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Results for “expression profiling”

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PubMed2003

Early prognosis of the development of renal chronic allograft rejection by gene expression profiling of human protocol biopsies.

BACKGROUND: Chronic allograft rejection (CR) is the major cause of failure of long-term graft survival and is so far irreversible. Early prognosis of CR by molecular markers before overt histologic manifestation would be a valuable aid for the optimization of treatment regimens and the design of clinical CR trials. Oligonucleotide microarray-based approaches have proven to be useful for the diagnosis and prognosis of a variety of diseases and were chosen for the unbiased identification of prognostic biomarkers. METHODS: Renal allograft biopsies were taken at month 6 posttransplantation (PT) from two groups who were, at that time, healthy recipients: one group developed CR at month-12 PT, the other group remained healthy. Gene expression profiles from the two groups at month-6 PT biopsies were analyzed to identify differentially expressed genes with prognostic value for CR development at month 12. RESULTS: A set of 10 genes was identified that showed differential expression profiles between the two patient groups and had a complete separation of the 15% to 85% quantile range for each individual gene. This set of genes was sufficient to allow the correct prediction of the occurrence or nonoccurrence of CR in 15 of 17 (88%) patients using cross-validation (occurrence for a patient was predicted on the basis of the other patients' data only). In addition, a correct prediction could be made that a recipient with a normal biopsy 12 months PT developed CR within the following 6 months. CONCLUSIONS: Identified expression patterns seem to be highly prognostic of the development of renal CR.

Adult↗

PubMed2003

Disease-associated expression profiles in peripheral blood mononuclear cells from patients with advanced renal cell carcinoma.

Expression profiling has demonstrated that transcriptomes of primary malignancies differ from those in normal tissue. It is unknown, however, whether there exist "surrogate" transcriptional markers in peripheral blood mononuclear cells (PBMCs) of patients with solid tumors. We identified transcripts expressed differentially between PBMCs from renal cell carcinoma patients and normal subjects, some of which appear to reflect specific immune responses of circulating cells. We also identified small sets of predictor genes distinguishing PBMCs from renal cell carcinoma patients and normal volunteers with high accuracy. The present findings have important implications for diagnosis and future clinical pharmacogenomic studies of antitumor therapies.

Adult↗

PubMed2004

Exploring interactions between rat hepatocytes and nonparenchymal cells using gene expression profiling.

Cocultivation of primary hepatocytes with a plethora of nonparenchymal cells (from within and outside the liver) has been shown to support hepatic functions in vitro. Despite significant investigation into this phenomenon, the molecular mechanism underlying epithelial-nonparenchymal interactions in hepatocyte cocultures remains poorly understood. In this study, we present a functional genomic approach utilizing gene expression profiling to isolate molecular mediators potentially involved in induction of liver-specific functions by nonparenchymal cells. Specifically, primary rat hepatocytes were cocultivated with closely related murine fibroblast cell types (3T3-J2, NIH-3T3, mouse embryonic fibroblasts) to allow their classification as "high," "medium," or "low" inducers of hepatic functions. These functional responses were correlated with fibroblast gene expression profiles obtained using Affymetrix GeneChips. Microarray data analysis provided us with 17 functionally characterized candidate genes in the cell communication category (cell surface, extracellular matrix, secreted factors) that may be involved in induction of hepatic functions. Further analysis using various databases (i.e., PubMed, GenBank) facilitated prioritization of the candidates for functional characterization. We experimentally validated the potential role of two candidates in our coculture model. The cell surface protein, neural cadherin (N-cadherin), was localized to hepatocyte-fibroblast junctions, while adsorbed decorin up-regulated hepatic functions in pure cultures as well as cocultures with low-inducing fibroblasts. In the future, identifying mediators of hepatocyte differentiation may have implications for both fundamental hepatology and cell-based therapies (e.g., bioartificial liver devices). In conclusion, the functional genomic approach presented in this study may be utilized to investigate mechanisms of cell-cell interaction in a variety of tissues and disease states.

Animals↗

PubMed2001

Gene expression profile in response to chromium-induced cell stress in A549 cells.

Chromium (Cr) is a trace element required for life. Biological activities of Cr are complicated and remain to be fully investigated. It is known that the valence of Cr plays an important role in the biological activities of Cr. For example, Cr (VI) is classified as a metal carcinogen, but Cr (III) is widely used as a nutritional supplement. Establishment of a gene expression profile for Cr-induced cellular response is necessary to facilitate investigation of the biological activities of Cr. In the present study, a large-scale gene expression analysis was conducted using RNA of human lung epithelial cells after in vitro exposure to Cr (VI). Utilizing high-density oligonucleotide arrays representing 2400 genes, we observed that expression of 150 genes was up-regulated, and that of 70 genes were down-regulated by Cr (VI). Functional analysis of these responsive genes led to an outline of potential biological activities of Cr in six aspects. The gene expression profile reveals that Cr may involves in redox stress, calcium mobilization, energy metabolism, protein synthesis, cell cycle regulation and carcinogenesis in the cell. The results provide a critical clue for understanding molecular mechanisms of the biological activities of Cr.

Calcium↗

PubMed2003

Specific differences in gene expression profile revealed by cDNA microarray analysis of glutathione S-transferase placental form (GST-P) immunohistochemically positive rat liver foci and surrounding tissue.

Glutathione S-transferase placental form (GST-P), one of the glutathione S-transferases family of detoxification enzymes, is a very useful marker of rat liver pre-neoplastic lesions. We here investigated the gene expression profile in GST-P positive foci as compared with surrounding GST-P negative areas in the same liver of rats treated with diethylnitrosamine and then 2-acetylaminofluorene combined with partial hepatectomy. GST-P positive foci were harvested by laser microdissection and total RNAs were extracted to allow gene expression profiles to be assessed by cDNA microarray assays. Transaldolase, rat aflatoxin B1 aldehyde reductase and gamma-glutamylcysteine synthetase were found as up-regulated genes and regucalcin as a down-regulated gene, in line with findings for hepatocellular carcinomas. The results indicate that the approach adopted is useful for understanding mechanisms of hepatocarcinogenesis and identification of new markers for rat liver pre-neoplastic foci.

Animals↗

PubMed2000

Comprehensive gene expression profile of a normal human liver.

To investigate the gene expression profile of a normal human liver, we performed serial analysis of gene expression (SAGE), which allows the quantitative and simultaneous analysis of thousands of genes expressed in tissue. Polyadenylated RNA was obtained from a bulk normal human liver sample and SAGE was performed. Reverse transcriptase-polymerase chain reaction (RT-PCR) was also performed in each of 3 different normal liver samples to evaluate the validity of the profile in each individual. A total of 30,982 tags were sequenced, 8,596 of which were unique. The genes highly expressed in the normal liver were those encoding plasma proteins (>21.8% of total transcripts), cytoplasmic proteins (>8.6%), enzymes (>4.8%), protease inhibitors (>1.7%), complements (>1.1%), and coagulation factors (>0.75%). About 13.9% of all transcripts encoded genes not reported in GenBank thus far. This study identifies candidate genes to be examined in relation to various human liver diseases, including viral hepatitis, liver cirrhosis, and hepatocellular carcinoma.

Adult↗

PubMed2005

Expression profile of serotonin4 (5-HT4) receptors in adrenocortical aldosterone-producing adenomas.

OBJECTIVE: We aimed to investigate the expression profile of serotonin4 (5-HT4) receptors in adrenocortical aldosterone-producing adenoma (APA) tissues in comparison with normal adrenal cortex. DESIGN AND METHODS: Total 5-HT4 receptor mRNAs were quantified by real-time quantitative polymerase chain reaction (PCR) assay, and the mRNAs encoding the 5-HT4 receptor isoforms were characterized by reverse transcription (RT)-PCR in seven normal adrenal cortices and 11 APA tissues. The distribution of 5-HT4 receptor mRNAs was investigated by in situ hybridization in both normal adrenal and APA tissues, and the presence of 5-HT in APA tissues was studied by immunohistochemistry. RESULTS: Real-time PCR analysis revealed that 5-HT4 receptor mRNA expression was 4.7-47 times higher in APA tissues than in normal glands. In situ hybridization studies showed that 5-HT4 receptor mRNAs were expressed in both zona glomerulosa and zona fasciculata/reticularis of the normal cortex and in groups of APA steroidogenic cells disseminated in the tumor tissues. Characterization of 5-HT4 receptor splice variants by RT-PCR revealed different profiles of expression in APAs versus normal adrenals. Isoforms (a) and (b) were not expressed in any APA but were present in the majority of normal adrenocortical tissues. Conversely, isoform (d) was expressed in 5/11 APAs but only in 1/7 adrenals. Immunohistochemical studies revealed the presence of 5-HT-immunoreactivity in both mast cells and clusters of steroidogenic cells in APA tissues. CONCLUSION: Our results show overexpression and different splicing of the 5-HT4 receptor in APA tissues in comparison with normal adrenocortical tissue. They also demonstrate the presence of 5-HT in both mast cells and tumor steroidogenic cells, providing evidence for a possible autocrine/paracrine activation of aldosterone secretion within adenoma tissues.

Adrenal Cortex Neoplasms↗

PubMed1993

SpOct, a gene encoding the major octamer-binding protein in sea urchin embryos: expression profile, evolutionary relationships, and DNA binding of expressed protein.

We have characterized a sea urchin gene, SpOct, that encodes a 78-kDa POU-domain protein related to mammalian Oct-1 and Oct-2. The SpOct protein binds octamer elements in the promoters of the alpha H2B (Bell et al., 1992, Dev. Biol. 150, 363-371) and CyIIIa actin genes, and it closely resembles the major octamer-binding activity obtained from sea urchin blastula nuclear lysates in the size of its DNase I footprint on a canonical octamer element and in its relative binding affinity (Kr) for the octamer element versus poly(dAT) (1.4 x 10(4)). Moreover, partial protein sequences obtained from affinity-purified octamer-binding protein match sequences present in SpOct. These data suggest that SpOct is closely related to, if not identical with, the major octamer-binding activity in blastula nuclear extracts. RNA gel blots reveal four forms of SpOct mRNA, ranging in size from 4 to 12 kb. They are regulated coordinately in the embryo: all are present in the unfertilized egg, increase 28-fold in amount by the 8-hr blastula stage, and decline 6-fold by the 12-hr blastula stage. The same four size classes of SpOct mRNAs are present in several adult tissues, although their relative amounts vary. The temporal profile of SpOct mRNA expression in embryos closely resembles that of the alpha histone H2B gene. Our previous work (Bell et al., 1992) showed that expression of the alpha H2B gene in blastula-stage embryos was entirely dependent on an octamer element. Together, these data strongly suggest that SpOct may be the key regulator of the alpha H2B gene.

Amino Acid Sequence↗

PubMed2002

Expression profile of the channel catfish spleen: analysis of genes involved in immune functions.

Both qualitative and quantitative patterns of tissue-specific gene expression can be determined using gene profiling. Expressed sequence tag (EST) analysis is an efficient approach not only for gene discovery and examining gene expression, but also for development of molecular resources useful for functional genomics. As part of an ongoing transcriptome analysis of channel catfish (Ictalurus punctatus), EST analysis was conducted for gene annotations and profiling using a complementary DNA library developed from messenger RNA of the spleen. A total of 1204 spleen cDNA clones were analyzed. Of the 1204 clones, 665 clones (55.2%) were identified as orthologs of known genes from other organisms by BLAST searches and 539 clones (44.8%) as unknown gene clones. In total 147 novel genes were identified, and annotations were made to 118 of them. In addition, 389 novel EST clusters were identified. Expression profile was analyzed in relation to metabolic functional groups. A total of 28 known genes were involved in immune functions, of which 10 were identified for the first time in channel catfish. Microsatellite-containing clones were also identified that may be potentially useful for genome mapping. This work contributed to the Catfish Gene Index, and toward a Unigene set useful for functional genomics research concerning spleen gene functions in relation to disease defenses.

Journal Article↗

PubMed2005

Gene expression profiling of potato responses to cold, heat, and salt stress.

In order to identify genes involved in abiotic stress responses in potato, seedlings were grown under controlled conditions and subjected to cold (4 degrees C), heat (35 degrees C), or salt (100 mM NaCl) stress for up to 27 h. Using an approximately 12,000 clone potato cDNA microarray, expression profiles were captured at three time points following initiation of the stress (3, 9, and 27 h) from two different tissues, roots and leaves. A total of 3,314 clones could be identified as significantly up- or down-regulated in response to at least one stress condition. The genes represented by these clones encode transcription factors, signal transduction factors, and heat-shock proteins which have been associated with abiotic stress responses in Arabidopsis and rice, suggesting similar response pathways function in potato. These stress-regulated clones could be separated into either stress-specific or shared-response clones, suggesting the existence of general response pathways as well as more stress-specific pathways. In addition, we identified expression profiles which are indicative for the type of stress applied to the plants.

Cold Temperature↗

PubMed2003

Development of a Corynebacterium glutamicum DNA microarray and validation by genome-wide expression profiling during growth with propionate as carbon source.

A DNA microarray was developed to analyse global gene expression of the amino acid-producing bacterium Corynebacterium glutamicum. PCR products representing 93.4% of the predicted C. glutamicum genes were prepared and spotted in quadruplicate onto 3-aminopropyltrimethoxysilane-coated glass slides. The applicability of the C. glutamicum DNA microarray was demonstrated by co-hybridisation with fluorescently labelled cDNA probes. Analysis of the technical variance revealed that C. glutamicum genes detected with different intensities resulting in ratios greater than 1.52 or smaller than -1.52 can be regarded as differentially expressed with a confidence level of greater than 95%. In a validation example, we measured changes of the mRNA levels during growth of C. glutamicum with acetate and propionate as carbon sources. Acetate-grown C. glutamicum cultures were used as reference. At the 95% confidence interval, 117 genes revealed increased transcript levels in the presence of propionate, while 43 genes showed a decreased expression compared with the acetate-grown culture. Global expression profiling confirmed the induction of the prpD2B2C2 gene cluster already known to be essential for propionate degradation via the 2-methylcitrate cycle. Besides many genes of unknown function, the paralogous prpD1B1C1 gene cluster as well as fasI-B (encoding fatty-acid synthase IB), dtsR1 and dtsR2 (components of acyl-CoA carboxylases), gluABCD (glutamate transport system), putP (proline transport system), and pyc (pyruvate carboxylase) showed significantly increased expression levels. Differential expression of these genes was confirmed by real-time reverse transcription (RT) PCR assays.

Carbon↗

PubMed2005

Distinction of desmoplastic melanoma from non-desmoplastic melanoma by gene expression profiling.

Desmoplastic melanoma (DM) is a variant of melanoma characterized by the presence of amelanotic fusiform melanocytes dispersed in a prominent collagenous stroma. DM behaves differently from conventional non-desmoplastic melanoma (NDM). It has a higher tendency for local recurrence and is less likely to metastasize to regional lymph nodes. In this study, we explored the possibility of distinguishing DM from NDM by gene expression profiling. RNA samples from ten primary cutaneous melanomas of similar depth of invasion were analyzed using the Affymetrix U133A oligonucleotide platform. Four tumors were DM, five were ND, and one tumor showed combined features of desmoplastic and conventional. Hierarchical cluster analysis clearly separated DM from NDM. The expression of a number of melanocyte differentiation genes was decreased in DM compared with NDM, which corresponded to immunohistochemical results. Various genes were upregulated in DM, including neurotrophic factors and genes involved in extracellular matrix production. A novel finding was the high expression of clusterin in DM, which was confirmed by immunohistochemical studies. Our results from gene expression profiling validate the distinction of DM from NDM. They also provide the opportunity to learn more about the biology of DM which had previously not yet been associated with this variant of melanoma.

Biomarkers, Tumor↗

PubMed2005

OP-142 gene expression profile of nonfunctional human pancreatic islets: predictors of transplant failure?

Islet culture has become a standard part of most successful protocols for clinical islet transplantation. To date, however, islets are transplanted based on crude measures of viability, purity and in vitro insulin production without adequate prior assessment of the potential for in vivo function. The purpose of this study was to define the gene expression profiles of human islets associated with in vivo function using a nonimmune NOD-scid mouse model. Human islets from eight isolations were maintained in culture for 7 to 14 days in Memphis serum-free media until transplanted. The RNA was extracted from 10,000 IEQ using RNASTAT-60. The gene expression profiles were analyzed using high-density Affymetrix U133A GeneChips and Genespring software. An aliquot of 2000 IEQ from each islet preparation was also transplanted into NOD-scid animals (n = 5) for in vivo function assessments. Islet function was assessed by measurements of human C-peptide at days 7 and 14 posttransplant. Human C-peptide levels were determined by radioimmunoassay. Gene analysis of nonfunction islets (4 of 8 islet preparations) showed high relative levels of expression of proinflammatory genes and low relative levels of genes directed toward insulin processing and secretion as well as islet integrity. Overexpression of hypoxia and proinflammatory genes may result in reduced insulin secretion and lead to islet destruction posttransplantation. Identifying and validating those genes could allow the development of a potency assay for human transplantation that would be very useful for screening human islet preparations before clinical transplant.

Adult↗

PubMed2006

Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation mechanisms in vivo.

Alternative splicing of pre-mRNAs allows multicellular organisms to create a huge diversity of proteomes from a finite number of genes. But extensive studies in vitro or in cultured cells have not fully explained the regulation mechanisms of tissue-specific or developmentally regulated alternative splicing in living organisms. Here we report a transgenic reporter system that allows visualization of expression profiles of mutually exclusive exons in Caenorhabditis elegans. Reporters for egl-15 exons 5A and 5B showed tissue-specific profiles, and we isolated mutants defective in the tissue specificity. We identified alternative-splicing defective-1 (asd-1), encoding a new RNA-binding protein of the evolutionarily conserved Fox-1 family, as a regulator of the egl-15 reporter. Furthermore, an asd-1;fox-1 double mutant was defective in the expression of endogenous egl-15 (5A) and phenocopied egl-15 (5A) mutant. This transgenic reporter system can be a powerful experimental tool for the comprehensive study of expression profiles and regulation mechanisms of alternative splicing in metazoans.

Alternative Splicing↗

PubMed2006

Clues to neuro-degeneration in Niemann-Pick type C disease from global gene expression profiling.

BACKGROUND: Niemann-Pick Type C (NPC) disease is a neurodegenerative disease that is characterized by the accumulation of cholesterol and glycosphingolipids in the late endocytic pathway. The majority of NPC cases are due to mutations in the NPC1 gene. The precise function of this gene is not yet known. METHODOLOGY/PRINCIPAL FINDINGS: Using cDNA microarrays, we analyzed the genome-wide expression patterns of human fibroblasts homozygous for the I1061T NPC1 mutation that is characterized by a severe defect in the intracellular processing of low density lipoprotein-derived cholesterol. A distinct gene expression profile was identified in NPC fibroblasts from different individuals when compared with fibroblasts isolated from normal subjects. As expected, NPC1 mutant cells displayed an inappropriate homeostatic response to accumulated intracellular cholesterol. In addition, a number of striking parallels were observed between NPC disease and Alzheimer's disease. CONCLUSIONS/SIGNIFICANCE: Many genes involved in the trafficking and processing of amyloid precursor protein and the microtubule binding protein, tau, were more highly expressed. Numerous genes important for membrane traffic and the cellular regulation of calcium, metals and other ions were upregulated. Finally, NPC fibroblasts exhibited a gene expression profile indicative of oxidative stress. These changes are likely contributors to the pathophysiology of Niemann-Pick Type C disease.

Alzheimer Disease↗

PubMed2004

Gene expression profiling shows that macrophages derived from mouse embryonic stem cells is an improved in vitro model for studies of vascular disease.

Macrophages (Mphi) play an important role in the initiation and progress of the atherogenic process. They contribute to the growth of atherosclerotic plaque by affecting lipoprotein metabolism, matrix homeostasis, lipoprotein modification and cholesterol accumulation. Access to in vitro Mphi models is therefore important for understanding the mechanisms involved in the transition of the relatively simple fatty streak to more complex type of lesions. The aim of the present work was to compare the expression profile of macrophages differentiated from the hematopoietic lineage to peritoneal mouse macrophages and two commonly used mouse macrophage cell lines (J774.A1 and RAW264.7). Our results showed that the embryonic stem cell-derived macrophages (ES Mphi) had a more similar expression profile to peritoneal macrophages than the two mouse macrophage cell lines. The ES Mphi had unchanged expression of the majority of cholesterol efflux mediators when compared to mouse peritoneal macrophages, whereas the cell lines showed altered expression of several of these genes. A key gene in this process is apolipoprotein E, which is expressed in ES Mphi but not in macrophage cell lines. In conclusion, ES Mphi are likely to provide a better in vitro model than mouse Mphi cell lines to study macrophage involvement in atherosclerosis.

Animals↗

PubMed1998

Expression profiles of P2-receptor isoforms P2Y1 and P2Y2 in the rat lens.

PURPOSE: To verify at the molecular level that P2 receptors are expressed in the lens and to determine their expression profiles. METHODS: The reverse transcription-polymerase chain reaction (RT-PCR) was used to screen rat lens epithelial and fiber cells for the expression of the ionotropic P2X2 receptor and the G-protein-linked receptor isoforms P2Y1 and P2Y2. Northern blot analysis was used to confirm the level of expression of P2Y1 and P2Y2. The profile of P2-receptor isoform expression in the lens was identified using an indirect RT-PCR in situ hybridization procedure on paraffin sections of whole rat eyes. RESULTS: P2X2-receptor transcripts could not be detected in lens epithelial or fiber cells. P2Y1- and P2Y2-receptor transcripts were detected in lens fiber cells but not in the epithelial cells. Their expression profiles were maximal in the lens cortex and mostly overlapped each other, except that transcripts for the P2Y2-receptor isoform appeared earlier in the not yet fully elongated fiber cells in the lens bow region. CONCLUSIONS: The molecular data support physiological evidence previously reported by others that P2Y receptors are expressed in the lens and identifies cortical fiber cells as the principal site of expression.

Animals↗

PubMed2006

When will tumor gene expression profiling be incorporated into clinical breast cancer decision making?

DNA microarray based gene expression analysis of primary breast cancers is not in general clinical use in spite of the widespread enthusiasm for the approach. However, several studies have identified gene expression patterns, or "signatures" that are predictive of disease outcome and assays based on these findings have become commercially available. Additional studies are required to further define gene signatures that can be used to help tailor the therapy best suited to for an individual patient. Recent gene expression profiling studies using cell line models to identify downstream transcriptional targets of oncogenic signaling pathways may help achieve this goal.

Breast Neoplasms↗