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Results for “differential expression”

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At least 469 records · Page 26Linked to original sources
PubMed2006

Identification of differentially expressed genes in cutaneous squamous cell carcinoma by microarray expression profiling.

BACKGROUND: Carcinogenesis is a multi-step process indicated by several genes up- or down-regulated during tumor progression. This study examined and identified differentially expressed genes in cutaneous squamous cell carcinoma (SCC). RESULTS: Three different biopsies of 5 immunosuppressed organ-transplanted recipients each normal skin (all were pooled), actinic keratosis (AK) (two were pooled), and invasive SCC and additionally 5 normal skin tissues from immunocompetent patients were analyzed. Thus, total RNA of 15 specimens were used for hybridization with Affymetrix HG-U133A microarray technology containing 22,283 genes. Data analyses were performed by prediction analysis of microarrays using nearest shrunken centroids with the threshold 3.5 and ANOVA analysis was independently performed in order to identify differentially expressed genes (p < 0.05). Verification of 13 up- or down-regulated genes was performed by quantitative real-time reverse transcription (RT)-PCR and genes were additionally confirmed by sequencing. Broad coherent patterns in normal skin vs. AK and SCC were observed for 118 genes. CONCLUSION: The majority of identified differentially expressed genes in cutaneous SCC were previously not described.

Adolescent↗
PubMed2001

Differential expression of signal transducers and activators of transcription during human adipogenesis.

Signal Transducers and Activators of Transcription (STATs) display unique expression patterns upon induction of differentiation of murine 3T3-L1 preadipocytes into adipocytes. During differentiation, expression of STAT1 and STAT5 increase, while STAT3 and STAT6 remain relatively unchanged. Here, we determined whether human subcutaneous preadipocytes expressed STATs and if the pattern of expression changed during adipogenesis. We found by Western blot analysis that freshly isolated preadipocytes expressed STAT1, STAT3, STAT5, and STAT6, but not STAT2 and STAT4. Induction of preadipocyte differentiation with 1-methyl-3-isobutylxanthine, dexamethasone, insulin, and BRL49653 decreased expression of STAT1, and increased expression of STAT3 and STAT5. STAT6 expression did not change during adipogenesis. Changes in expression of CCAAT/enhancer binding protein beta (C/EBPbeta), C/EBPdelta, C/EBPalpha, and peroxisome proliferator-activated receptor gamma were similar to murine cell lines. These results suggest that unlike the traditional adipogenic transcription factors, unique differences exist in STAT expression patterns between murine and human adipose cells.

Adipocytes↗
PubMed2002

Profiling genes differentially expressed in NGX6 overexpressed nasopharyngeal carcinoma cells by cDNA array.

PURPOSE: To investigate the role of the NGX6 gene in carcinoma proliferation and profile the downstream genes regulated by NGX6 in a nasopharyngeal carcinoma (NPC) cell line. METHODS: We established a NPC cell line with NGX6 overexpression by gene transfection. Subsequently, a high-density cDNA array was used to identify differentially expressed genes in NGX6-overxepressed cells. Four differentially expressed genes or EST(expressed sequence tags) were examined using Northern blot. Furthermore, flow cytometry was employed to analyze the percentages of cells in the G(0)-G(1), S, and G(2)-M phase of the cell cycle in a NGX6 overexpression cell line. RESULTS: Fifty-five genes and ESTs were differentially expressed after NGX6 transfection in a cDNA array assay. Several genes related to cell cycle and transcription regulation were identified using this technique. Flow cytometry analysis showed NGX6 overexpression can increase the length of the G(1) phase of the cell cycle in NPC cells. CONCLUSION: We demonstrated the existence of a panel of genes that can be regulated by NGX6. Overexpression of NGX6 can influence the distribution of the cell cycle in NPC cells. Further studies are necessary to elucidate the exact function of these genes and their relationship to NGX6 expression.

Carcinoma↗
PubMed2004

Localization and differential expression of arginase II in the kidney of male and female mice.

Arginase II (AII) has been almost exclusively studied in male mammalian kidneys. Our investigations were conducted to localize AII gene expression in the female mouse kidney, and to analyze the differential expression of AII gene at the transcriptional and translational levels in the kidneys of female and male mice. Total RNAs and soluble proteins extracted from renal zones and whole kidneys were analyzed by Northern and Western blots, respectively. Mitochondrial and cytosolic proteins were analyzed by Western blot. L-[guanidino-14C]arginine hydrolysis by AII was detected in microdissected tubules and the 14CO2 released from [14C]urea hydrolysis was quantified. The results of these experiments showed that: (1) both AII mRNA and protein were highly expressed in the deep cortex and the outer stripe of the outer medulla, (2) urea was produced mainly in the proximal straight tubules (PST), (3) the 38-kDa AII protein was more abundant in the mitochondria than the cytosol, and (4) the renal content of AII mRNA and protein was about three-fold higher in female than in male mice. In conclusion, in both genders, AII gene expression is restricted to the PST and localized into mitochondria. AII gene is differentially expressed in the kidney of female and male mice since higher levels of AII mRNA, protein and activity were observed in the kidneys of the former than those of the latter. Renal AII gene expression was gender-dependent in mice but not in rats. Finally, in the PST of females, L-arginine-derived ornithine may be a precursor for the renal production of L -glutamate and L-glutamine because high levels of AII, ornithine aminotransferase and glutamine synthetase are expressed in this nephron segment.

Animals↗
PubMed2003

Modulation of GdCl3 and Angelica sinensis polysaccharides on differentially expressed genes in liver of hepatic immunological injury mice by cDNA microarray.

AIM: To study the modulating effect of GdCl(3) and Angelica Sinensis polysaccharides (ASP) on differentially expressed genes in liver of hepatic immunological mice by cDNA microarray. METHODS: Hepatic immunological injury was induced by lipopolysaccharide (LPS ip, 0.2 mg/kg(-1)) in bacillus calmetteguerin (BCG ip, 1 mg/kg(-1)) primed mice; A single dose of 20 mg/kg(-1) GdCl(3) was simultaneously pretreated and 30 mg/kg(-1) ASP (ig, qdX7 d) was administrated when the BCG+LPS was primed. The mice were sacrificed at the end of the 7(th) day after ip LPS for 6 h and the liver was removed quickly. The PCR products of 512 genes were spotted onto a chemical material-coated glass plate in array. The DNAs were fixed to the glass plate after series of treatments. The total RNAs were isolated from the liver tissue, and were purified to mRNAs by Oligotex. Both mRNAs from the normal liver tissue and the liver tissue from the mice with hepatic immunological injury or that pretreated with GdCl(3) or ASP were reversely transcribed to cDNAs with the incorporation of fluorescent dUTP to prepare the hybridization probes. The mixed probes were hybridized to the cDNA microarray. After high-stringent washing, the cDNA microarray was scanned for fluorescent signals and showed differences between the two tissues. RESULTS: Among the 512 target genes, 18 differed in liver tissue of hepatic immunological injury mice, and 6 differed in those pretreated by ASP, 7 differed in those pretreated by GdCl(3). CONCLUSION: cDNA microarray technique is effective in screening the differentially expressed genes between two different kinds of tissue. Further analysis of those obtained genes will be helpful to understand the molecular mechanism of hepatic immunological injury and to study the intervention of drug. Both ASP and GdCl(3) can decrease the number of the differentially expressed genes in liver tissue of mice with hepatic immunological injury.

Angelica sinensis↗
PubMed2003

Differential expression of DOC-1 in microsatellite-unstable human colorectal cancer.

The precise genetic mechanism of malignant transformation in DNA mismatch repair deficient, microsatellite-unstable colorectal cancer (CRC) has yet to be elucidated. We employed cDNA microarray to identify patterns of gene expression among CRC cell lines and to compare directly lines with and without microsatellite instability. This study was undertaken to test the hypothesis that microsatellite-unstable CRC cell lines demonstrate specific patterns of gene expression that differ significantly from those observed among microsatellite-stable CRC. Multiple differential expression patterns were identified. Genes demonstrating differential expression included deleted-in-oral-cancer-1 (DOC-1), a highly conserved growth suppressor. DOC-1 expression correlated with microsatellite status, with significantly decreased expression in microsatellite-unstable cell lines and constitutive expression in microsatellite-stable cell lines. We also observed alterations in the biologic behavior of p12(DOC-1)-deficient cell lines, with increased S phase and decreased apoptosis compared to microsatellite-stable (DOC-1+) cell lines. Transfection of p12(DOC-1) into SW48, which lacks p12(DOC-1) expression, resulted in cell cycle and apoptosis profiles similar to other p12(DOC-1)+ cell lines. These results support the hypothesis that microsatellite-unstable CRC is characterized by novel patterns of gene expression different from those associated with microsatellite-stable CRC, and demonstrate that p12(DOC-1) has tumor suppressor potential in colon epithelial cells.

Apoptosis↗
PubMed2001

Identification and isolation of differentially expressed genes in osmotically stressed human oral keratinocytes.

Complementary DNA fragments which showed differential expression relative to unstressed controls were identified and isolated from human oral keratinocytes exposed to hyperosmotic stress. The up- or downregulation of the expression of nine of these cDNAs in response to osmotic stress was determined by Northern blotting. Sequence analysis showed that clones K-5 and K-46 contained identical sequences. Homology searches revealed that K-13 and K-33 were fragments of unknown genes. Among the upregulated cDNAs, K-16 and K-32 were 94 and 83% identical to chromosome 16 bacterial artificial chromosome (CIT987K-A-418G10) and a cDNA (ai49b01.sl) clone, respectively. Another clone, K-34, encoded a protein 73% identical to Bax epsilon. Among the downregulated genes, K-5/46 and K-45 were 99% identical to the og24d08.s1 cDNA clone and to mitochondrial genes for tRNAs and 12S and 16S ribosomal RNAs, respectively, while K-50 was 100% identical to KIAA0905 protein. The gene expression induced by osmotic stress occurred in parallel with the induction of apoptosis and a reduction in protein biosynthesis. This observation, together with the characteristics of the some of the differentially expressed genes, suggests that among the major events induced in oral keratinocytes by hyperosmotic stress are the induction of apoptosis and a decrease in protein biosynthesis, brought about by upregulation of pro-apoptotic genes and downregulation of genes involved in protein biosynthesis.

Amino Acid Sequence↗
PubMedDate not supplied

Identification of differentially expressed genes in prostatic epithelium in relation to androgen receptor CAG repeat length.

The CAG repeat within exon 1 of the androgen receptor (AR) has been associated with the development of prostate cancer. The shorter number of glutamine residues in the protein has been associated with a higher transcriptional activity of the AR and increased relative risk for prostate cancer. In an attempt to identify differentially expressed genes in prostate cancer in relation to AR CAG repeat length variation, in this study we used total mRNA from normal and tumor tissues from 2 prostate cancer patients with AR alleles containing 19 and 26 CAG repeats to perform differential-display RT-PCR analysis. We were able to identify 48 different transcripts that showed homology to several known genes associated with different biological pathways. Among the differentially expressed genes, ATRX and SFRP1 were further validated by quantitative RT-PCR. The transcripts of both ATRX and SFRP1 genes proved to be down-regulated in most of the prostate tumors analyzed by quantitative RT-PCR. Hypermethylation of the promoter region of the SFRP1 gene was found in 17.5% (7/40) of the cases analyzed and was associated with the loss of SFRP1 expression (p=0.014). The differentially expressed genes identified in this study are implicated in several cellular pathways that, when up- or down-regulated, might play a role in the tumorigenic process of the prostate.

Aged↗
PubMed1992

Differential expression of vimentin in rat prostatic tumors.

Differential hybridization analysis was used to identify molecular differences between a relative benign and a highly aggressive rat prostatic tumor derived from the Dunning R-3327-H adenocarcinoma. From the several differentially expressed mRNAs identified, we here report the characterization of pBUS51 which encodes a transcript highly expressed in all-anaplastic Dunning tumors. Only a very low expression was detectable in normal rat prostate or in the differentiated tumors of the Dunning system. Nucleotide sequence analysis and computer-assisted database comparison revealed that pBUS51 was highly homologous to vimentin and therefore likely the rat homolog of this protein.

Amino Acid Sequence↗
PubMed1997

Differential expression of estrogen receptors alpha and beta mRNA during differentiation of human osteoblast SV-HFO cells.

Estrogens have been shown to be essential for maintaining a sufficiently high bone mineral density and ER alpha expression has been demonstrated in bone cells. Recently, a novel estrogen receptor, estrogen receptor beta (ERbeta) has been identified. Here we demonstrate that also ERbeta is expressed in human osteoblasts, and that ER alpha and ERbeta are differentially expressed during human osteoblast differentiation. ERbeta mRNA expression increased gradually during osteoblast culture, resulting in an average increase of 9.9+/-5.3 fold (mean+/-S.D., n=3) at day 21 (mineralization phase) as compared to day 6 (proliferation phase). In contrast, ER alpha mRNA expression levels increased only slightly until day 10 (2.3+/-1.7 fold) and then remained constant. The observed differential regulation of ER alpha and beta is suggestive for an additional functional role of ERbeta to ER alpha in bone metabolism.

Cell Differentiation↗
PubMed2005

[The effect of 20(R)-ginsenoside Rg3 on the differential expression of cell signaling genes and other related genes in human lung adenocarcinoma cell line A549].

OBJECTIVE: To study the effect of 20(R)-ginsenoside Rg3 [20(R)-Rg3] on the differential expression of cell signaling genes and other related genes in human lung adenocarcinoma cell line A549. METHODS: The cell line A549 was cultured with 20(R)-Rg3 (10(-6) mol/L) for 72 h, RNA was extracted, and the differential expression of cell signaling genes and other related genes were detected with DNA microarray. RESULTS: A total of 3 490 genes were detected, and the expression of 24 genes were changed after the addition of 20(R)-Rg3. Two cell signaling genes & transducin genes were up-regulated. Two cystoskeleton & locomotion genes were up-regulated. Three proto-oncogene & anti-oncogene genes were down-regulated. Two of the translation & synthetical genes were down-regulated, and 1 of them was up-regulated. One DNA recombination gene and one metabolism gene were down-regulated. CONCLUSION: 20(R)-Rg3 showed significant effect on the differential expression of cell signaling genes and other related genes in human lung cell line A549.

Adenocarcinoma↗
PubMed2000

Differential expressions of protein kinase C isozymes during proliferation and differentiation of human skeletal muscle cells in vitro.

The mechanism of skeletal muscle regeneration in vivo can be well modeled in vitro by culturing skeletal muscle cells. In these cultures mononuclear satellite cells fuse to form polynuclear myotubes by proliferation and differentiation. The aim of this study was to determine how the different protein kinase C (PKC) isozymes were expressed during differentiation of human skeletal muscle in vitro. The expressions of desmin, used as a muscle-specific intermediate filament protein marker of differentiation, and of different PKC isozymes were detected by single and double immunohistochemical labeling, and by Western blot analysis. In skeletal muscle cells we could identify five PKC isozymes (PKC alpha, -gamma, -etha, -theta and -zeta). The expressions of PKC alpha and -zeta did not change significantly during differentiation; their levels of expression were high in the early immature cells and remained unchanged in later phases. In contrast, the expression levels of PKC gamma and -etha increased with differentiation. Furthermore, the cellular localization of PKC gamma markedly altered during differentiation, with a perinuclear-nuclear to cytoplasmic translocation. The change in the level of expression of PKC theta during differentiation showed different pattern; its expression was high during the early phases, but a decreased immunostaining was detected in the matured, well-differentiated myotubes. We conclude, therefore, that cultured human skeletal muscle cells possess a characteristic PKC isozyme pattern, and that the different phases of differentiation are accompanied by different expression patterns of the various isozymes. These data suggest the possible functional and differential roles of PKC isozymes in human skeletal muscle differentiation.

Cell Differentiation↗
PubMed2000

Differentially expressed mRNAs in androgen-independent but not androgen-dependent Shionogi carcinoma.

UNLABELLED: Recently, a new and highly effective method termed suppressive subtractive hybridization (SSH) has been introduced to clone differentially expressed mRNAs. Genes expressed in androgen-independent but not in androgen-dependent tumors, and vice versa, are obviously significant to delineate the mechanisms of androgen dependency/independency of these tumors. Mouse mammary cancer (Shionogi carcinoma-115) has been extensively used to analyze the mechanism of androgen-dependent cancer growth. METHODS: We cloned androgen-independent and androgen-dependent Shionogi carcinoma-115 specific mRNAs by the SSH method. Cloned sequences were compared with known sequences using NCBI BLAST across the Internet. Two clones were positive for cDNA insert when androgen-independent cDNA was used as tester cDNA, while no clones were positive using the androgen-dependent tester cDNA. One of the former was mouse protein kinase C beta-II while the other was a new DNA sequence. Mouse protein kinase C beta-II mRNA and the new mRNA were shown to be differentially expressed by RT-PCR analysis in androgen-independent but not androgen-dependent Shionogi carcinoma. Two mRNA species differentially expressed in androgen-independent but not androgen-dependent Shionogi carcinoma were cloned by the SSH method. The significance of these mRNAs for androgen-dependency/independency of Shionogi carcinoma should be explained in future studies.

Androgens↗
PubMed2004

Mixture models for assessing differential expression in complex tissues using microarray data.

MOTIVATION: The use of DNA microarrays has become quite popular in many scientific and medical disciplines, such as in cancer research. One common goal of these studies is to determine which genes are differentially expressed between cancer and healthy tissue, or more generally, between two experimental conditions. A major complication in the molecular profiling of tumors using gene expression data is that the data represent a combination of tumor and normal cells. Much of the methodology developed for assessing differential expression with microarray data has assumed that tissue samples are homogeneous. RESULTS: In this paper, we outline a general framework for determining differential expression in the presence of mixed cell populations. We consider study designs in which paired tissues and unpaired tissues are available. A hierarchical mixture model is used for modeling the data; a combination of methods of moments procedures and the expectation-maximization algorithm are used to estimate the model parameters. The finite-sample properties of the methods are assessed in simulation studies; they are applied to two microarray datasets from cancer studies. Commands in the R language can be downloaded from the URL http://www.sph.umich.edu/~ghoshd/COMPBIO/COMPMIX/.

Algorithms↗
PubMed2004

Differential expression of the skeletal muscle proteome in mdx mice at different ages.

The mdx mouse is the most commonly used animal model for Duchenne muscular dystrophy (DMD), a disease caused by the absence of dystrophin. Although much has been done to elucidate the structure and function of dystrophin and the dystrophin-associated glycoprotein complex (DGC), little is known about the cascade of molecular events triggered by the absence of dystrophin that lead to muscle degeneration. To study the molecular basis of DMD, we decided to systematically study the skeletal muscle proteome in mdx mice at different ages. By using two-dimensional (2-D) gel electrophoresis, we defined changes in the protein expression pattern between mdx and control muscles. Approximately 46 differentially expressed proteins from the cytosolic fraction of mdx hindlimb muscles at three months of age were detected by 2-D gel analysis, of which 24 were identified by matrix assisted laser desorption/ionization- mass spectrometry. Most of the proteins fell into five groups of functionally related proteins. These functional categories are (i) metabolism and energy production, (ii) serine protease inhibitor family, (iii) growth and differentiation, (iv) calcium homeostasis, and (v) cytoskeletal reorganization and biogenesis. The potential roles of the differentially expressed proteins are discussed in the context of the mdx phenotype. Finally, we analyzed alterations of protein expression in mdx mice at one and six months of age to determine how protein expression changes with disease progression.

Animals↗
PubMed2003

alpha-Synuclein maps to a quantitative trait locus for alcohol preference and is differentially expressed in alcohol-preferring and -nonpreferring rats.

Total gene expression analysis (TOGA) was used to identify genes that are differentially expressed in brain regions between the alcohol-naive, inbred alcohol-preferring (iP), and -nonpreferring (iNP) rats. alpha-Synuclein, expressed at >2-fold higher levels in the hippocampus of the iP than the iNP rat, was prioritized for further study. In situ hybridization was used to determine specific brain regions and cells expressing alpha-synuclein in the iP and iNP rats. Similar to alpha-synuclein mRNA levels, protein levels in the hippocampus were higher in iP rats than iNP rats. Higher protein levels were also observed in the caudate putamen of iP rats compared with iNP rats. Sequence analysis identified two single nucleotide polymorphisms in the 3' UTR of the cDNA. The polymorphism was used to map the gene, by using recombination-based methods, to chromosome 4, within a quantitative trait locus for alcohol consumption that was identified in the iP and iNP rats. A nucleotide exchange in the iNP 3' UTR reduced expression of the luciferase reporter gene in SK-N-SH neuroblastoma cells. These results suggest that differential expression of the alpha-synuclein gene may contribute to alcohol preference in the iP rats.

3' Untranslated Regions↗
PubMed2002

[Screening of differentially expressed genes in the mouse hematopoietic stromal cells after long-term culture].

Hematopoietic stromal cells, being the essential ingredient of the hematopoietic microenvironment, play very important roles in the control and regulation of self-renewal, proliferation and differentiation of hematopoietic stem cells (HSC) via complex interactions of cell-cell, cell-humoral and cell-extracellular matrix. Evidence from in vivo experiment has proved that HSC derived from normal mice could reconstitute hematopoiesis of mice with HSC defects but failed to reconstitute hematopoiesis of those mice with microenvironment defects, showing the importance of hematopoietic microenvironment in the maintenance of hematopoiesis in vivo. A well-known long-term culture (LTC) system established by Dexter demonstrated in another way that stromal cell layer in the system could support ex vivo hematopoiesis for several months, even more than one year under the optimal conditions. It, however, has not been demonstrated that what is the key elements and in which way the ex vivo hematopoiesis could be maintained for so long time. As the inventions for the large-scale screening methodologies the suppression subtractive hybridization (SSH) was chosen for the screening differentially expressed genes expressed by LTC cultured stromal cells but not by the uncultured bone marrow cells (BMC). mRNA extracted from both cultured adherent cells (tester) and BMC (driver) were hybridized according to the protocol provided by CLONTECH. Total of 130 clones differentially expressed by cultured cells were randomly picked up and 106 ESTs were obtained after sequencing. They represent 26 identical or similar genes and 7 novel genes after the bioinformatics analysis. 5 of the novel genes with the entire open reading frame, without functional clues, have been cloned into the mammalian expression vectors and the functions of them in the control of proliferation and differentiation of HSC will be further exploring. The most interesting discovery is that 3 novel genes have signal peptides, implying the potential discovery of novel growth factors as 80% known growth factors have signal peptides. Our experimental results suggest that: (a) based on the results of subtractive efficiency, the SSH could be a reliable method to screen differentially expressed genes; (b) gene expression may be regulated by multiple factors, even conditioning-dependent, in this experiment the genes expressed by bone marrow stromal cells are LTC-cultivation inducible; (c) it is possible to find interesting genes or special gene after relatively large-scale screen.

Animals↗
PubMed2002

Differential expression of the Quox-1 gene in normal human cells, early human embryo, and tumor cells.

Quox-1 is the only gene in the hox family whose expression occurs throughout the developing central nervous system. The differential expression of the Quox-1 gene was studied in normal human tissues and tumor tissues. Marked expression of Quox-1 was detected in early human embryos, LCE cells, and HeLa cells, with weak to zero expression being detected in various normal human tissues. Immunocytochemistry analysis further confirmed that the Quox-1 protein was absent in normal human leukocytes. However, high levels of Quox-1 product were found in leukocytes of acute lymphocyte leukemia patients and in patients with a subtype of acute nonlymphocyte leukemia. In addition, Southern blot analysis showed that the genomic DNA of LCE, HeLa, and normal human leukocyte cells had a DNA rearrangement of the Quox-1 gene, suggesting that the rearrangement of genomic DNA might be the cause of differential expression in normal human tissues and tumor tissues. The data implied that the overexpression of Quox-1 was associated with tumors, and that there may be links between the processes of embryogenesis and carcinogenesis.

Alternative Splicing↗