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PubMed1999

Combining SSH and cDNA microarrays for rapid identification of differentially expressed genes.

Comparing patterns of gene expression in cell lines and tissues has important applications in a variety of biological systems. In this study we have examined whether the emerging technology of cDNA microarrays will allow a high throughput analysis of expression of cDNA clones generated by suppression subtractive hybridization (SSH). A set of cDNA clones including 332 SSH inserts amplified by PCR was arrayed using robotic printing. The cDNA arrays were hybridized with fluorescent labeled probes prepared from RNA from ER-positive (MCF7 and T47D) and ER-negative (MDA-MB-231 and HBL-100) breast cancer cell lines. Ten clones were identified that were over-expressed by at least a factor of five in the ER-positive cell lines. Northern blot analysis confirmed over-expression of these 10 cDNAs. Sequence analysis identified four of these clones as cytokeratin 19, GATA-3, CD24 and glutathione-S-transferase mu-3. Of the remaining six cDNA clones, four clones matched EST sequences from two different genes and two clones were novel sequences. Flow cytometry and immunofluorescence confirmed that CD24 protein was over-expressed in the ER-positive cell lines. We conclude that SSH and microarray technology can be successfully applied to identify differentially expressed genes. This approach allowed the identification of differentially expressed genes without the need to obtain previously cloned cDNAs.

Antigens, CD↗
PubMed2000

Identification and characterization of a novel gene KE04 differentially expressed by activated human dendritic cells.

To better understand the molecular mechanisms of dendritic cells (DC) function, we isolated differentially expressed genes in Ag-activated DC by a PCR-based subtractive hybridization technique. A novel full-length cDNA, KE04, was thus isolated from KLH-activated human PBMC-derived DC. KE04 cDNA encoded a 346-aa protein devoid of functionally indicative motifs. KE04 protein showed 64% identity with a Caenorhabditis elegans protein and 83% identity with a human putative protein. Distant relationship was also found with other prokaryotic and eukaryotic proteins. Differential expression of KE04 in activated DC other than nonactivated DC was confirmed at both mRNA and protein levels. KE04 mRNA expression was detectable in various human tissues and cell lines by Northern blot and RT-PCR. Western blot and confocal microscopy analysis indicated that its cytolocalization was intracellular. Our data suggest the potential involvement of KE04 in DC activation and will facilitate the research of molecular mechanism of DC function.

Amino Acid Sequence↗
PubMed2006

Mixture models for detecting differentially expressed genes in microarrays.

An important and common problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. As this problem concerns the selection of significant genes from a large pool of candidate genes, it needs to be carried out within the framework of multiple hypothesis testing. In this paper, we focus on the use of mixture models to handle the multiplicity issue. With this approach, a measure of the local FDR (false discovery rate) is provided for each gene. An attractive feature of the mixture model approach is that it provides a framework for the estimation of the prior probability that a gene is not differentially expressed, and this probability can subsequently be used in forming a decision rule. The rule can also be formed to take the false negative rate into account. We apply this approach to a well-known publicly available data set on breast cancer, and discuss our findings with reference to other approaches.

Animals↗
PubMed1990

Differential expression of a Mr approximately 90,000 cell surface transferrin receptor-related glycoprotein on murine B16 metastatic melanoma sublines selected for enhanced brain or ovary colonization.

A cell surface Mr approximately 90,000 glycoprotein (gp90) was found in higher amounts on brain-colonizing than on lung-colonizing murine B16 melanoma sublines. The possible role of gp90 in determining the brain-associated metastatic properties of B16 cells was examined by purifying the glycoprotein and studying the effects of anti-gp90 on the growth, adhesion, and organ colonization properties of B16 cells. The specificity of the anti-gp90 was demonstrated in immunoprecipitation studies where a cell surface- or metabolically labeled Mr approximately 90,000 glycoprotein of pI approximately 4 was exclusively found upon two-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing conditions. Immunoprecipitation analysis, enzyme-linked immunosorbent assays, and the lectin-binding properties of gp90 on lectin affinity columns indicated that it is a Mr approximately 180,000 disulfide-linked dimer, probably related to the transferrin receptor. B16 sublines selected for various organ colonization properties differentially expressed gp90, bound 125I-labeled transferrin, and responded differently to purified transferrin in proliferation assays in relation to their metastatic properties (B15b greater than O13 greater than F10 greater than F1). Anti-gp90 immunoglobulin G affected the growth of brain-colonizing B16-B15b more than B16-F1 cells, but had no effect on the adhesion of B16-B15b or -F1 cells to microvessel endothelial cells in vitro, and anti-gp90 immunoglobulin G F(ab')2 had little effect on the brain colonization properties of B16-B15b cells in syngeneic mice. In blocking assays, anti-gp90 inhibited the binding of 125I-labeled transferrin to B16-B15b cells in a dose-dependent manner. The results suggest that the differential growth-stimulating effects of transferrin on highly metastatic B16 melanoma cells may be due to their differential expression of a Mr approximately 90,000 glycoprotein that is related to the transferrin receptor. In organ sites, such as the brain, differential expression of a transferrin-like receptor may allow metastatic cells to respond to low concentrations of growth factors known to be present in certain organs.

Animals↗
PubMed1986

Differential expression of metastasis-associated cell surface glycoproteins and mRNA in a murine large cell lymphoma.

A metastatic variant cell subline of the Abelson virus-transformed murine large lymphoma/lymphosarcoma RAW117 has been selected in vivo ten times for liver colonization. Highly metastatic subline RAW117-H10 forms greater than 200 times as many gross surface liver tumor nodules as the parental line RAW117-P. Analysis of cellular proteins and glycoproteins indicates reduced expression of murine Moloney leukemia virus-associated p15, p30, and gp70, and increased expression of a sialoglycoprotein, gp150, in the highly metastatic H10 cells. Northern analyses of oncogene expression suggested that mRNA of various oncogenes was expressed equally or not expressed in the RAW117 cells of differing metastatic potential. Differential gene expression was examined using a cDNA library of 17,600 clones established from poly A+ mRNA isolated from H10 cells. The cDNA library was screened by the colony hybridization technique using probes made from both RAW117-P and -H10 cells. Approximately 99.5% of these cDNA clones were expressed identically in P and H10 cells. Of the few differentially expressed cDNA clones (approx. 150/17,600), one-half of these were identified as Moloney leukemia virus sequences in a separate probing with a radiolabeled Moloney leukemia virus probe. The remainder of the differentially expressed mRNA detected by colony hybridization of the cDNA library were expressed at higher levels (approx. 1/6) or lower levels (approx. 1/3) in the highly metastatic H10 cells.

Animals↗
PubMed1993

Differential expression of human nicotinic acetylcholine receptor alpha subunit variants in muscle and non-muscle tissues.

The nicotinic acetylcholine receptor (nAChR) is an oligomeric transmembrane glycoprotein consisting of four homologous subunits in stoichiometry of alpha 2, beta (gamma or epsilon). Recently the presence of a novel exon (P3A) in human alpha AChR gene has been reported. Two variants of the human alpha subunit arise from alternate RNA splicing, one with and one without the P3A exon. However, the evolutionary origin of the P3A exon and the regulation of the expression of the two variants in human muscle and non-human tissues is currently unknown. Examination of genomic DNA from various species shows that the P3A exon sequence is present only in hominoids, old world and new world primates species and is absent in the muscle cDNA or genomic DNA from rat, mouse or dog, indicating that P3A exon is evolutionary conserved for at least 50 million years. The P3A+ variant of alpha subunit was found to be constitutively expressed in skeletal muscle, brain, heart, kidney, liver, lung and thymus, while P3A-variant was differentially expressed only in skeletal muscle. Thus it appears that the P3A+ variant is generated by 'default' selection by the splicing machinery, while expression of the P3A- variant is regulated by tissue-specific factors in the skeletal muscle. Mechanisms regulating differential expression of the alpha subunit variants may be pertinent to the pathophysiology of myasthenia gravis.

Amino Acid Sequence↗
PubMed2006

Investigation of differentially expressed proteins due to the inhibitory effects of berberine in human liver cancer cell line HepG2.

The investigation of differentially expressed proteins was used together with other techniques to study the inhibitory effects of two different doses of berberine in human liver cancer cell line HepG2. For HepG2 cells treated with 24.0 mg l(-1) of berberine, an increase in the sub G(0) phase that was indicative of cell death was observed in cell cycle analysis with flow cytometry. However, no significant increase in sub G(0) was observed in HepG2 cells treated with 4.0 mg l(-1) of berberine. Using flow cytometric analysis, significant activation of caspase 3 was not observed with HepG2 cells treated with 4.0 and 24.0 mg l(-1) of berberine. In this work, labeling of cells with stable isotope was not used in the proposed method developed. The whole cell lysates from the control and treated cells were digested with trypsin and the peptides were separated by two-dimensional (cation exchange and reversed phase) liquid chromatography and tandem mass spectrometry. Our preliminary data showed that the proposed platform provided a rapid approach to study the molecular mechanism due to the inhibitory effects of different doses of the berberine on HepG2 cell lines. This included a network of proteins involved in mitogen-activated protein kinase (MAPK) phosphorelay systems, metabolism, regulation of cell cycle and DNA damage response. The differentially expressed proteins identified using the current approach were consistent with the data obtained from cell cycle analysis with flow cytometry.

Berberine↗
PubMed1989

A dual-labeling method for identifying differentially expressed genes: use in the identification of cDNA clones that hybridize to RNAs whose abundance in tomato flowers is potentially regulated by gibberellins.

A method for identifying cDNA clones that hybridize to differentially expressed RNAs is described. Briefly, the RNA population in which the RNAs of interest are more abundant is used as a template for the synthesis of 35S-labeled cDNAs and another RNA population in which the RNAs of interest are less abundant is used as a template for the synthesis of 32P-labeled cDNAs. The labeled cDNAs are pooled and hybridized to plaque or colony lifts constructed from a cDNA library. Clones that hybridize to RNAs that are differentially expressed are identified using differential autoradiography/fluorography to discriminate between the 32P and 35S isotopes. We have used this method to identify cDNA clones that hybridize to mRNAs that are more abundant in the flowers of wild-type tomato than in the flowers of mutants that have low endogenous levels of gibberellins.

Autoradiography↗
PubMed2005

Identifying genes with differential expression in gemcitabine-resistant pancreatic cancer cells using comprehensive transcriptome analysis.

Pancreatic cancer is often unresectable at diagnosis, and chemotherapy using gemcitabine is now the standard treatment for advanced pancreatic cancer. However, acquired resistance to gemcitabine resulting in therapeutic failure is often encountered. Therefore, we sought to identify genes that determine gemcitabine resistance by evaluating the relationship between gene expression profiles and gemcitabine sensitivity to provide molecular targets for overcoming gemcitabine resistance. First, the gemcitabine concentration needed for 50% growth inhibition was examined in six pancreatic cancer cell lines. By exposing MIA PaCa-2 cells to long-term gemcitabine, we established gemcitabine-resistant cells. The gene expression profiles of the six pancreatic cancer cell lines and gemcitabine-resistant cells were determined using cDNA microarray analysis. By comparing the results, 30 genes were identified as differentially expressed genes correlated with gemcitabine sensitivity. Differentially expressed genes in the parental cell lines were also examined, and six overlapping genes were identified as genes correlated with gemcitabine sensitivity in both assays. Of these genes, the down-regulated expression of TNFSF6 protein, also known as Fas ligand, was confirmed in the gemcitabine-resistant cell line. These results should provide therapeutic molecular targets for overcoming gemcitabine resistance.

Antimetabolites, Antineoplastic↗
PubMed2003

Regulation and differential expression of the c-maf gene in differentiating cultured cells.

The Maf transcription factors are involved in a variety of developmental and cellular differentiation processes, but their role in the differentiation of mesenchymal cells has not been described. Here, we have analyzed c-maf expression during the differentiation of adipocytes and muscle cells in cultured systems. The expression of c-maf mRNA was down-regulated during adipogenesis and up-regulated during myogenesis. In adipogenesis, the c-maf mRNA was down-regulated 58h after switching to the differentiation medium and just after PPARgamma2 mRNA was induced. A transient transfection analysis of a reporter gene containing the 5(')-flanking region of the c-maf gene showed that PPARgamma2 represses c-maf gene expression. We previously found that c-Maf, c-Jun, and Pax6 bind to and stimulate the c-maf gene. The PPARgamma2 repression of c-maf expression seems to be due, at least in part, to inhibition of the transactivation functions of c-Maf, c-Jun, and Pax6. The repression of c-maf was partly reversed by CBP, suggesting that these transcription factors compete for CBP or related transcription co-factors. In myogenesis, there was a differentiation-dependent stimulation of c-maf mRNA expression. The increased expression correlated with myoD expression. A transient transfection analysis showed that myoD stimulated a c-maf reporter gene through binding to two typical E-box elements located between 160 and 180 nucleotides upstream of the cap site. Binding of MyoD to the E-boxes was confirmed by a gel mobility shift assay and DNaseI footprinting analysis. Combined, these results suggest that the c-maf gene plays an important role during the differentiation of adipocyte and muscle cells from mesenchymal fibroblast cells.

Adipocytes↗
PubMed1989

Glucocorticoid- and progesterone-specific effects are determined by differential expression of the respective hormone receptors.

Although glucocorticoids and progestins control vastly different physiological processes, the receptors mediating the effects of these hormones interact with the same DNA sequences. Transfer experiments involving synthetic genes and in vitro binding studies have shown that progesterone and glucocorticoid receptors both recognize the same 15-base pair DNA element (TGTACAGGATGTTCT), raising the question of how the two steroids affect gene expression selectively. We considered the possibility that their selectivity arises from either the differential expression of the receptors in target cells or the differential dependence of receptor function on additional transcription factors. To test these alternatives we introduced a progesterone-receptor expression plasmid into the rat hepatoma cell line Fto2B-3 which contains glucocorticoid receptor but is devoid of progesterone receptor. We report that expression of the progesterone receptor in Fto2B-3 cells renders endogenous glucocorticoid-regulated genes inducible by progestins. Our data show that the responsiveness of a cell to external stimuli can be reprogrammed by the expression of a single transcription factor and that differential expression of hormone receptors is at least one mechanism by which steroid-specific gene activation is achieved.

Animals↗
PubMed2006

Investigation of differentially expressed genes in the ventricular myocardium of senescent rats.

Aging alters a variety of physiological functions of the heart. The molecular basis of the age-related functional changes has not been fully understood. Differential gene expression provides the basis for many fundamental cellular processes associated with development and aging. The identification and cloning of genes whose expression is modulated by aging can be of importance for our better understanding of these age-related phenomena. In order to isolate and characterize gene products differentially expressed in senescent hearts, we applied a differential display method for screening those genes in rat ventricular myocardium. Total RNAs were isolated from 2-month-old (young) and 24-month-old rat (senescent) ventricles by the acid-guanidium-phenol-chloroform method. The first-strand synthesis of the cDNAs from each RNA was carried out with oligo-d(T) primers. The differential display screening was performed with three arbitrary primers and eight anchor primers, and the products were isolated on a 6% denaturing polyacrylamide gel. The bands showing differential expression were excised and subcloned into T-vector. We selected 19 upregulated clones and 66 downregulated clones in aged rat hearts. The differential expression of those candidate genes was confirmed by reverse Northern blot analysis. The selected genes were sequenced by dye-terminator methods. Among 31 clones, 15 clones were unknown. The known products included alpha-myosin heavy chain, cytochrome oxidase subunit, H(+)-transporting ATP synthase F0 complex subunit c isoform 3 (ATP5G3), and Na(+)-K(+)-Cl(-) cotransporter. The RT-PCR differential display method effectively identified genes differentially expressed in senescent hearts, and may be a useful tool for investigating factors responsible for age-related physiological changes.

Aging↗
PubMed1997

Differential expression of the HsKin17 protein during differentiation of in vitro reconstructed human skin.

In eukaryotic cells, various proteins homologous to the E. coli RecA protein are involved in the elimination of DNA damage. These proteins contribute to the repair of double-strand breaks and to genetic recombination. The mouse Kin17 protein is recognised by antibodies directed against the RecA protein. Kin17 has a zinc-finger domain allowing binding to curved DNA stretching over illegitimate recombination junctions. In the present study, we identified the human counterpart of the mouse Kin17 protein (named HsKin17) in skin cells. We employed an in vitro reconstructed skin model composed of an epidermal sheath lying on a dermal matrix with human fibroblasts embedded in rat collagen type I. The maturation programme (proliferation versus differentiation) of keratinocytes was highly dependent on stromal cells. Immunohistochemical staining of frozen sections obtained from skin specimens was monitored by an interactive laser cytometer. In this way we analysed protein levels in both dermal and epidermal compartments. After having characterised the epithelium, we focused our attention on HsKin17 expression. We detected HsKin17 in human keratinocytes. HsKin17 protein levels increased in proliferating epithelial keratinocytes after 7 days of culture. After 2 weeks of culture, epidermal sheaths acquired most of the differentiated features of mature epithelium. At this time, HsKin17 protein dropped below measurable levels in the stratum corneum, and diminished in nucleated cells. This study showed that HsKin17 is expressed in human reconstructed epithelium under conditions of hyperproliferation.

Adult↗
PubMed1999

Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes.

A new and highly effective method, termed suppression subtractive hybridization (SSH), has been developed for the generation of subtracted cDNA libraries. It is based primarily on a technique called suppression PCR, and combines normalization and subtraction in a single procedure. The normalization step equalizes the abundance of cDNAs within the target population and the subtraction step excludes the common sequences between the target and driver populations. As a result only one round of subtractive hybridization is needed and the subtracted library is normalized in terms of abundance of different cDNAs. It dramatically increases the probability of obtaining low-abundance differentially expressed cDNA and simplifies analysis of the subtracted library. The SSH technique is applicable to many molecular genetic and positional cloning studies for the identification of disease, developmental, tissue-specific, or other differentially expressed genes. This chapter provides detailed protocols for the generation of subtracted cDNA and differential screening of subtracted cDNA libraries. As a representative example we demonstrate the usefulness of the method by constructing a testis-specific cDNA library as well as using the subtracted cDNA mixture as a hybridization probe. Finally, we discuss the characteristics of subtracted libraries, the nature and level of background nondifferentially expressed clones in the libraries, as well as a procedure for the rapid identification of truly differentially expressed cDNA clones.

Animals↗
PubMedDate not supplied

Differential expression of protein kinase C isozymes and small GTP-binding proteins during HL60 cell differentiation by retinoic acid and cyclic AMP: relation with phospholipase D (PLD) activation.

The differential expression of protein kinase C (PKC) isozymes and small GTP-binding proteins, and their relation to O2 generation and phospholipase D (PLD) activation were analyzed during the differentiation of human promyelocytic HL60 cells to neutrophil-like cells induced by either retinoic acid (RA) or dibutyryl cyclic AMP (dbcAMP). In response to either one of the inducers, nitroblue tetrazolium (NBT) reduction activity time-dependently increased. Although PLD activity was upregulated by dbcAMP-treatment, only a slight increase was observed in RA-treated cells. Small GTP-binding proteins Rac1, Rap1, and RhoA, which are reported to be implicated in O2- generation or PLD activation, were already expressed in undifferentiated HL60 cells and their significant changes were not detected during differentiation. The mRNAs of the cytosolic components of NADPH oxidase system, p47phox and p67phox, were present in trace amounts in undifferentiated cells. However, they rapidly increased in response to RA or dbcAMP. In response to either RA or dbcAMP, the increases were observed in cPKC isozymes (alpha, beta I, beta II) but not in other subtypes (delta, epsilon, theta, zeta) by both RT-PCR and Western blot analyses. In dbcAMP-treated cells PKC alpha increased remarkably, whereas PKC beta I and beta II mainly elevated in RA-treated cells. These results suggest the possibility that cPKCs are closely related to cell differentiation and that PKC alpha is involved in PLD activation.

Bucladesine↗
PubMed2000

Differential expression of cholesteryl ester transfer protein in the liver and plasma of fasted and fed transgenic mice.

Because cholesteryl ester transfer protein (CETP) is considered a potential target in the treatment of atherosclerosis, several reports have focused on the regulation of this enzyme, and there is evidence that insulin may be a regulatory factor. The present study examines the differential expression of the human CETP gene between physiologic conditions that are accompanied by low (fasted) and high (fed) insulin levels. CETP expression was examined in plasma and tissues of transgenic mice expressing the human CETP minigene after 12 hours of fasting (n = 20) or ad libitum feeding (n = 20) with normal mouse chow. Plasma cholesteryl ester transfer activity (CETA) was 20% higher in fed than in fasted mice, reflecting higher levels of CETP (P < 0.05). This observation was accompanied by higher liver mRNA in fed mice (100%, P < 0.05), as determined by ribonuclease protection assays, as well as by higher CETA (23%, P < 0.05) and CETP mass (29%, P < 0.05) in the particulate fraction of liver homogenates. These parameters of liver CETP expression correlated well with each other, as well as with plasma CETA. CETP in the liver particulate fraction was found as a doublet (approximately 70 and 65 kDa), which resolved to a single band (approximately 60 kDa) upon deglycosylation. No differences in CETP expression were observed in pooled adipose tissue samples from fed and fasted mice. Insulin and glucose were not related to any plasma or tissue parameter of CETP expression. In summary, the concerted, differential expression of CETP in the liver of fed and fasted transgenic mice appears to contribute to higher plasma CETP levels in fed mice, but the precise role of insulin and glucose in regulating CETP expression under fasted and fed conditions needs to be defined.

Journal Article↗
PubMed2003

DNA microarray analysis of genes differentially expressed in diet-induced (cafeteria) obese rats.

OBJECTIVE: To better understand the molecular basis of dietary obesity, we examined adipose tissue genes differentially expressed in an obesity model using DNA microarray analysis. RESEARCH METHODS AND PROCEDURES: We assessed the expression level of over 12,500 transcripts in epididymal fat pads from (cafeteria) obese and control rats with the aid of the array technology. RESULTS: Cafeteria (obese) rats weighed 50% more and had 2.5-fold higher levels of epididymal fat and elevated levels of circulating leptin. Adipose genes differentially expressed in obese and control rats were categorized into five groups: macronutrient metabolism, transcription factors, hormone receptor and signal transduction, redox and stress proteins, and cellular cytoskeleton. Interestingly, the expression levels of a number of genes involved in lipid metabolism such as glycerol-3-phosphate dehydrogenase, stearoyl coenzyme A desaturase, together with the transcription factors implicated in adipocyte differentiation (CAAT/enhancer binding protein-alpha and peroxisome proliferator-activated receptor-gamma), were significantly increased in obese animals compared with control. The most up-regulated transcripts were the ob (49.2-fold change) and the fatty acid-binding protein genes (15.7- fold change). In contrast, genes related to redox and stress protein were generally down-regulated in obese animals compared with the control. DISCUSSION: Our study showed that in diet-induced obesity, the expression levels of some important genes implicated in lipid metabolism were up-regulated, whereas those related to redox and stress protein were down-regulated in obese animals compared with control. This pattern of gene expression may occur in human obesity cases after high-fat intake.

Adipocytes↗
PubMed2001

[Construction of a subtracted cDNA library of differentially expressed genes in human normal liver tissue and primary hepatocellular carcinoma tissue].

OBJECTIVE: To construct a subtracted cDNA library of differentially expressed genes in human normal liver tissue and primary hepatocellular carcinoma (HCC) tissue. METHODS: Using the suppression subtractive hybridization (SSH), a novel technique has been described recently. cDNA fragments of missing or low expressing tumor suppressor genes in HCC tissue were isolated using paracancerous normal liver tissue and HCC tissue as targets. Then these cDNA fragments were directly inserted into T/A cloning vector to set up the subtractive library. Amplification of the library was carried out with transformation of E.coli by high voltage electroperforation. One hundred positive bacteria clones were randomly picked and identified using enzyme restriction method. RESULTS: The amplified library contained more than 4,000 positive bacteria clones. Random analysis of 100 clones with enzyme restriction method showed that all clones contained 200-600 bp inserts. CONCLUSIONS: A subtracted cDNA library of differentially expressed genes in human normal liver tissue and HCC tissue is constructed successfully with SSH and T/A cloning techniques. The library is efficient and lays solid foundation for screening and cloning new and specific missing or low expressing tumor suppressor genes of HCC.

Carcinoma, Hepatocellular↗