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Results for “differential expression”

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PubMed2004

Differential expression of the chitin synthase genes of Aspergillus nidulans, chsA, chsB, and chsC, in response to developmental status and environmental factors.

To understand the role of the chitin synthase genes of Aspergillus nidulans, we analyzed the expression of chsA, chsB, and chsC both by Northern blotting and by a vital reporter system with sgfp encoding a modified version of green fluorescent protein, sGFP. chsA was expressed specifically during asexual differentiation, but not during either vegetative growth or sexual differentiation. The expression of chsB was ubiquitous throughout the fungal body and relatively independent of the change in developmental status of the cells. chsC was expressed moderately during sexual development as well as during the early phase of vegetative growth, but was expressed weakly in old vegetative mycelia and in asexual structures. Furthermore its expression was spatially differentiated, i.e., relatively strong in young cleistothecia and in mature ascospores, but negligible in Hülle cells. Osmostress caused by high concentrations (up to 1.2M) of KCl or NaCl stimulated the expression of chsA and chsC, but not that of chsB. Sodium acetate, especially at high concentration (3%), strongly enhanced the expression of all the three genes. Neither heat shock nor the sugar carbon sources tested (glucose, sucrose, or lactose) affected the expression of any of the three chitin synthase genes.

Aspergillus nidulans↗
PubMed2005

Differential expression of chlamydial signal transduction genes in normal and interferon gamma-induced persistent Chlamydophila pneumoniae infections.

Characteristic features of the persistent chlamydial developmental cycle, associated with chronic infections in both humans and animals, include the generation of non-replicative, morphologically aberrant bodies which are distinct from normal propagating reticulate bodies. Previous studies have correlated these morphological and metabolic changes with differential expression of diverse functional subsets of chlamydial genes. To further investigate these correlations, we compared mRNA expression of predicted chlamydial signal transduction genes between normal Chlamydophila pneumoniae A-03 infections in HEp-2 cells and those treated with gamma interferon (IFN-gamma) by using real-time RT-PCR. Inspection of the Cp. pneumoniae genome revealed at least 39 candidate signal transduction genes, of which 30 were differentially expressed in Cp. pneumoniae mediated persistence. Functional sub-groups of differentially expressed signal transduction genes include chlamydial GTPases (hflX, ychF, yhbZ and yphC), linked to bacterial cellular processes such as cell cycle control and ribosome assembly and stability. Other up-regulated signal transduction genes sharing similarity to bacterial stress response genes (htrA, surE, lytB and hrcA) were also detected. The transcriptional changes observed for the majority of signal transduction genes appear to be unique for Cp. pneumoniae, as similar changes were not observed in recent whole genomic analysis of C. trachomatis IFN-gamma mediated persistence. These results suggest that chlamydial signal transduction genes play potentially important roles in the establishment and maintenance of Cp. pneumoniae persistence, likely as part of the IFN-gamma response stimulon as described for C. trachomatis, but with considerable differences in the transcriptional profile.

Cell Line↗
PubMed2004

[Analysis of differentially expressed lung metastasis-associated proteins in adenoid cystic carcinoma cell lines].

OBJECTIVE: To analyze differentially expressed metastasis-associated proteins in Adenoid cystic carcinoma cell lines of human salivary gland by proteomics. METHODS: Protein expression alterations of ACC-2 and ACC-M cells were described by 2-D gels. After image analysis by software, proteins of interest were excised from the gels and identified by matrix assisted laser desorption ionization time-of-flight mass spectrometer. RESULTS: 12 protein spots showed significantly differential expression patterns between two cell lines. In the identified protein candidates, transketolase, modulator recognition factor 2, Dim1p homolog, splicing factor (arginine/serine-rich 9) and v-Ha-ras l oncogene were all lowly expressed in the poorly metastatic ACC-2 cell and significantly upregulated in highly metastatic ACC-M cell, while type I collagen pro alpha and tumor necrosis factor (ligand) superfamily member 4 showed a high expression in ACC-2 cells and a low expression in ACC-M cells. Pirin (spot 6) just appears in ACC-2 cell and was not detectable in ACC-M cell, while retinal homeobox protein was just detected in ACC-M cell and did not appear in ACC-2 cell. CONCLUSIONS: The proteins may be involved in the adenoid cystic carcinoma lung metastasis through different mechanisms. Our work may contribute to discover diagnostic markers and therapeutic targets.

Carcinoma, Adenoid Cystic↗
PubMed2001

Cloning of differentially expressed genes in an HIV-1 resistant T cell clone by rapid subtraction hybridization, RaSH.

An HIV-1 resistant T cell clone R1c2 has been generated that carries mutant, latent HIV-1 in a minority of the cell population. Resistant cells express HIV-1 receptors CD4 and CXCR4 and display resistance to infection by wild type (wt) HIV-1 at the level of virus transcription. To begin to define the repertoire of genes modulated in R1c2 cells that correlate with and potentially control expression of the HIV-1 resistance phenotype we have employed a rapid subtraction hybridization (RaSH) technique. For this approach, cDNA libraries were prepared from double-stranded cDNAs that were enzymatically digested into small fragments, ligated to adapters, PCR amplified followed by incubation of tester and driver PCR fragments. The RaSH scheme resulted in the cloning of genes displaying differential expression between HIV-1 resistant (R1c2) and susceptible (SupT1) cells, including known genes and those not described in current DNA databases. Analysis of the pattern of expression of the differentially expressed genes documented eleven genes with enhanced (HR clones) and six genes with reduced (HS clones) expression in HIV-1 resistant versus HIV-1 susceptible T-cell clones.

Cell Line↗
PubMed2001

Detection of differentially expressed genes in HeLa x fibroblast hybrids using subtractive suppression hybridization.

To understand genetic differences and similarities between tumorigenic and nontumorigenic HeLa x fibroblast hybrid cells, subtractive suppression hybridization (SSH), based on suppression PCR and a combination of normalization and subtraction in a single procedure, was used. Using the nontumorigenic CGL1 and tumorigenic CGL3, forward (CGL1-CGL3) and reverse (CGL3-CGL1) subtracted libraries were constructed. Among 192 clones, seven were identified as differentially expressed genes specific for either CGL1 or CGL3. All seven were not reported previously as differentially expressed genes in this hybrid system. In the forward subtraction, p16 was isolated, indicating the involvement of the loss of tumorigenic phenotype. Subsequent transfection of wild-type p16 to the tumorigenic CGL3 showed growth suppression in colony formation assay; however, no tumor suppression was observed when the transfectant was inoculated into nude mice. These results indicate that: (a) SSH is a suitable method to identify differentially expressed genes in two types of cells; and (b) although p16 plays some roles in growth suppression, the p16-transfected CGL3 is still capable to proliferate in vivo.

Animals↗
PubMed1994

Differential expression of cyclophilin isoforms during keratinocyte differentiation.

Cyclophilin A, the major intracellular binding protein for the immunosuppressive drug cyclosporin A (CsA), was studied in human keratinocytes during differentiation both in vivo and in vitro. Analysis of cyclophilin by gel-filtration radiobinding-assay with tritiated CsA showed one specific radioactive peak at 17 kDa. By this technique, the levels of cyclophilin (mean 55.23 +/- 8.43 pmol/mg protein) did not significantly differ during keratinocyte differentiation. When the protein extracts from calcium-induced differentiating keratinocytes and normal human skin were analysed by PAGE radiobinding-assay, two specific radioactive CsA-binding peaks were detected. The major peak (RF 0.13) was expressed in all samples (mean 47.32 +/- 17.53 pmol/mg protein) whereas the minor peak (RF 0.23) was dramatically decreased about 6-fold in abnormally differentiated skin (psoriasis) as well as in non-differentiated keratinocytes. At least six [3H]CsA-binding isoforms with pI values ranging from 5.58 to 7.75 were detected by isoelectrofocusing autoradio-blotting-assay in normal human skin; three of them immunoreacted with antibodies to cyclophilin. These results demonstrated the presence of several cyclophilin isoforms in human epidermal cells and an expression which correlated with the differentiation of human keratinocytes both in vivo and in vitro.

Amino Acid Isomerases↗
PubMed2006

Genes differentially expressed in oropharyngeal tonsils and mandibular lymph nodes of tuberculous and nontuberculous European wild boars naturally exposed to Mycobacterium bovis.

Bovine tuberculosis, caused by Mycobacterium bovis (Mycobacterium tuberculosis complex), is a zoonotic disease that affects cattle worldwide. The bacterium infects other animal species, both domesticated and wild, and this range of hosts complicates attempts to control or eradicate the disease. Despite advances in the characterization of the mechanisms involved in host-pathogen interactions and host cell responses to M. tuberculosis complex in human, bovine and mouse cells, differentially expressed genes in tissue biopsies of naturally occurring tuberculous and nontuberculous exposed individuals have been poorly characterized. In this study, differential gene expression was analysed using suppression-subtractive hybridization in oropharyngeal tonsils and mandibular lymph nodes of field-collected tuberculous and nontuberculous European wild boars from a tuberculosis-endemic area of Spain. Real-time PCR and semiquantitative reverse-transcriptase PCR of selected genes confirmed the results of the suppression-subtractive hybridization analysis. Protein expression of selected differentially expressed genes was analysed by radial immunodiffusion or immunohistochemistry. Differential gene expression varied among tuberculous and non-tuberculous groups and between tonsils and lymph nodes. Single and multiple cellular mechanisms were affected, including signal transduction, immune response, inflammation, stress, apoptosis/antiapoptosis, cell structure, adhesion and transport, protein and DNA/RNA metabolism and enzymatic processes. These results demonstrate the modulation of gene expression by mycobacterial infection in tonsils and mandibular lymph nodes of European wild boars naturally exposed to M. bovis, and provide a basis for defining host-pathogen interactions and the mechanism of protective immunity.

Animals↗
PubMed2003

Differentially expressed genes in the liver of thioacetamide treated rats.

Thioacetamide is a hepatotoxic and hepatocarcinogenic compound that affects liver metabolism, inhibits mRNA transport and induces enlargement of the nucleolus. To investigate the effect of thioacetamide at the molecular level, differential display RT-PCR was conducted. Analysis of nineteen differentially expressed genes demonstrated that ten cDNAs have their expression inhibited while the other nine were positively affected by thioacetamide. Two of the cDNAs were homologous to known genes-TAP and ankyrin-binding glycoprotein-1, two corresponded to repetitive sequences and seven were homologous to expressed sequence tags. The differential expression of some of the isolated cDNAs was confirmed by northern hybridization. It is proposed that since the product of TAP is involved in mRNA transport, thioacetamide inhibition of TAP expression might, at least partially, explain the thioacetamide-induced swelling of the nucleolus.

Animals↗
PubMed2002

Multivariate approach for selecting sets of differentially expressed genes.

An important problem addressed using cDNA microarray data is the detection of genes differentially expressed in two tissues of interest. Currently used approaches ignore the multidimensional structure of the data. However it is well known that correlation among covariates can enhance the ability to detect less pronounced differences. We use the Mahalanobis distance between vectors of gene expressions as a criterion for simultaneously comparing a set of genes and develop an algorithm for maximizing it. To overcome the problem of instability of covariance matrices we propose a new method of combining data from small-scale random search experiments. We show that by utilizing the correlation structure the multivariate method, in addition to the genes found by the one-dimensional criteria, finds genes whose differential expression is not detectable marginally.

Algorithms↗
PubMed2005

The influence of missing value imputation on detection of differentially expressed genes from microarray data.

MOTIVATION: Missing values are problematic for the analysis of microarray data. Imputation methods have been compared in terms of the similarity between imputed and true values in simulation experiments and not of their influence on the final analysis. The focus has been on missing at random, while entries are missing also not at random. RESULTS: We investigate the influence of imputation on the detection of differentially expressed genes from cDNA microarray data. We apply ANOVA for microarrays and SAM and look to the differentially expressed genes that are lost because of imputation. We show that this new measure provides useful information that the traditional root mean squared error cannot capture. We also show that the type of missingness matters: imputing 5% missing not at random has the same effect as imputing 10-30% missing at random. We propose a new method for imputation (LinImp), fitting a simple linear model for each channel separately, and compare it with the widely used KNNimpute method. For 10% missing at random, KNNimpute leads to twice as many lost differentially expressed genes as LinImp. AVAILABILITY: The R package for LinImp is available at http://folk.uio.no/idasch/imp.

Algorithms↗
PubMed2002

Differential expression of inducible nitric oxide synthase is associated with differential Toll-like receptor-4 expression in chicken macrophages from different genetic backgrounds.

The purpose of this study was to examine iNOS gene expression and activity in macrophages from different chicken genetic lines against various bacterial LPS. Furthermore, the possible involvement of surface LPS receptors as candidates for differential iNOS gene induction in these genetic lines of chicken was also examined. Sephadex-elicited abdominal macrophages (1 x 10(6)) as well as iNOS hyper-responder macrophages from a transformed chicken macrophage cell line, MQ-NCSU, were exposed to 5 microg/ml LPS from E. coli, Shigella flexneri, Serratia marcensces, and Salmonella typhimurium. Nitrite levels were quantitated in the culture supernatant fractions of macrophages after 24h by the Griess method. The results showed that macrophages from K-strain (B(15)B(15)) (range from two separate trials: 31-89 microM) and MQ-NCSU (22-81 microM) were high responders whereas macrophages from both GB1 (B(13)B(13)) (15-38 microM) and GB2 (B(6)B(6)) (7-15 microM) chickens were low responders against all LPSs used. Northern blot analysis revealed that K-strain macrophages expressed higher intensity of 4.5Kb iNOS mRNA (iNOS/beta-actin ratio) than macrophages from GB2 regardless of the LPS source. To elucidate possible molecular mechanism(s) involved in iNOS gene expression in these two strains of chickens, the constitutive expression of LPS-related macrophage cell surface receptors, CD14, Toll-like receptor-2 (TLR2), and Toll-like receptor-4 (TLR4), was examined via flow cytometry using anti-human CD14, TLR2 and TLR4 antibodies. CD14 surface expression and intensity was not different between macrophages from K-strain or GB2 chickens. In contrast, while the overall percentage of TLR4-positive macrophages was the same (K-strain, trial 1=92%, trial 2=62%; GB2, trial 1=91%, trial 2=64%), the mean fluorescence intensity (MFI), an indicator of receptor number, was significantly higher (P=0.05) in K-strain macrophages (MFI: trial 1=145; trial 2=131) than GB2 macrophages (MFI: trial 1=101; trial 2=98). Furthermore, TLR2 (a previously thought candidate as LPS signaling molecule) positive cell numbers were higher in K-strain than the GB2 macrophages in one of the two trials with no difference in the intensity of TLR2 expression in either trial. These findings suggest that the observed differences in iNOS expression and activity among the K-strain (hyper-responder) and GB2 (hypo-responder) chickens are, at least in part, due to differential expression of TLR4 (an LPS signaling molecule), leading to more intense LPS-mediated activation of K-macrophages.

Animals↗
PubMed2002

Differentially expressed genes associated with mouse lung tumor progression.

To detect altered gene expression associated with mouse lung tumor progression, we compared the gene expression profile of lung adenocarcinomas with that of lung adenomas and normal lungs. Autoradiographic analysis showed that among the 588 genes surveyed, 152 genes were detected and the remaining 436 genes did not give any signals. A gene-specific semiquantitative reverse transcription polymerase chain reaction method was used to confirm the expression profile. A total of 29 genes was found to be differentially expressed in mouse lung tumors when compared to normal lungs. The pattern of expression, either underexpression or overexpression, was the same for 10 genes between adenocarcinomas and adenomas. Among them, seven genes were overexpressed, two genes were underexpressed and one gene was lost. Interestingly, 19 genes showed differential expression or increased incidence or difference in level of change between lung adenomas and adenocarcinomas, including Stat1, ADAP, IGFBP-6, PDGF-A, TGF-beta2, Int-3, VEGFR2, BAX, BAG-1, c-Jun, FasL, TRAIL, YB-1, CD31, Cdc42, B-raf, Rab-2, Abi-1, and ACE. These genes can be designated as candidate 'lung tumor progression' (LTP) genes because their expression changes may specifically affect lung tumor progression in mice. Further analyses of these candidate LTP genes may provide new leads for elucidation of lung tumor progression in mice.

Adenocarcinoma↗
PubMed1989

Differential expression of the receptors for epidermal growth factor and insulin in the developing human placenta.

The detailed cellular distribution of epidermal growth factor (EGF) receptors and insulin receptors during the development of the human placenta was examined. We show that EGF receptors are expressed by villous cytotrophoblast cells in first trimester human placentae. However, where these cells proliferate to form extravillous cytotrophoblast cell columns, there is a dramatic decrease in EGF receptor expression. There is no such differential expression of insulin receptors on this cell population. In contrast, both EGF-and insulin-receptors are present throughout gestation on the microvillous membrane of the terminally differentiated and non-proliferative syncytiotrophoblast although, at term, EGF-but not insulin-receptors are also found on the basolateral membrane of this epithelium. We further show that EGF receptors isolated from first trimester and term human placentae have functional tyrosine kinase activities but differ in their extent of glycosylation. These results suggest that EGF receptors probably play several distinct functional roles in these epithelial cells depending on their proliferative capacity and differentiation status.

Adenosine Triphosphate↗
PubMedDate not supplied

Identification and quantification of differentially expressed proteins in E-cadherin deficient SCC9 cells and SCC9 transfectants expressing E-cadherin by dimethyl isotope labeling, LC-MALDI MS and MS/MS.

A strategy based on isotope labeling of peptides and liquid chromatography matrix-assisted laser desorption ionization mass spectrometry (LC-MALDI MS) has been employed to accurately quantify and confidently identify differentially expressed proteins between an E-cadherin-deficient human carcinoma cell line (SCC9) and its transfectants expressing E-cadherin (SCC9-E). Proteins extracted from each cell line were tryptically digested and the resultant peptides were labeled individually with either d(0)- or d(2)-formaldehyde. The labeled peptides were combined and the peptide mixture was separated and fractionated by a strong cation exchange (SCX) column. Peptides from each SCX fraction were further separated by a microbore reversed-phase (RP) LC column. The effluents were then directly spotted onto a MALDI target using a heated droplet LC-MALDI interface. After mixing with a MALDI matrix, individual sample spots were analyzed by MALDI quadrupole time-of-flight MS, using an initial MS scan to quantify the dimethyl labeled peptide pairs. MS/MS analysis was then carried out on the peptide pairs having relative peak intensity changes of greater than 2-fold. The MS/MS spectra were subjected to database searching for protein identification. The search results were further confirmed by comparing the MS/MS spectra of the peptide pairs. Using this strategy, we detected and compared relative peak intensity changes of 5480 peptide pairs. Among them, 320 peptide pairs showed changes of greater than 2-fold. MS/MS analysis of these changing pairs led to the identification of 49 differentially expressed proteins between the parental SCC9 cells and SCC9-E transfectants. These proteins were determined to be involved in different pathways regulating cytoskeletal organization, cell adhesion, epithelial polarity, and cell proliferation. The changes in protein expression were consistent with increased cell-cell and cell-matrix adhesion and decreased proliferation in SCC9-E cells, in line with E-cadherin tumor suppressor activity. Finally, the accuracy of the MS quantification and subcellular localization for 6 differentially expressed proteins were validated by immunoblotting and immunofluorescence assays.

Amino Acid Sequence↗
PubMed2004

Differential expression of TGF-beta isoforms during differentiation of HaCaT human keratinocyte cells: implication for the separate role in epidermal differentiation.

The three mammalian isoforms of transforming growth factor-beta(TGF-beta1, beta2, beta3) are potent regulators of cell growth, differentiation, and extracellular matrix deposition. To study their role in skin differentiation, we investigated the expression of TGF-beta isoforms on cell growth and differentiation induction of the human keratinocyte cell line, HaCaT by elevating the Ca(2+) concentration. An ELISA and RT-PCR assay revealed secreted TGF-beta 1 protein and TGF-beta 1 mRNA were increased during calcium-induced differentiation. In contrast, major differences were seen for TGF-beta 2 and TGF-beta 3 mRNA which were decreased during differentiation, but TGF-beta 2 and TGF-beta3 protein were not evident on an ELISA. These results suggest different functions for each TGF-beta isoforms in epidermal differentiation, such that TGF-beta 1 is associated with the more differentiated state, and TGF-beta 2 and TGF-beta 3 may be associated the more proliferated state.

Cell Differentiation↗
PubMed1993

Differential expression of a human sperm-specific isozyme in seminoma cells transplanted in Scid-nu(str) mice.

An isozyme of human sperm-specific lactate dehydrogenase, LDH-X (C4) (EC 1.1.1.27), which is expressed only in differentiated germ cells (spermatozoa, spermatids and primary spermatocytes after midpachytene), appeared in the xenografted tumor cells of human seminoma and its metastatic lesions (lymph node and kidney) in scid (severe combined immunodeficiency)-nude(streaker) double mutant mice, though it was not expressed in the original tumor of the patient. The morphological pattern of seminoma cells also changed in the xenografts and metastatic lesions as in normal spermatogenesis. Thus, the human seminoma cells showed differential expression of the sperm-specific isozyme in parallel with their morphological changes. However, the sperm-specific isozyme disappeared in the mitotically dividing seminoma cells which were newly established from the LDH-X positive xenograft.

Adult↗
PubMed2001

Differential expression of 14 genes in amyotrophic lateral sclerosis spinal cord detected using gridded cDNA arrays.

In order to obtain insight into the aetiology and pathogenesis of amyotrophic lateral sclerosis (ALS), high-density gene discovery arrays (GDA human version 1.2) containing 18 400 non-redundant EST cDNAs pooled from different tissue libraries have been used to monitor gene expression in lumbar spinal cord from ALS cases compared with controls. Quantitative filter analysis revealed differential expression of cDNAs normalized to internal standards. These candidates have been further investigated and their expression in spinal cord characterized in a panel of ALS and control subjects. Significant differential expression was obtained for 14 genes, 13 being elevated (up to six-fold) and one decreased (by 80%) in ALS. Amongst those elevated in ALS were thioredoxin and glial fibrilary acid protein, which have already been shown to be up-regulated in ALS, thus supporting the reliability of this approach. The other differentially regulated transcripts confirmed in the expression studies represent potential candidates in ALS pathogenesis being involved in antioxidant systems, neuroinflammation, the regulation of motor neurone function, lipid metabolism, protease inhibition and protection against apoptosis. The use of the GDA system has greatly facilitated the screening and retrieval of sequence information and has generated useful information on the cascade of molecular events occurring in ALS and potentially may highlight new candidates playing a role in the aetiology and progression of this disease.

Adolescent↗
PubMed2003

Improved detection of differentially expressed genes in microarray experiments through multiple scanning and image integration.

The variability of results in microarray technology is in part due to the fact that independent scans of a single hybridised microarray give spot images that are not quite the same. To solve this problem and turn it to our advantage, we introduced the approach of multiple scanning and of image integration of microarrays. To this end, we have developed specific software that creates a virtual image that statistically summarises a series of consecutive scans of a microarray. We provide evidence that the use of multiple imaging (i) enhances the detection of differentially expressed genes; (ii) increases the image homogeneity; and (iii) reveals false-positive results such as differentially expressed genes that are detected by a single scan but not confirmed by successive scanning replicates. The increase in the final number of differentially expressed genes detected in a microarray experiment with this approach is remarkable; 50% more for microarrays hybridised with targets labelled by reverse transcriptase, and 200% more for microarrays developed with the tyramide signal amplification (TSA) technique. The results have been confirmed by semi-quantitative RT-PCR tests.

False Negative Reactions↗