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At least 613 records · Page 34Linked to original sources
PubMed1999

Differential expression of human lysyl hydroxylase genes, lysine hydroxylation, and cross-linking of type I collagen during osteoblastic differentiation in vitro.

The pattern of lysyl hydroxylation in the nontriple helical domains of collagen is critical in determining the cross-linking pathways that are tissue specific. We hypothesized that the tissue specificity of type I collagen cross-linking is, in part, due to the differential expression of lysyl hydroxylase genes (Procollagen-lysine,2-oxyglutarate,5-dioxygenase 1, 2, and 3 [PLOD1, PLOD2, and PLOD3]). In this study, we have examined the expression patterns of these three genes during the course of in vitro differentiation of human osteoprogenitor cells (bone marrow stromal cells [BMSCs]) and normal skin fibroblasts (NSFs). In addition, using the medium and cell layer/matrix fractions in these cultures, lysine hydroxylation of type I collagen alpha chains and collagen cross-linking chemistries have been characterized. High levels of PLOD1 and PLOD3 genes were expressed in both BMSCs and NSFs, and the expression levels did not change in the course of differentiation. In contrast to the PLOD1 and PLOD3 genes, both cell types showed low PLOD2 gene expression in undifferentiated and early differentiated conditions. However, fully differentiated BMSCs, but not NSFs, exhibited a significantly elevated level (6-fold increase) of PLOD2 mRNA. This increase coincided with the onset of matrix mineralization and with the increase in lysyl hydroxylation in the nontriple helical domains of alpha chains of type I collagen molecule. Furthermore, the collagen cross-links that are derived from the nontriple helical hydroxylysine-aldehyde were found only in fully differentiated BMSC cultures. The data suggests that PLOD2 expression is associated with lysine hydroxylation in the nontriple helical domains of collagen and, thus, could be partially responsible for the tissue-specific collagen cross-linking pattern.

Adolescent↗
PubMed1992

Two FGF receptor genes are differentially expressed in epithelial and mesenchymal tissues during limb formation and organogenesis in the mouse.

Fibroblast growth factors (FGFs) can influence the growth and differentiation of cultured cells derived from neuroectoderm, ectoderm or mesenchyme. The FGFs interact with a family of at least four closely related receptor tyrosine kinases that are products of individual genes. To investigate the role of FGFs in the growth and differentiation of embryonic tissues and to determine whether the individual FGF receptor genes might have specific functions, we compared the localization of mRNA for two FGF receptor genes, FGFR1 (the flg gene product) and FGFR2 (the bek gene product), during limb formation and organogenesis in mouse embryos (E9.5-E16.5). Although the two genes were coexpressed in some tissues, the differential expression of FGFR1 and FGFR2 in most embryonic tissues was striking. FGFR1 was expressed diffusely in mesenchyme of limb buds, somites and organ rudiments. In contrast, FGFR2 was expressed predominantly in the epithelial cells of embryonic skin and of developing organs. The differential expression of FGFR1 and FGFR2 in mesenchyme and epithelium respectively, suggests the receptor genes are independently regulated and that they mediate different functions of FGFs during development.

Animals↗
PubMed2004

Retinoic acid and retinoid X receptors are differentially expressed in thyroid cancer and thyroid carcinoma cell lines and predict response to treatment with retinoids.

Therapy for patients with advanced thyroid carcinoma is limited. Clinical and in vitro studies suggest that some patients with advanced thyroid cancer may respond to therapy with retinoic acid. mRNA expression of the six retinoic acid (RAR) and retinoid X receptor (RXR) isoforms (RARalpha, -beta, -gamma and RXRalpha, -beta, -gamma) was measured in four human thyroid cell lines, and protein expression was subsequently measured in 10 thyroid cancer cell lines. Two isoforms, RARbeta and RXRgamma, were differentially expressed in the four cell lines. Comparison of 10 thyroid tumors and matched normal thyroid tissue confirmed differential tumor expression of RARbeta and RXRgamma and lack of the RXRgamma isoform in normal thyroid tissue. Cell lines expressing both RARbeta and RXRgamma demonstrated significant growth suppression when treated with retinoids, whereas cell lines lacking these isoforms were unaffected. Expression of RARbeta, the isoform associated with suppression of tumor growth in other cancer types, was not affected by treatment with retinoids in the thyroid cancer cell lines. LG346 increased apoptosis and decreased cells in the S-phase in an anaplastic carcinoma cell line, suggesting that this retinoid causes growth suppression of these cells by multiple mechanisms. In summary, we identified the RARbeta and RXRgamma isoform to be differentially expressed in thyroid cancer cell lines and tumor tissue. These isoforms seem to predict response to retinoid therapy in thyroid cancer cell lines.

Antineoplastic Agents↗
PubMed1992

Differential expression of ras protooncogenes during in vitro differentiation of human erythroleukemia cells.

We have compared the expression of the ras protooncogene family (H-, K-, and N-ras) in leukemia cell differentiation utilizing as a model K562 and HEL erythroleukemia cells treated either with 1-beta-arabinofuranosylcytosine or 12-O-tetradecanoylphorbol-13-acetate (TPA). 1-beta-D-Arabinofuranosylcytosine induced terminal erythroid differentiation of K562 cells, while TPA induced myeloid differentiation of K562 and HEL cells, resulting in myelomonocytic-like cells expressing macrophagic and megakaryocytic markers. H-ras mRNA levels showed a dramatic decrease in K562 cells subjected to erythroid and myelomonocytic differentiation. The same result was found at the protein level for p21H-ras. Expression of K-ras and N-ras in K562 cells also decreased with differentiation, although significant mRNA levels remained despite cessation of cell proliferation. The decrease in K-ras expression was greater for TPA-treated cells than for 1-beta-arabinofuranosylcytosine-treated cells. TPA-induced myelomonocytic differentiation in HEL cells also resulted in a dramatic down-regulation of H-ras mRNA levels. Thus, by using a leukemia cell line able to differentiate along two different lineages, our results reveal a lineage-specific modulation of ras gene family expression.

Cell Differentiation↗
PubMed1999

Identification, N-terminal region sequencing and similarity analysis of differentially expressed proteins in Paracoccidioides brasiliensis.

Paracoccidioides brasiliensis is the causal agent of paracoccidioidomycosis, which is a systemic mycosis in Latin America. This human pathogen is a dimorphic fungus existing as mycelium (26 degrees C) and in infected tissues as a yeast form (36 degrees C). The in vitro differentiation process is reversible and dependent on temperature shift. In the present study, the total proteins from both forms of P. brasiliensis (isolate Pb01) were analysed by two-dimensional electrophoresis. Differentially expressed proteins were identified. Two of these proteins, PbM46 (mycelium) and PbY20 (yeast), were submitted to automated protein sequencing of their N-terminal regions. The 15 amino acid residue sequence of PbM46, AITKIFALKVYDSSG, is similar to enolases from several sources, and specially those from Saccharomyces cerevisiae (80%) and Candida albicans (67%), when compared to the NR database at NCBI using the BLASTP program. The 34 amino acid residue sequence of PbY20, APKIAIVFYSLYGHIQKLAEAQKKGIEAAGGTAD, could probably represent an allergen protein since it is very similar (90%) to the minor allergen protein of Alternaria alternata and 82% similar to the allergen protein of Cladosporium herbarum. This comparative analysis of proteins from mycelium and yeast forms has allowed the identification and characterization of differentially expressed proteins, probably related to differential gene expression in P. brasiliensis.

Amino Acid Sequence↗
PubMed2003

Differential expression of HLA class II genes associated with disease susceptibility and progression in rheumatoid arthritis.

OBJECTIVE: Rheumatoid arthritis (RA)-associated HLA class II genes are assumed to promote susceptibility to and/or progression of the disease. Among the various modes of action proposed so far is the effect of the differential expression of HLA class II genes in different types of antigen-presenting cells on the Th1/Th2 balance. The aim of this study was to investigate the differential expression of genes encoded within the RA-associated HLA-DR4 superhaplotype and within the neutral DR7 and DR9 superhaplotypes. METHODS: The promoters encoded within these 3 haplotypes were first analyzed for sequence polymorphisms. To test for functional consequences, we assumed that the binding of nuclear factors to the promoter elements was correlated with the transcription activity, and we used surface plasmon resonance technology. To that end, oligonucleotides representing the polymorphic regulatory sequences and nuclear extracts from a monocyte cell line and a B cell line were used. RESULTS: While the promoters of the highly polymorphic HLA-DRB1*04, *07, and *09 alleles showed comparable binding of nuclear factors, differential binding was observed for the 2 promoters that drive the relatively nonpolymorphic DRB4 alleles in linkage disequilibrium with DRB1. Interestingly, analysis of RA patients positive for DR4, DR7, and DR9 revealed the segregation of radiographic progression with the stronger of the 2 DRB4 promoters, independent of the DRB1 allele. Moreover, DRB1*04 alleles in RA patients showed a reduced association with the DRB4 splice variant, completely preventing DRB4 expression. CONCLUSION: Our findings represent the first evidence of a correlation between the differential expression of HLA class II genes and both the susceptibility and the progression of RA.

Adult↗
PubMed2003

An empirical bayesian method for differential expression studies using one-channel microarray data.

Gene expression microarrays have become powerful tools in many areas of biological and biomedical research. These technologies allow researchers to measure the expression levels of thousands of genes in a tissue or cell sample simultaneously. One of the most common types of microarray experiments is simply an exploratory study to compare two samples (e.g. tumor and normal tissue) and look for a list of genes that might be differentially expressed between the two. Differential expression is typically measured by computing a t-statistic or similar statistic for each gene. The genes are then ranked according to the absolute value of the t-statistic, and the twenty or fifty best candidates might be studied in follow-up experiments. When sample sizes are small, the t-statistic can be problematic, because variances are estimated poorly and the "top 20" list is often dominated by the genes with the lowest variance estimates. Lönnstedt and Speed (2001) proposed an empirical Bayes method for avoiding this problem, and showed that their approach has lower false positive and false negative rates than t-statistic-based methods. However, their method was designed mainly for the two-channel microarray, which produces paired data. It is not suitable for technologies such as one-channel arrays that produce unpaired data. We propose a simplification for Lönnstedt and Speed's method, and then extend it to unpaired data with two or more independent treatments. We demonstrate our method on both simulated and real data. When the number of replicates is small, gene rankings based on our statistic appear to be much more reliable than rankings based on the t-statistic.

Journal Article↗
PubMed2003

Strategy for elucidating differentially expressed genes in leiomyomata identified by microarray technology.

OBJECTIVE: cDNA microarray technology identifies genes that are differentially expressed between tissues. Our previous study identified several genes that might contribute to the fibroid phenotype. We therefore sought to confirm genes involved in three distinct signal transduction pathways. DESIGN: Evaluation of differential mRNA and protein expression of Dlk, Frizzled-2, and CD-24 in fibroids compared with adjacent myometrium. University hospital. PATIENT(S): Five women undergoing medically indicated hysterectomy for symptomatic fibroids. INTERVENTION(S): Microarray analysis of up to 33000 genes, reverse transcriptase-polymerase chain reaction (RT-PCR), real-time RT-PCR, Western blot, and immunohistochemistry. MAIN OUTCOME MEASURE(S): Expression of mRNA transcripts and protein in fibroid compared with myometrium.A more extensive microarray confirmed differential expression of Frizzled-2 and CD-24 but did not confirm Dlk overexpression. RT-PCR and real-time PCR demonstrated equivalent Dlk mRNA expression between fibroid and myometrium (ratio, 1.02), a slight Frizzled-2 overexpression (ratio, 2.09), and robust CD-24 overexpression in fibroids (ratio, 12.35). Western blot and immunohistochemistry confirmed Frizzled-2 overexpression, but did not confirm Dlk overexpression. CONCLUSION(S): Microarray technology is the first phase of tissue evaluation, but changes in gene expression must be confirmed. Confirmed genes can then be used to generate hypotheses testing their involvement in fibroid development.

Antigens, CD↗
PubMed2004

Identification of membrane proteins differentially expressed in human papillomavirus type 16 E5-transfected human keratinocytes by nanoelectrospray ionization mass spectrometry.

Membrane proteins differentially expressed in human papillomavirus type 16 (HPV-16) E5-transfected HaCaT cells have been identified. Membrane proteins were isolated and separated by two-dimensional gel electrophoresis. Spots showing quantitative differences between E5-transfected and control cells were extracted and the proteins were identified by nanoelectrospray ionization mass spectrometry. A total of 24 spots was analysed. Among the proteins showing differential expression, a decreased amount of calnexin and increased expression of hsp70, proteins both involved in maturation and transport of MHC class I complexes to the plasma membrane, were noticed. These findings correlate with the decreased surface expression of MHC class I molecules described in E5-expressing cells, HPV-positive cervical lesions and cervical carcinomas. These results stress the value of the proteomic approach, as used here in the experimental design, which allows the correlation of changes in host gene expression with biological functions of viral genes.

Histocompatibility Antigens↗
PubMed2006

Elevated levels of phosphorylated fibrinogen-alpha-isoforms and differential expression of other post-translationally modified proteins in the plasma of ovarian cancer patients.

We evaluated the differentially expressed proteins in the plasma of ovarian cancer (OVC) patients using 2-D SDS-polyacrylamide gel electrophoresis (SDS-PAGE) with post-translational modification (PTM) specific stains after the removal of six high-abundance proteins. The pooled plasma from patients with stage III or IV OVC was compared to a pooled postmenopausal age-matched control. Several proteins were identified as differentially expressed in the plasma of OVC patients. Among them, the phosphorylated fibrinogen-alpha-chain isoform (containing fibrinopeptide-A) was found to be up-regulated. Previously in our laboratory, phosphorylated fibrinopeptide-A was found to be up-regulated in the low molecular weight fraction of serum derived from OVC patients. We examined the levels of phosphorylated fibrinogen-alpha-chain in each patient that constituted the pooled plasma using Western blot, mass spectrometry (MS), and PTM specific stains. Phosphoprotein bands containing fibrinogen-alpha-chain fragments showed up-regulation in all OVC patients.

Aged↗
PubMed2002

Isolation of differentially expressed genes from white spot virus (WSV) infected Pacific blue shrimp (Penaeus stylirostris).

To isolate novel cellular factors that are activated or repressed upon WSV infection, the RNA fingerprints of healthy and WSV infected blue shrimp ( Penaeus stylirostris) were compared using the mRNA differential display technique. Thirty-two unique differentially expressed, and one constitutively expressed, cDNA sequences were retrieved. Six of 32 cDNAs showed similarities with the database entries: cDNA 10G32-142 to a shrimp arginine kinase, 22C48-201 to shrimp mitochondrial ATPase gene; 22C47-197, 21G49-203 and 20A55-268 to shrimp ESTs and 20G50-206 to a WSV gene, ORF 116. The constitutively expressed gene showed significant similarity to a yeast elongation factor 1-alpha gene. The expression of a subset of differentially expressed genes (13 of 32) was further evaluated by real-time RT-PCR. Ten of 13 genes showed statistically significant changes in expression between healthy and WSV infected animals suggesting that these genes may play an important role in WSV pathogenesis.

Amino Acid Sequence↗
PubMed2005

Microarray analysis of differentially expressed genes in rat frontal cortex under chronic risperidone treatment.

Long-term administration of antipsychotic drugs can induce differential expression of a variety of genes in the brain, which may underscore the molecular mechanism of the clinical efficacy and/or side effects of antipsychotic drugs. We used cDNA microarray analysis to screen differentially expressed genes in rat frontal cortex under 4 weeks' treatment of risperidone (1 mg/kg). Using real-time quantitative PCR, we were able to verify eight genes, whose expression were significantly upregulated in rat frontal cortex under chronic risperidone treatment when compared with control animals. These genes include receptor for activated protein kinase C, amida, cathepsin D, calpain 2, calcium-independent receptor for alpha-latrotoxin, monoamine oxidase B, polyubiquitin, and kinesin light chain. In view of the physiological function of these genes, the results of our study suggest that chronic risperidone treatment may affect the neurotransmission, synaptic plasticity, and proteolysis of brain cells. This study also demonstrates that cDNA microarray analysis is useful for uncovering genes that are regulated by chronic antipsychotic drugs treatment, which may help bring new insight into the molecular mechanism of antipsychotic drugs.

Animals↗
PubMed2005

The immunomodulatory proteins B7-DC, B7-H2, and B7-H3 are differentially expressed across gestation in the human placenta.

Placental trophoblast cells form a cellular barrier between the potentially immunogenic fetus and maternal leukocytes. Trophoblasts subvert maternal immunity by producing surface-bound and soluble factors that interact with maternal leukocytes. Here, we describe the distribution of three members of the expanding family of B7 immunomodulatory molecules: B7-DC, B7-H2, and B7-H3. B7-DC and B7-H3 inhibit antigen-stimulated lymphocyte activation while B7-H2 serves in a regulatory capacity, often promoting a Th2 immunophenotype. First trimester and term placentas, purified trophoblast cells, choriocarcinoma cell lines, and human umbilical vein endothelial cells were analyzed for B7 family RNA and protein expression. Transcripts and proteins for all three B7s were present throughout gestation but were differentially expressed within the trophoblast and the stroma. Whereas B7-DC was prominent on the syncytiotrophoblast of early placenta, it was absent from the trophoblast at term. In contrast, B7-H2 and B7-H3 were prominent on the extravillous trophoblast throughout gestation. Lastly, stromal cells, including macrophages and endothelial cells, differentially expressed B7-DC, B7-H2, and B7-H3, depending on gestational age. Thus, all three of these newly discovered B7 proteins are differentially positioned at the maternal-fetal interface such that they could steer maternal leukocytes away from a harmful immune response and toward a favorable one.

Antigens, CD↗
PubMed2004

[Detection of differentially expressed genes in hepatocellularcarcinoma cells SMMC-7721 treated with Typhonium giganteum extract by mRNA differential display].

OBJECTIVE: To screen and identify the differentially expressed genes in hepatocellular carcinoma cells SMMC-7721 responsing to the aqueous extract from dried powdered rhizomes of Typhonium giganteum (AEoTGE). METHOD: The response of hepatocellular carcinoma cells SMMC-7721 to AEoTGE was explored with the technique of mRNA differential display. RESULT: After hepatocarcinoma cells SMMC-7721 were treated by AEoTGE for 36 hours, 1 gene expression was upgrade and 1 gene expression was downgrade induced by AEoTGE. CONCLUSION: The research has provided important clues for the molecular mechanism of how hepatocarcinoma cells responseing to T. giganteum.

Araceae↗
PubMed2005

Identification of differentially expressed genes in papillary thyroid carcinomas with and without rearrangements of the tyrosine kinase receptors RET and/or NTRK1.

BACKGROUND: The transforming capacities of RET and/or NTRK1 chimeric oncogenes as well as the molecular background of non-rearranged papillary thyroid carcinomas (PTCs) remain to be elucidated. To assess altered gene expression, we examined PTCs with and without tyrosine kinase receptor rearrangements by mRNA differential display (DD). MATERIALS AND METHODS: Six of 13 PTCs examined harbored RET chimeras (3x RET/PTC1, 1x RET/PTC3) and/or NTRK1 chimeras (2x trk, 1x TRK-T3, 2 unknown TRK hybrids). The method of DD analysis was refined by a novel fragment-recovery technique using a high-performance fluorescence scanner. RESULTS: Of 500 up- or down-regulated mRNA transcripts, 19 selected fragments were recovered, cloned, sequenced, and identified. The accuracy and high degree of reproducibility of the method was demonstrated. Differential expression of gene products with potential association to cell proliferation or tumor progression was observed, such as 14-3-3beta and Rab27a. Moreover, several gene products with unknown functions were demonstrated in PTCs bearing RET or NTRK1 hybrids versus rearrangement-negative PTCs, including a homologue of the Ig kappa light chain constant region. CONCLUSIONS: Candidate transcripts with presumed tumorigenic potential in other solid tumors may prove to be relevant in the progression of PTCs, too. Most promising is the isolation of several differentially expressed, yet unknown, genes that may open new insights in the pathogenesis or progression of PTC.

Adolescent↗
PubMed2005

A robust statistical method for detecting differentially expressed genes.

DNA microarray technology allows researchers to monitor the expressions of thousands of genes under different conditions, and to measure the levels of thousands of different DNA molecules at a given point in the life of an organism, tissue or cell. A wide variety of different diseases that are characterised by unregulated gene expression, DNA replication, cell division and cell death, can be detected early using microarrays. One of the major objectives of microarray experiments is to identify differentially expressed genes under various conditions. The detection of differential gene expression under two different conditions is very important in biological studies, and allows us to identify experimental variables that affect different biological processes. Most of the tests available in the literature are based on the assumption of normal distribution. However, the assumption of normality may not be true in real-life data, particularly with respect to microarray data.A test is proposed for the identification of differentially expressed genes in replicated microarray experiments conducted under two different conditions. The proposed test does not assume the distribution of the parent population; thus, the proposed test is strictly nonparametric in nature. We calculate the p-value and the asymptotic power function of the proposed test statistic. The proposed test statistic is compared with some of its competitors under normal, gamma and exponential population setup using the Monte Carlo simulation technique. The application of the proposed test statistic is presented using microarray data. The proposed test is robust and highly efficient when populations are non-normal.

Journal Article↗
PubMed2005

[Study on differentially expressed genes of ulcerative colitis in the rat treated by herbs-partitioned moxibustion].

OBJECTIVE: To probe the mechanism of herbs-partitioned moxibustion for treatment of ulcerative colitis. METHODS: The rats with ulcerative colitis were randomly divided into 3 groups, normal control group, model group, and herbs-partitioned moxibustion group. The rats in the herbs-partitioned moxibustion group were treated by herbs-partitioned moxibustion at bilateral Tianshu (ST 25). BiostarR-40s gene chip was applied to detect the differentially expressed gene of their colonic tissues and fluorescence quantitative polymerase chain reaction was employed to confirm the results of the microarray analysis with interleukin-1 beta messenger RNA (IL-1beta mRNA) expression. RESULTS: Of 174 differential expression genes identified, 28 genes (including 7 known genes) elevated in rats of ulcerative colitis were down-regulated and 146 genes (including 42 known genes) reduced in the rat of ulcerative colitis were up-regulated after herbs-partitioned moxibustion treatment. CONCLUSION: Many abnormally expressed genes are involved in occurrence of ulcerative colitis and herbs-partitioned moxibustion can regulate expression of IL-1beta and other genes to exert therapeutic effect.

Animals↗
PubMed1989

Differential expression of members of a cyanobacterial psbA gene family in response to light.

The genome of the cyanobacterium Synechococcus sp. strain PCC 7942 contains three psbA genes encoding two forms of the D1 protein: form I, the product of psbAI, differs from form II, the product of both psbAII and psbAIII, at 25 of 360 residues. D1 is essential for photosynthesis as a core component of the photosystem II reaction center. Translational gene fusions between each of the Synechococcus psbA genes and the Escherichia coli lacZ gene were inserted into the chromosome of wild-type Synechococcus sp. at the respective psbA loci to serve as in vivo reporters of psbA expression. beta-Galactosidase activities indicated differential expression of the psbA-lacZ gene fusions related to light availability. Expression of psbAI was 500-fold greater than expression of psbAII and 50-fold greater than psbAIII under similar conditions. As light intensity decreased from 600 microE.m-2.s-1 to 2 microE.m-2.s-1, expression of the psbAI reporter increased eightfold while expression of the psbAII and psbAIII reporters decreased 10-fold, suggesting differential production of the two forms of D1 in photosystem II in response to light availability. Relative levels of psbA-lacZ fusion transcripts directly reflected beta-galactosidase activities in the transformants, although the fusion transcripts were less stable than native psbA messages.

Chlorophyll↗