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Expression Values (expression + value)
Selected AbstractsLow expression of XIAP-associated factor 1 in human colorectal cancersJOURNAL OF DIGESTIVE DISEASES, Issue 1 2005Tian Le MA OBJECTIVE: Eight cellular homologs of the inhibitors-of-apoptosis proteins (IAP) have been identified in humans and of them, the X-linked IAP (XIAP) is the most potent. XIAP-associated factor 1 (XAF1) is a newly discovered XIAP-binding protein that negatively regulates the caspase-inhibiting activity of XIAP. It is either not expressed or present at extremely low levels in many cancer cell lines. The aims of the present study were: (i) to investigate the expression of XAF1 in human colorectal cancers (CRC) both in vitro and in vivo, and (ii) to evaluate the possibility of XAF1 as a new tumor marker. METHODS: The expression of XAF1 in four human colon cancer cell lines (Colo205, Colo320, SW1116, LoVo) and in samples from 70 patients with CRC was analyzed by reverse transcriptase-polymerase chain reaction. XAF1 concentrations were also detected in the peripheral circulation of the 70 patients, as well as three traditional circulating cancer-associated antigens. RESULTS: A low concentration of XAF1 mRNA was detectable in the three colon cancer cell lines other than Colo205, which showed the strongest expression of XAF1. The expression of XAF1 in tissue was relatively lower in primary CRC compared with a relatively higher level in benign colorectal tumors (P < 0.01). Although the XAF1 expression in circulation of those with CRC was also lower than in those with benign tumors, there was no statistical significance (P > 0.05). CONCLUSIONS: The present results suggest that the low expression of XAF1 in tumor tissue coincides with a similar level in the peripheral circulation, which contributes at least part to the malignant behavior of CRC. Integrating the XAF1 relative expression value with the other three traditional tumor biomarkers created a four-parameter assay that significantly improved the rate of diagnosis of CRC. [source] Prognostic significance of CD38 and CD20 expression as assessed by quantitative flow cytometry in chronic lymphocytic leukaemiaBRITISH JOURNAL OF HAEMATOLOGY, Issue 6 2003Eric D. Hsi Summary. CD38 expression on chronic lymphocytic leukaemia (CLL) cells is a poor prognostic factor, however, methods for measuring this vary. The QuantiBRITETM flow cytometry (FC) system yields an absolute antigen expression value (antibodies bound/cell, ABC) and may be useful in standardizing CD38 expression analysis. We evaluated cryopreserved pretreatment CLL cells for CD20 ABC, CD38 ABC, and percentage of CD38+ B cells from 131 patients requiring therapy. The 92 patients (70%) with , 100 CD38 ABC had worse overall survival (OS; 34% at 5 years) compared with those with <,100 CD38 ABC (70% at 5 years, mortality hazard ratio 2·30, 95% confidence interval 1·28,4·12; two-tailed P = 0·003). Among the 64 patients with <,30% CD38+ cells, OS of the 25 with , 100 ABC was worse than that of the 39 with <,100 ABC (P = 0·018). OS of patients with <,30% CD38+ cells and , 100 ABC was actually similar to that of patients with , 30% CD38+ cells. BrightCD20 expression (, 20 000 ABC) was not associated with a worse OS (P = 0·10). The presence of , 100 CD38 ABC in CLL patients requiring therapy is an unfavourable prognostic factor for OS and quantitative FC may be superior to percentage CD38+ cell assessment. Prospective trials are required to determine more precisely the prognostic significance of absolute expression levels in fresh CLL cells. [source] Time course analysis of gene expression during light-induced photoreceptor cell death and regeneration in albino zebrafishDEVELOPMENTAL NEUROBIOLOGY, Issue 8 2007Sean C. Kassen Abstract Constant intense light causes apoptosis of rod and cone photoreceptors in adult albino zebrafish. The photoreceptors subsequently regenerate from proliferating inner nuclear layer (INL) progenitor cells that migrate to the outer nuclear layer (ONL) and differentiate into rods and cones. To identify gene expression changes during this photoreceptor regeneration response, a microarray analysis was performed at five time points during the light treatment. The time course included an early time point during photoreceptor death (16 h), later time points during progenitor cell proliferation and migration (31, 51, and 68 h) and a 96 h time point, which likely corresponds to the initial photoreceptor differentiation. Mean expression values for each gene were calculated at each time point relative to the control (0 h light exposure) and statistical analysis by one-way ANOVA identified 4567 genes exhibiting significant changes in gene expression along the time course. The genes within this data set were clustered based on their temporal expression patterns and proposed functions. Quantitative real-time PCR validated the microarray expression profiles for selected genes, including stat3 whose expression increased markedly during the light exposure. Based on immunoblots, both total and activated Stat3 protein expression also increased during the light treatment. Immunolocalization of Stat3 on retinal tissue sections demonstrated increased expression in photoreceptors and Müller glia by 16 h of light exposure. Some of the Stat3-positive Müller cells expressed PCNA at 31 h, suggesting that Stat3 may play a role in signaling a subset of Müller cells to proliferate during the regeneration response. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007. [source] SNP discovery, expression and association analysis for the SDHD gene in pigsJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2007S.E.F. Guimaraes Summary The SDHD gene was examined for single nucleotide polymorphisms (SNP) as well as for expression changes in the Longissimus dorsi muscle of commercial pigs with different potential for growth. Three SNPs, including one previously described in the coding region and two new ones in the 3,-UTR, were found. The normalized expression of SDHD was correlated with growth, meat quality and sensory traits (p < 0.05). For the commercial pigs used in this study, as well as a Berkshire × Yorkshire resource population, the SNPs have been associated (p < 0.05) with: growth, carcass composition, meat quality and sensory traits. Despite the fact that the described SNPs were not significantly associated with the normalized expression values, the SDHD SNPs and expression were associated with growth and meat quality traits in pigs. [source] Gene expression normalization in a dual-compartment system: a real-time quantitative polymerase chain reaction protocol for symbiotic anthozoansMOLECULAR ECOLOGY RESOURCES, Issue 2 2009ANDERSON B. MAYFIELD Abstract Traditional real-time quantitative polymerase chain reaction protocols cannot be used accurately with symbiotic organisms unless the relative contribution of each symbiotic compartment to the total nucleic acid pool is known. A modified ,universal reference gene' protocol was created for reef-building corals and sea anemones, anthozoans that harbour endosymbiotic dinoflagellates belonging to the genus Symbiodinium. Gene expression values are first normalized to an RNA spike and then to a symbiont molecular proxy that represents the number of Symbiodinium cells extracted and present in the RNA. The latter is quantified using the number of genome copies of heat shock protein-70 (HSP70) amplified in the real-time quantitative polymerase chain reaction. Gene expression values are then normalized to the total concentration of RNA to account for differences in the amount of live tissue extracted among experimental treatments and replicates. The molecular quantification of symbiont cells and effect of increasing symbiont contributions to the nucleic acid pool on gene expression were tested in vivo using differentially infected sea anemones Aiptasia pulchella. This protocol has broad application to researchers who seek to measure gene expression in mixed organism assemblages. [source] Activation of human T lymphocytes under conditions similar to those that occur during exposure to microgravity: A proteomics studyPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 7 2005Angela Risso Abstract A number of experiments, conducted under microgravity conditions, i.e. in space shuttle biolaboratories or in ground based systems simulating the conditions occurring in microgravity, show that in hypogravity, in vitro human lymphocyte activation is severely impaired. However, very early stimulation steps of T lymphocytes are not compromised, since CD69 receptor, the earliest membrane activation marker, is expressed by T cells at a level comparable to that observed on 1 g activated lymphocytes. Since CD69 engagement, together with submitogenic doses of phorbol esters, transduces an activation signal to T lymphocytes, we undertook a comparative study on the stimulation mediated through this receptor on human CD3+ cells cultured under conditions similar to those which occur during exposure to microgravity, i.e. in clinorotation, or at 1 g. During the early hours of activation, increased levels of intracellular calcium and increased mitochondrial membrane potential were detectable in clinorotating as well as in 1 g cells. However, after 48 hours clinorotation, interleukin 2 production by T lymphocytes was significantly reduced and cell proliferation was greatly decreased. By means of a differential proteomics approach on T cells activated in clinorotation or at 1 g for 48 hours, we were able to detect statistically significant quantitative protein alterations. Seven proteins with modified expression values were identified; they are involved in nucleic acids processing, proteasome regulation and cytoskeleton structure. [source] Gene expression of cytokine receptors in HL60 cells exposed to a 50 Hz magnetic fieldBIOELECTROMAGNETICS, Issue 5 2002Jiliang Zhou Abstract The effects of a 50 Hz extremely low frequency (ELF) sinusoidal magnetic field (MF) on the expression of genes relating to cytokine receptors were studied in HL60 cells. Transcription levels of tumor necrosis factor receptor (TNFR) p55 and p75, interleukin-6 receptor-, (IL-6R,) and transforming growth factor-, receptor 1 (TGF,R1) were quantified in cells exposed to an intensity of 0.1 or 0.8 mT for periods ranging from 30 min to 72 h. Cells treated with 10 nM of phorbol 12-myristate 13-acetate (PMA) for 8 h served as a positive control. Gene expression values were assessed by the ribonuclease protection assay (RPA) and normalized to those of the noninducible gene GAPDH. The results showed that MF exposure at 0.1 and 0.8 mT for 72 h increased TNFR p75 and IL-6R, mRNA expression in HL60 cells. No significant change in gene expression levels of TNFR p55 and TGF,R1 was observed under any of the exposure conditions. In addition, we report here for the first time that IL-6R, mRNA expression can be suppressed by PMA in HL60 cells. Bioelectromagnetics 23:339,346, 2002. © 2002 Wiley-Liss, Inc. [source] Efficiency of Functional Regression Estimators for Combining Multiple Laser Scans of cDNA MicroarraysBIOMETRICAL JOURNAL, Issue 1 2009C. A. Glasbey Abstract The first stage in the analysis of cDNA microarray data is estimation of the level of expression of each gene, from laser scans of hybridised microarrays. Typically, data are used from a single scan, although, if multiple scans are available, there is the opportunity to reduce sampling error by using all of them. Combining multiple laser scans can be formulated as multivariate functional regression through the origin. Maximum likelihood estimation fails, but many alternative estimators exist, one of which is to maximise the likelihood of a Gaussian structural regression model. We show by simulation that, surprisingly, this estimator is efficient for our problem, even though the distribution of gene expression values is far from Gaussian. Further, it performs well if errors have a heavier tailed distribution or the model includes intercept terms, but not necessarily in other regions of parameter space. Finally, we show that by combining multiple laser scans we increase the power to detect differential expression of genes. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Correlative analysis of gene expression profile and prognosis in patients with gliomatosis cerebriCANCER, Issue 16 2009Oscar Fernando D'Urso PhD Abstract BACKGROUND: In modern clinical neuro-oncology, the pathologic diagnoses are very challenging, creating significant clinical confusion and affecting therapeutic decisions and prognosis. METHODS: TP53 and PTEN gene sequences were analyzed, and microarray expression profiling was also performed. The authors investigated whether gene expression profiling, coupled with class prediction methodology, could be used to determine the prognosis of gliomatosis cerebri in a more consistent manner than standard pathology. RESULTS: The authors reported the results of a molecular study in 59 cases of gliomatosis cerebri, correlating these results with prognosis. The well-known prognostic factors of gliomas (ie, age, Karnofsky performance status, histology [grade 2 vs 3], and contrast enhancement) were found to be predictive of response or outcome in only a percentage of patients but not in all patients. The authors identified a 23-gene signature that was able to predict patient prognosis with microarray gene expression profiling. With the aim of producing a prognosis tool that is useful in clinical investigation, the authors studied the expression of this 23-gene signature by real-time quantitative polymerase chain reaction. Real-time expression values relative to these 23 gene features were used to build a prediction method able to distinguish patients with a good prognosis (those more likely to be responsive to therapy) from patients with a poor prognosis (those less likely to be responsive to therapy). CONCLUSIONS: The results of the current study demonstrated not only a strong association between gene expression patterns and patient survival, but also a robust replicability of these gene expression,based predictors. Cancer 2009. © 2009 American Cancer Society. [source] | |||||||||||||