated that pks4 encoded a 2009-amino acid polypeptide consisting of four functional domains: β-ketoacyl synthase (KS), acyltransferase (AT), acyl carrier (ACP), and thioesterase (TE). Disruption of pks4 resulted in the loss of both pks4 transcripts and bikaverin biosynthesis in G. fujikuroi cultures. Expression of pks4 is strongly repressed by high amounts of ammonium and basic pH. Unexpectedly, pks4 was overexpressed in mutants of the regulatory gene, areA, which is responsible for the activation of nitrogen assimilation genes. Three additional polyketide synthase genes have been cloned from G. fujikuroi MP-C by heterologous hybridization. The presence of these four PKS genes demonstrates the diversity of polyketide biosynthetic pathways in this fungus.

Decreased sulfotransferase SULT1C2 gene expression in DPT-induced polycystic kidney

The pathogenesis of polycystic kidney disease (PKD) remains unclear despite the identification of the genes responsible for hereditary PKD. In this study, we investigated the alteration of gene expressions in an acquired PKD model induced by 2-amino-4,5-diphenylthiazole (DPT) using the differential display method. Kidney mRNA from a Sprague-Dawley rat fed with 1% DPT for 4 days and from a control rat was compared by the RT-PCR differential display method. Differentially expressed bands were re-amplified and subcloned. Using these subclones as probes, the changes in gene expressions were confirmed by Northern blot analysis. Subsequently, mouse kidney cDNA library was screened. The isolated 1.5-kb cDNA contained an open reading frame encoding 296 amino acids, which shared 94.3% identity with rat SULT1C2 sulfotransferase, and was considered to be its mouse ortholog (GenBank Accession No. AY005469). Mouse SULT1C2 mRNA was abundant in the kidney and stomach among normal mouse tissues. The expression of SULT1C2 mRNA was decreased in the rat kidney after DPT feeding but not in the stomach. Mouse SULT1C2 was expressed successfully using pET plasmid vector and E. coli. The recombinant 34-kD protein was capable of catalyzing the sulfation of p-nitrophenol at a Km of 3.1 mmol/L, by utilizing 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as the sulfate donor. Although the physiological substrate and function of SULT1C2 have yet to be elucidated, its down-regulation could be involved in the cystic changes of tubules by decreasing the sulfation of the tubular basement membrane components.

Modified Differential Display Method with Double-Stranded cDNA, a More Efficient Approach

Modified Differential Display Method with Double-Stranded cDNA, a More Efficient Approach

Modified Differential Display Method with Double-Stranded cDNA, a More Efficient Approach

Modified Differential Display Method with Double-Stranded cDNA, a More Efficient Approach

Dietary protein modifies hepatic gene expression associated with oxidative stress responsiveness in growing pigs.

Understanding the basis for differences in nutrient requirements and for nutrient effects on health and performance requires an appreciation of the links between nutrition and gene expression. We developed and applied molecular probes to characterize diet-associated postabsorptive hepatic gene expression in growing pigs chronically fed protein-restricted diets based on either casein (CAS) or soy protein isolate (SPI). Eighty-eight expressed sequence tags (ESTs) were identified on the basis of diet-related changes in expression, by using an mRNA differential display method. Expression profiling based on transcription analysis by real-time reverse transcriptase-polymerase chain reaction showed that the SPI diet significantly changed the pattern of gene expression as compared with the CAS diet and allowed identification of coregulated genes. The expression of six genes involved in the metabolism of stress response (glutathione S-transferase, peptide methionine sulfoxide reductase, apolipoprotein A-I, organic anion transport polypeptide 2, calnexin, heat shock transcription factor 1) exhibited significant changes in the transcription level and indicated an increased oxidative stress response in pigs fed the SPI diet. Hierarchical clustering of gene expression data of all 33 ESTs analyzed across 14 pigs fed the two different diets resulted in clustering of genes related to the oxidative stress response with genes related to the regulation of gene expression and neuronal signaling.

Related genes in lung cancer tissues associated with residential high radon exposure

Objective: To investigate the related genes in lung cancer tissues associated with residential high radon exposure. Methods: Differentially expressed gene fragments in lung cancer and normal lung tissues were discovered by differential display and reverse Northern blot hybridization method. The fragments positive in lung cancer and negative in normal lung tissue were determined. Results: Seven differential displayed fragments were sequenced. One of them named NA7 is 95% homologous with AI208667 in EAT of Genbank. Another fragment named NG2 is up to 98% homologous with five fragments. The remained one CA1 may be a new gene fragment. Conclusion: 3 gene fragments were discovered from lung cancer and normal lung tissues of high radon exposure resident.

Progestin upregulates G-protein-coupled receptor 30 in breast cancer cells.

A differential display method was used to study genes the expression of which is altered during growth inhibition induced by medroxyprogesterone acetate (MPA). A transcript of G-protein-coupled receptor 30 (GPR30) was upregulated by MPA in estrogen-treated MCF-7 breast cancer cells. Northern-blot analysis showed a progestin-specific primary target gene, which was enhanced by progesterone and different progestins, but not by dihydrotestosterone or dexamethasone, and which was abrogated by antiprogestin RU486. The dose-dependent and time-dependent increase in GPR30 mRNA expression correlated with MPA-induced growth inhibition in MCF-7 cells. Additionally, GPR30 upregulation by progestin correlated with growth inhibition when a comparison was made between different breast cancer cell lines. The ERK1/ERK2 pathway is capable of inducing progesterone receptor-dependent and ligand-dependent transcription. Thus we sought to establish whether different MAPK pathway inhibitors affect progestin-induced GPR30 mRNA regulation. The regulation of GPR30 was independent of ERK pathway activation, but the p38 pathway inhibitor induced GPR30 expression, which suggested a potential gene regulation pathway. These data demonstrate a new progestin target gene, the expression of which correlates with growth inhibition.

Screening of multidrug-resistance-related genes in gastric cancer SGC7901 cell line with different mRNA differential display methods

Objective The comparison of Staining silver mRNA differential display with autoradiography mRNA differential display method was performed during Isolating and cloning the multidrug\|resistance\|related genes in gastric cancer SGC7901 cell line. Methods To establish drug\|resistance human gastric cancer SGC7901/VCR cell induced by vincristine. Different drug\|resistance related genes in SGC7901/VCR were screened with staining silver and autoradiography mRNA differential display method. Results The mRNA differential display method with silver staining was short time, lower cost, and convenience for acting. Autoradiography mRNA differential display method, which can get more differential low\|abundance DNA bands, was superior to silver staining method. There was no difference during re\|amplifying of differential DNA bands, cloning, sequencing, hybridization for identification and false positive rate using them. Conclusion The silver staining mRNA differential display method was better for rapid screening of high\|abundance differential expressed genes; the later was benefited for visualizing more differential expressed genes between SGC7901 cell and SGC7901/VCR cell.

S100P expression in human esophageal epithelial cells: Human esophageal epithelial cells sequentially produce different S100 proteins in the process of differentiation

Extracellular calcium ions (Ca2+) are important in regulating the differentiation of keratinocytes and squamous epithelial cells. To clarify the mechanisms involved in the differentiation of human esophageal epithelial cells (EECs), we used the primary culture of human EECs, which can be differentiated by increasing the concentration of extracellular Ca2+, and tried to reveal the extracellular Ca2+ inducible genes using a differential display (DD) method. We found that the calcium-binding protein S100P showed a Ca2+-inducible expression in the EECs. Our immunohistochemical study demonstrated that differentiated large EECs expressing S100P overlie immature proliferating cells which lack S100P immunoreactivity. S100P was detected in vivo in the suprabasal layers of the epithelium. These findings indicate that S100P expression is closely associated with differentiation of human EECs. We also investigated the expression of other S100 proteins, including S100A2, S100A6, and CAAF1 (S100A12), in human EECs. Most of the immature EECs were positive for S100A2 and S100A6, whereas the S100A12-producing cells were similar to the S100P-producing cells. In vivo, S100A12 was strongly detected on all epithelial cells except for basal and proliferating cells. S100A2 was detected on all of the epithelial cells. S100A6 was preferentially seen in the cells of basal layers. These findings suggest that within EECs S100 proteins might play important roles in cell differentiation during specific stages. Among them, S100P expression is unique in that this protein is transiently expressed during the early stage of differentiation. Anat Rec 267:60–69, 2002. © 2002 Wiley-Liss, Inc.

Isolation of Blast Fungal Cerebroside Elicitor-responsive Genes in Rice Plants

To study molecular interactions that occur between the rice plant and the rice blast fungus upon infection, we isolated five elicitor-responsive genes from rice (Orysa sativa cv. Akitakomachi) treated with cerebroside elicitor derived from the blast fungus (Magnaporthe grisea) by the mRNA differential display method. Homology searches with isolated cDNA clones revealed that one cDNA shared strong similarities with the mammalian selenium-binding protein (SBP) (1). Three others had homologies with Arabidopsis thaliana putative β-1,3-glucanase (2), rice glucose-6-phosphate/ phosphate translocator (3) and A. thaliana kinase-like protein (4), respectively. The last one was not homologous to any known genes (5). Transcripts of the three genes (1, 3, 5) were induced by the rice blast fungus; two of the genes (1, 5) were quickly elevated in response to infection with an avirulent race of the fungus. On the other hand, a transcript of the other gene (3) was quickly elevated in response to the infection with a virulent race. These unique elicitor-responsive genes in rice may provide new understanding of host defense mechanisms against the blast fungus.

S100P expression in human esophageal epithelial cells: Human esophageal epithelial cells sequentially produce different S100 proteins in the process of differentiation.

Extracellular calcium ions (Ca(2+)) are important in regulating the differentiation of keratinocytes and squamous epithelial cells. To clarify the mechanisms involved in the differentiation of human esophageal epithelial cells (EECs), we used the primary culture of human EECs, which can be differentiated by increasing the concentration of extracellular Ca(2+), and tried to reveal the extracellular Ca(2+) inducible genes using a differential display (DD) method. We found that the calcium-binding protein S100P showed a Ca(2+)-inducible expression in the EECs. Our immunohistochemical study demonstrated that differentiated large EECs expressing S100P overlie immature proliferating cells which lack S100P immunoreactivity. S100P was detected in vivo in the suprabasal layers of the epithelium. These findings indicate that S100P expression is closely associated with differentiation of human EECs. We also investigated the expression of other S100 proteins, including S100A2, S100A6, and CAAF1 (S100A12), in human EECs. Most of the immature EECs were positive for S100A2 and S100A6, whereas the S100A12-producing cells were similar to the S100P-producing cells. In vivo, S100A12 was strongly detected on all epithelial cells except for basal and proliferating cells. S100A2 was detected on all of the epithelial cells. S100A6 was preferentially seen in the cells of basal layers. These findings suggest that within EECs S100 proteins might play important roles in cell differentiation during specific stages. Among them, S100P expression is unique in that this protein is transiently expressed during the early stage of differentiation.

Identification of the interferon regulatory factor 5 gene (IRF-5) as a direct target for p53

Interferon regulatory factors (IRFs) regulate transcription of interferon genes through DNA sequence-specific binding to these targets. Using a differential display method for examining gene expression in p53-defective cells infected with adenovirus containing wild-type p53, we found that expression of interferon regulatory factor 5 (IRF-5) mRNA was increased in the presence of exogenous p53. An electrophoretic mobility-shift assay showed that a potential p53 binding site (p53BS) detected in exon 2 of the IRF-5 gene could in fact bind to p53 protein. Moreover, a heterologous reporter assay revealed that the p53BS possessed p53-dependent transcriptional activity. Expression of IRF-5 was induced in p53+/+ cells (MCF7 and NHDF), but not inp53-/- cells (H1299) when DNA was damaged by gamma-irradiation, UV-radiation, or adriamycin treatment in a wild-type p53-dependent manner. These results suggest that IRF-5 is a novel p53-target, and that it might mediate the p53-dependent immune response.

Characterization of a prolactin-regulated gene in reproductive tissues using the prolactin receptor knockout mouse model.

Prolactin (PRL) exerts pleiotropic physiological effects in various cells and tissues, although it is mainly considered as a regulator of reproduction and cell growth. Null mutation of the prolactin receptor (PRLR) gene leads to female sterility due to a failure of embryo implantation. Using this mouse model and the method of mRNA differential display, we identified PRL target genes that are regulated during the peri-implantation period. We characterized 1 among the 45 isolated genes, UA-3, which is regulated in the uterus as well as in the ovary during early pregnancy. This gene corresponds to a P311 mouse cDNA that was originally identified for its high expression in late-stage embryonic brain and adult cerebellum. We report here that UA-3 is present in numerous tissues as well as in ovary and uterus at the site of blastocyst apposition, and that its expression is hormonally regulated. Moreover, in situ hybridization reveals high expression in ovarian granulosa cells and in uterine epithelium. Recently, it has been suggested that P311 expression is tightly regulated at several levels by mechanisms that control cellular growth, transformation, motility, or a combination of these. Taken together, these results suggest that P311 could be involved in these processes during pregnancy, although its function remains to be clearly established.

Differential display of protein tyrosine kinase cDNAs from human fetal and adult brains.

Here we describe a differential display method for surveying the expression of most protein tyrosine kinases and applying it to cDNAs from human fetal and adult brains. The method involves two selective steps for processing the mRNA. At each step, degenerate oligonucleotide primers derived from highly conserved regions of the catalytic domain of the kinases are used. In the display with BstYI and BsiHKI digests of the cDNA, 65% and 59% of a total of 72 and 63 bands, respectively, represented fragments from a total of 27 different tyrosine kinases. The expression levels of the kinases in the display were comparable with those measured by RT-PCR. This method offers a relatively specific way to display differentially expressed gene families in any tissue and cell type.

Yellow lupine gene encoding stearoyl-ACP desaturase--organization, expression and potential application.

A gene for the delta9 desaturase specific to stearoyl-ACP (acyl carrier protein) was identified from yellow lupine (Lupinus luteus) cDNA and genomic libraries through the differential display method. The desaturase transcript appears in plants infected with Bradyrhizobium sp. (Lupinus) as revealed by Northern hybridization, RT-PCR and expression of beta-glucuronidase under the desaturase promoter. A small amount of desaturase transcript was also detected in uninfected plants, which suggests that the gene does not belong to the strict nodule-specific sequences. The desaturase provides unsaturated fatty acids for additional cell membrane synthesis. During nodule and symbiosome development a peribacteroid membrane is formed and the requirement for membrane surface increases, thus the level of desaturase expression is also higher. Transgenic plants of Nicotiana tabacum with overexpression of the full-length lupine stearoyl-ACP desaturase sequence were obtained. They revealed higher content of unsaturated fatty acids (especially oleic acid) in comparison with control plants.

Genes responding to vernalization in hexaploid wheat.

Genotype-specific gene expression in response to vernalization in common wheat was examined by the differential display method. Two near-isogenic lines of Vrn-A1 ( Vrn-A1 for the spring type and vrn-A1 for the winter type) were treated by vernalization of developing embryos in detached-ear cultures. This treatment was effective to promote vrn-A1 genotypes to head at a time equivalent to that of Vrn-A1. Differential cDNA fragments were isolated by the RT-PCR method from embryos subjected to vernalization treatments for 2- and 4-weeks at DAP10 and DAP20 stages, respectively. Among 110 differential cDNA fragments isolated, 48 were examined for their chromosomal locations and designated as wec ( wheat- embryo cold treatment) genes. Seven wec genes showed genotype-specific expression in response to vernalization. The statistical analysis utilizing two recombinant inbred lines showed that four wec genes were significantly associated with heading factors.

Thymosin-β4 Regulates Motility and Metastasis of Malignant Mouse Fibrosarcoma Cells

We identified a thymosin-beta4 gene overexpression in malignant mouse fibrosarcoma cells (QRsP-30) that were derived from clonal weakly tumorigenic and nonmetastatic QR-32 cells by using a differential display method. Thymosin-beta4 is known as a 4.9-kd polypeptide that interacts with G-actin and functions as a major actin-sequestering protein in cells. All of the six malignant fibrosarcoma cell lines that have been independently converted from QR-32 cells expressed high levels of thymosin-beta4 mRNA and its expression in tumor cells was correlated with tumorigenicity and metastatic potential. Up-regulation of thymosin-beta4 in QR-32 cells (32-S) transfected with sense thymosin-beta4 cDNA converted the cells to develop tumors and formed numerous lung metastases in syngeneic C57BL/6 mice. In contrast, antisense thymosin-beta4 cDNA-transfected QRsP-30 (30-AS) cells reduced thymosin-beta4 expression, and significantly lost tumor formation and metastases to distant organs. Vector-alone transfected cells (32-V or 30-V cells) behaved like their parental cells. We observed that tumor cell motility, cell shape, and F-actin organization is regulated in proportion to the level of thymosin-beta4 expression. These findings indicate that thymosin-beta4 molecule regulates fibrosarcoma cell tumorigenicity and metastasis through actin-based cytoskeletal organization.