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PubMed1999

MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.

The trend toward high-throughput techniques in molecular biology and the explosion of online scientific data threaten to overwhelm the ability of researchers to take full advantage of available information. This problem is particularly severe in the rapidly expanding area of gene expression experiments, for example, those carried out with cDNA microarrays or oligonucleotide chips. We present an Internet-based hypertext program, MedMiner, which filters and organizes large amounts of textual and structured information returned from public search engines like GeneCards and PubMed. We demonstrate the value of the approach for the analysis of gene expression data, but MedMiner can also be extended to other areas involving molecular genetic or pharmacological information. More generally still, MedMiner can be used to organize the information returned from any arbitrary PubMed search.

Databases, Factual↗
PubMed1998

lambda RNA internal standards quantify sensitivity and amplification efficiency of mammalian gene expression profiling.

There is an increasing interest in being able to document simultaneous levels of multiple mRNAs from limited amounts of mammalian tissue. The combination of amplified antisense RNA (aRNA) and reverse Northern blot analysis is one technology that allows the measurement of relative levels of multiple mRNAs. However, potential problems exist with this approach, such as (i) unknown amplification efficiencies and sensitivity of detection, (ii) an inherent 3' bias of amplified products and (iii) cross-hybridization of homologous mRNAs with the gene targets. Each of these potential problems was addressed experimentally by the use of poly(A) RNA internal standards synthesized from lambda phage (lambda) DNA. The results showed detection levels of as few as 10 copies of the poly(A) RNA internal standards. The internal standards aid in the optimization of reaction conditions and also reduce dependence on traditional "housekeeping" genes whose mRNA levels might or might not change. The overall results of these experiments highlight and extend the general usefulness of amplified antisense aRNA and reverse Northern blot analysis to study mRNA expression profiles.

Animals↗
PubMed1999

Gene expression profiling of fibroblasts resistant toward oncogene-mediated transformation reveals preferential transcription of negative growth regulators.

The signal-transducing Ras proteins are important driving forces of diverse cellular processes such as proliferation, neoplastic transformation, differentiation and growth inhibition. As a step toward understanding the complex mechanisms underlying cellular responses, gene expression patterns were examined in two phenotypically normal fibroblast lines which differ in their sensitivity toward oncogene-mediated transformation. Suppression subtractive hybridization (SSH) was used to establish a subtracted cDNA library specific for the REF52 cell line which, like normal diploid fibroblasts, is refractory toward neoplastic transformation induced by mutated HRAS oncogenes. In contrast, rat 208F control cells can be efficiently transformed by HRAS. The nucleotide sequence of 549 subtracted cDNA clones ('REF52 minus 208F') was determined. We identified 93 preferentially expressed gene fragments in resistant REF52 cells as compared to 208F cells. Seventeen of the 52 known genes (32.6%) are capable of inhibiting cell proliferation or of adversely affecting oncogenic signal transduction pathways. These results suggest that the anti-oncogenic properties of resistant REF52 cells are determined by multiple negative growth regulators. The preneoplastic state expressed in 208F cells is characterized by impairment of unexpectedly redundant control mechanisms. Our results also demonstrate that SSH is a powerful method for identifying specific transcriptional patterns in closely related cell types.

Cell Division↗
PubMed1995

Monitoring cell physiology by expression profiles and discovering cell type-specific genes by compiled expression profiles.

A gene expression profile is the list showing the expressed gene species and the abundance of their transcripts in a given cell or tissue. This list is made by constructing 3'-directed cDNA libraries consisting of only the 3'-termini of mRNA and sequencing randomly selected clones from such libraries: genes are identified by the sequences, and the composition of mRNA, which reflects gene activities, is measured from the frequency of appearance of the gene transcripts. For practical reasons, the number of sequenced clones has been limited to approximately 1000 per library at present, but the resulting profile covers almost all highly or moderately expressed genes, along with many less active genes. We constructed expression profiles from the HL60 human promyelocytic cell line and two of its derivatives, granulocytoids induced by DMSO and monocytoids induced by TPA. In HL60, a significant fraction of the abundantly expressed genes was for protein synthesis. Upon induction, these genes were partially or totally silenced; transcripts for proteins that characterize the granulocytes and monocyte-macrophages became abundant. By compiling and comparing different expression profiles, genes can be categorized into those expressed in diverse cell types and those active only in limited cell types. Although at present, the number of expression profiles that can be compiled is limited and this categorization is applicable only to abundantly expressed genes, 13 novel genes that may represent granulocyte- or monocyte-specific functions have been discovered.

Base Sequence↗
PubMed1999

Gene expression of vasoactive intestinal contractor/endothelin-2 in ovary, uterus and embryo: comprehensive gene expression profiles of the endothelin ligand-receptor system revealed by semi-quantitative reverse transcription-polymerase chain reaction analysis in adult mouse tissues and during late embryonic development.

Vasoactive intestinal contractor (VIC)/endothelin-2 (ET-2) is a 21 amino acid intestinal peptide characterized as a potent vasoactive and intestinal smooth muscle-contracting compound. To investigate the physiological roles of VIC/ET-2 further, we characterized the specificity of VIC gene expression relative to that of other members of the endothelin (ET) ligand-receptor system in adult mouse tissues and during embryonic development. Gene expression of ET-1, ET-3, ETA and ETB was ubiquitous in almost all tissues we examined while gene expression of VIC was localized to certain tissues. A high level of VIC gene expression was observed in ovary and uterus. The gene expression of VIC, relative to that of glyceraldehyde-3-phosphate dehydrogenase, was approximately 2.0%, 0.4%, and 2.3% in ovary, uterus, and intestine respectively, and was approximately 1.6 and 7. 1 times higher than that of ET-1 in ovary and intestine respectively. Thus, VIC may have some physiological role in adult ovary and uterus as well as intestine. In embryonic development, VIC gene expression sharply increased between 11 and 15 days post coitus and decreased after birth, suggesting an involvement in the later stages of embryonic development.

Animals↗
PubMed1999

Monitoring gene expression profile changes in ovarian carcinomas using cDNA microarray.

The development of cancer is the result of a series of molecular changes occurring in the cell. These events lead to changes in the expression level of numerous genes that result in different phenotypic characteristics of tumors. In this report we describe the assembly and utilization of a 5766 member cDNA microarray to study the differences in gene expression between normal and neoplastic human ovarian tissues. Several genes that may have biological relevance in the process of ovarian carcinogenesis have been identified through this approach. Analyzing the results of microarray hybridizations may provides new leads for tumor diagnosis and intervention.

Cloning, Molecular↗
PubMedDate not supplied

Transplantation of virally transduced cells into the dermis of immunocompetent and immunodeficient (SCID) mice to determine gene expression profile and differential donor cell survival.

Cell therapy and bioengineering hold great promise as therapeutic approaches using cells and cell-derived factors to treat various pathologic or trauma-induced states. One possible application is the transplantation of cells into wounded tissue to help regulate tissue repair. Cells engineered for optimal wound healing may help to minimize scarring following surgery or to enhance the rate of healing of chronic wounds. The purpose of the current study was to determine the effect of a viral insert, the LacZ-bearing, first generation adenovirus AdRGD, on the survival of dermally transplanted murine skin allogenic fibroblasts. The LacZ insert facilitated quantitation of both cell survival and gene expression and was used here to measure viable cell number. In addition to bearing the LacZ marker, the AdRGD vector is capable of carrying therapeutic gene inserts, so this study tested the feasibility of gene therapy for wound healing. Murine skeletal muscle PP6 (i.e., Pre-Plate 6) myogenic stem cells served as an alternate donor cell type. Cells were labeled with the LacZ-bearing AdRGD adenovirus vector and injected (50,000 cells/site) into the dorsal skin of adult normal, immunocompetent mice as well as in immunodeficient SCID mice. Skin biopsies were taken on days 0, 1, 2, 3, and 7 post-transplant, and assayed for LacZ expression. Soon after transplant (day 1), cell numbers underwent a transient decrease, but by day 2 post-transplant they were present in appreciable numbers. Between days 2-7 post-transplant, both allogenic fibroblasts and PP6 myogenic stem cells maintained survivability in similar numbers. Further, survival of transplanted cell types was similar in both normal, immunocompetent as well as SCID mice during this time period. There were no signs of acute inflammation or rejection in any of the samples. This study shows that AdRGD-transduced cells are not immunogenic in the mouse skin model and the cells show similar survival for the first 7 days post-transplantation independent of the cell type or immunocompetence of the host.

Animals↗
PubMed2000

Trophic actions of extracellular ATP: gene expression profiling by DNA array analysis.

In addition to Professor Burnstock's work on the short-term signaling actions of extracellular nucleotides and nucleosides, Geoff has had a long-standing interest in trophic actions of purines in development and in pathophysiological conditions which has been instrumental in encouraging my work in this area. The trophic actions of extracellular ATP, alone or in combination with polypeptide growth factors, may play an important role in brain development and may contribute to the reactive gliosis that accompanies brain injury and neurodegeneration. P2Y receptors in astrocytes are coupled to the ERK/MAPK cascade, a signal transduction mechanism crucial for cellular proliferation and differentiation. The mitogenic signaling pathway from P2Y receptors to ERK involves phospholipase D and a calcium-independent PKC isoform, PKCdelta. DNA array analysis reveals a number of changes in gene expression after P2Y receptor occupancy, indicating that this methodology will be a powerful tool in understanding the mechanisms underlying the trophic actions of extracellular nucleotides and nucleosides.

Adenosine Triphosphate↗
PubMed1997

Ordered differential display: a simple method for systematic comparison of gene expression profiles.

A method for display of 3'-end restriction fragments of cDNAs is proposed, extending the idea reported recently. First, representative pools of such fragments are selectively amplified using PCR suppression effect. Then, simplified subsets of these fragments suitable for comparison by PAGE are amplified by adapter-specific primers extended by two randomly picked bases at their 3'ends. By testing all possible combinations of extended primers the whole mRNA pool may be systematically investigated. The method was applied to search for molecular regional markers of freshwater planarian Dugesia tigrina .

Animals↗
PubMed1994

Intrathyroidal cytokine gene expression profiles in autoimmune thyroiditis.

Cytokines are thought to mediate the initiation and perpetuation of autoimmune thyroiditis. However, this concept is mainly based on in vitro findings and to date only interleukin (IL)-6 and interferon-gamma (IFN-gamma) have been detected in Graves' disease in vivo. The cytokine pattern produced by T-helper (Th) cells has important regulatory effects on the nature of the immune response. We therefore determined these cytokine mRNAs in Graves' disease and Hashimoto's thyroiditis. RNA was extracted by cesium chloride gradient centrifugation from the thyroid tissue of 12 patients undergoing thyroid resection for Graves' disease and from two patients being treated for Hashimoto's thyroiditis. Two patients with parathyroid adenomas and one patient with a goiter were used as controls. RNA was also extracted from normal human thyroid epithelial cells in primary culture. The cDNAs were prepared by reverse transcription and amplified for IL-2, -4, -5, -6 and -10 and IFN-gamma by polymerase chain reaction. All the cytokine mRNAs were detected in the Hashimoto's thyroid glands in large quantities. Six of the 12 Graves' disease thyroid glands showed, when compared with controls, an increased accumulation of transcripts for: IFN-gamma, IL-2, -4 and -10 or IL-2, -4 and IFN-gamma or IL-2 and IFN-gamma or IFN-gamma alone, each in one case or IL-2 alone in two cases. These cytokine profiles were not representative of a Th1 or Th2 phenotype. Increased amounts of cytokine mRNA in thyroid glands from Graves' disease patients were mostly associated with high microsomal antibody titres and/or prominent intrathyroidal lymphocytic infiltration.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMedDate not supplied

DNA microarrays in pediatric cancer.

Childhood cancer, like all cancer, is at heart a genetic disease. Consequently, fundamental understanding of the oncogenic process is likely to be beneficially addressed by genetic methodology. Current methods have largely focused on single-gene defects, like chimeric genes, which are present in many sarcomas and leukemias. Real understanding is more likely to derive from a genome-wide analysis of these malignancies. Recent technologic advances have made it possible to simultaneously assess the entire expressed gene profile, or transcriptome, of a given cancer. Foremost among these methods is gene expression profiling using DNA microarrays. Two basic approaches predominate: spotted arrays and photolithography arrays. Regardless of the method, the resulting information can be used to create disease profiles, but only if appropriate bioinformatic solutions are employed. Common analytic approaches include two-way expression comparisons, or scatter analyses; outlier gene analysis, to identify significantly dysregulated genes; dendrogram analyses, as pioneered by Eisen; cluster analyses to identify diagnostic or biologic groups; and various forms of functional analyses to identify relevant genes and biologic pathways. Studies of both adult and pediatric cancer have demonstrated the feasibility of such analyses to identify both diagnostic and prognostic groups of tumors. Acute childhood leukemias have been grouped into myelogenous and lymphoid, and even B- and T-cell subsets. Breast cancer prognostic groups have been identified on the basis of a small subset of expressed genes. In addition, preliminary data on childhood sarcomas appear to identify both diagnostic and prognostic subsets. Specifically, embryonal rhabdomyosarcoma could be distinguished from alveolar rhabdomyosarcoma, and even morphologically mixed embryonal and alveolar rhabdomyosarcoma showed similar gene expression profiles in both histologies. Further, collaborative studies using clustering analyses appear to identify prognostic groups of diverse sarcomas. Larger institutional and cooperative group studies are currently underway to validate these preliminary findings.

Animals↗
PubMed2000

Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain.

Expressed sequence tag (EST) analysis was conducted using a complementary DNA (cDNA) library made from the brain mRNA of channel catfish (Ictalurus punctatus). As part of our transcriptome analysis in catfish to develop molecular reagents for comparative functional genomics, here we report analysis of 1201 brain cDNA clones. Of the 1201 clones, 595 clones (49.5%) were identified as known genes by BLAST searches and 606 clones (50.5%) as unknown genes. The 595 clones of known gene products represent transcripts of 251 genes. These known genes were categorized into 15 groups according to their biological functions. The largest group of known genes was the genes involved in translational machinery (21.4%) followed by mitochondrial genes (6.2%), structural genes (3.1%), genes homologous to sequences of unknown functions (2.3%), enzymes (2.7%), hormone and regulatory proteins (2.5%), genes involved in immune systems (2.1%), genes involved in sorting, transport, and metal metabolism (1.8%), transcriptional factors and DNA repair proteins (1.6%), proto-oncogenes (1.2%), lipid binding proteins (1.2%), stress-induced genes (0.7%), genes homologous to human genes involved in mental diseases (0.6%), and development or differentiation-related genes (0.3%). The number of genes represented by the 606 clones of unknown genes is not known at present, but the high percentage of clones showing no homology to any known genes in the GenBank databases may indicate that a great number of novel genes exist in teleost brain.

Animals↗
PubMed2001

Profiling of differentially expressed genes induced by high linear energy transfer radiation in breast epithelial cells.

Methods to define patterns of gene expression have applications in a wide range of biological systems. Several molecular biological techniques are used to study expression patterns during the neoplastic progression of breast epithelial cells. In the present study, differential expression of human oncogenes/tumor suppressor genes in human breast epithelial cell lines irradiated with low doses of high linear energy transfer radiation and treated with estrogen was assessed with cDNA expression arrays. Transformed and tumorigenic cell lines were compared with the control cell line to identify differentially expressed genes during tumorigenic progression. Autoradiographic analysis showed that of the 190 genes analyzed, 49 genes showed a high level of altered expression, and 12 genes had minor differences in expression levels. Among these 49 genes, 17 genes were altered at all stages of transformation, 21 were altered only at the early stage, and the remaining 11 were at the late stage of transformation to the tumorigenic stage of progression. Among the 11 late stage-associated genes, seven genes were altered exclusively in the tumorigenic cell lines and in Tumor-T. Of the 17 all-stage genes, six were randomly selected, and we confirmed their altered expression by gene-specific semiquantitative reverse transcription polymerase chain reaction, followed by Northern blot analysis. The results showed that the mRNA expression patterns of all these genes were consistent with the expression pattern seen on the array. Among these six genes, five genes, including c-myc, puf, MNDA, c-yes, and Fra-1 showed upregulation, and the other gene, RBA/p48, showed downregulation in the transformed and tumorigenic cell lines compared with the control MCF-10F cell line. Investigation of these genes should help establish the molecular mechanisms of progression that are altered by radiation and estrogen treatment. A number of candidates reported here should be useful as biomarkers involved in breast carcinogenesis.

Alpha Particles↗
PubMed2001

Extracting biological information from DNA arrays: an unexpected link between arginine and methionine metabolism in Bacillus subtilis.

BACKGROUND: In global gene expression profiling experiments, variation in the expression of genes of interest can often be hidden by general noise. To determine how biologically significant variation can be distinguished under such conditions we have analyzed the differences in gene expression when Bacillus subtilis is grown either on methionine or on methylthioribose as sulfur source. RESULTS: An unexpected link between arginine metabolism and sulfur metabolism was discovered, enabling us to identify a high-affinity arginine transport system encoded by the yqiXYZ genes. In addition, we tentatively identified a methionine/methionine sulfoxide transport system which is encoded by the operon ytmIJKLMhisP and is presumably used in the degradation of methionine sulfoxide to methane sulfonate for sulfur recycling. Experimental parameters resulting in systematic biases in gene expression were also uncovered. In particular, we found that the late competence operons comE, comF and comG were associated with subtle variations in growth conditions. CONCLUSIONS: Using variance analysis it is possible to distinguish between systematic biases and relevant gene-expression variation in transcriptome experiments. Co-variation of metabolic gene expression pathways was thus uncovered linking nitrogen and sulfur metabolism in B. subtilis.

Arginine↗
PubMed2001

DNA microarray analysis of gene expression in endothelial cells in response to 24-h shear stress.

The recently developed DNA microarray technology provides a powerful and efficient tool to rapidly compare the differential expression of a large number of genes. Using the DNA microarray approach, we investigated gene expression profiles in cultured human aortic endothelial cells (HAECs) in response to 24 h of laminar shear stress at 12 dyn/cm(2). This relatively long-term shearing of cultured HAECs led to the modulation of the expression of a number of genes. Several genes related to inflammation and EC proliferation were downregulated, suggesting that 24-h shearing may keep ECs in a relatively noninflammatory and nonproliferative state compared with static cells. Some genes were significantly upregulated by the 24-h shear stress; these includes genes involved in EC survival and angiogenesis (Tie2 and Flk-1) and vascular remodeling (matrix metalloproteinase 1). These results provide information on the profile of gene expression in shear-adapted ECs, which is the case for the native ECs in the straight part of the aorta in vivo.

Adult↗
PubMed2000

Computational methods for gene expression-based tumor classification.

Gene expression profiles may offer more or additional information than classic morphologic- and histologic-based tumor classification systems. Because the number of tissue samples examined is usually much smaller than the number of genes examined, efficient data reduction and analysis methods are critical. In this report, we propose a principal component and discriminant analysis method of tumor classification using gene expression profile data. Expression of 2000 genes in 40 tumor and 22 normal colon tissue samples is used to examine the feasibility of gene expression-based tumor classification systems. Using this method, the percentage of correctly classified normal and tumor tissue was 87.0%. The combined approach using principal components and discriminant analysis provided superior sensitivity and specificity compared to an approach using simple differences in the expression levels of individual genes.

Analysis of Variance↗