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Results for “Gene expression profiling”

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PubMed2004

Profiling gene expression in kidney development.

Rapid determination of the expression levels of all genes can be achieved with microarrays. This technology is beginning to revolutionize the study of kidney development. Genome-wide expression studies of the developing rat, mouse and human kidneys have found thousands of expressed genes, with many hundreds showing changes in expression as a function of developmental time. The resulting gene expression profiles provide an important discovery function, identifying new genes and pathways not previously implicated in kidney organogenesis. In combination with microdissection techniques, microarrays further extend global gene expression analysis to discrete components or cell types within the kidney. The resulting detailed molecular portrait of normal kidney development provides a baseline for studies of the many mouse mutants available with abnormal kidney development.

Animals↗
PubMed2004

Gene expression profile of the mouse organ of Corti at the onset of hearing.

We describe the generation of an expressed sequence tag (EST) database of the mouse organ of Corti (OC). Over 20,000 independent clones were isolated, analyzed, and grouped into 8690 unique gene clusters. A large pool of novel genes unique to the OC was identified. Sequence alignments frequently revealed alternatively spliced forms of known genes potentially relevant in the OC function. We have also electronically mapped a subset of OC mouse ESTs to several syntenic regions associated with human autosomal and recessive deafness, which may prove useful for the identification of new positional candidates for these human diseases. The EST dataset is available as an interactive Web-based public database at. This resource provides both a view of the profile of gene expression in the OC at the onset of hearing and a tool to identify novel genes of importance in hearing.

Animals↗
PubMed2002

Gene expression profiling of apoptosis-related genes in human atherosclerosis: upregulation of death-associated protein kinase.

OBJECTIVE: Apoptosis substantially affects the cellularity and integrity of atherosclerotic plaques. It remains, however, unclear which key regulatory genes are involved. In this study, cDNA expression arrays were used to analyze transcript levels of 205 apoptosis-related genes in human carotid endarterectomy specimens versus nonatherosclerotic mammary arteries. METHODS AND RESULTS: Seventeen genes with a 2- to 5-fold relative expression difference were identified. One of the most apparent changes in human plaques was the overexpression of death-associated protein (DAP) kinase ( approximately 5-fold), a positive mediator of apoptotic cell death. Differential expression of DAP kinase mRNA in human plaques relative to mammary arteries was confirmed by quantitative reverse-transcription polymerase chain reaction. Western blotting and immunohistochemistry demonstrated enhanced levels of DAP kinase protein in the plaque with negligible expression in non-atherosclerotic vessels. DAP kinase was located predominantly in foam cells of smooth muscle cell (SMC) origin. Uptake of aggregated LDL by cultured aortic SMCs as well as exposure of SMCs to the short-chain acyl ceramide derivative N-hexanoyl-D-sphingosine (C6-ceramide) upregulated DAP kinase both at the mRNA and protein level. CONCLUSIONS: Our data demonstrate that cDNA array technology can identify novel genes that might participate in cell death pathways underlying atherogenesis.

Aged↗
PubMed2005

Laparoscopic donor nephrectomy gene expression profiling reveals upregulation of stress and ischemia associated genes compared to control kidneys.

We compared gene expression profiles from six donor kidneys prior to surgical manipulation to six kidneys removed after laparoscopic donor nephrectomy (LDN) and several hours of CO2 pneumoperitoneum. Biopsies were obtained from renal cortex and hybridized to Affymetrix HG-U133A GeneChips. For control kidneys, we identified 1380 genes present on all six samples that had a signal intensity >1,000. Functional classification of these revealed genes for cellular signaling (201; 15%), regulation of transcription (156; 11%), cellular transport (144; 10%) and cellular metabolism (111; 8%). A class comparison between the controls and LDN kidneys yielded 865 differentially expressed genes. Functional classification of the 502 genes differentially upregulated in LDN kidneys identified associations with apoptosis, cell adhesion, cell signaling, regulation of cell growth/proliferation, immune/inflammation, ischemia/stress response and proteolysis/peptidolysis. These data demonstrate an altered renal transcriptome induced by several hours of CO2 pneumoperitoneum and laparoscopic surgery characterized by upregulation of ischemia and injury associated genes.

Adult↗
PubMed2004

Gene expression profiles of cold-stored and fresh pollen to investigate pollen germination and growth.

In lily (Lilium longiflorum cv. Avita) pollen cold-stored (-20 degrees C) for 2 months, typical in vitro germination/growth was delayed by about 1 h compared with fresh pollen. We hypothesized that some proteins and mRNAs stored in mature pollen were degraded during storage periods and that re-synthesis of them was essential to resume normal germination and growth. Cold-stored and fresh pollen grains were used to investigate the regulatory mechanism of pollen germination and tube growth in terms of both total protein profile and gene expression. Total protein profiles of cold-stored pollen differed qualitatively and quantitatively from fresh pollen. Actinomycin D significantly inhibited both germination and tube growth of cold-stored pollen and later tube growth of fresh pollen but had no effect on fresh pollen germination and early tube growth. Suppression subtractive hybridization screening revealed 99 cDNAs enriched in fresh mature pollen, and 22 were selected for further characterization. Most of these 22 cDNAs gradually disappeared during cold storage, but full recovery was achieved by incubating the cold-stored pollen in culture medium for 2 h. Because of different sensitivities to cold storage and actinomycin D, the transcripts were divided into three groups according to their possible roles in pollen germination and tube growth. Several cDNAs encoding novel proteins showed pollen-specific expression patterns and may participate in drought tolerance (an Na+/H+ antiporter), endomembrane trafficking (DnaJ), division of the generative cell (Sgt1), pollen wall precursor uptake from stylar exudate (an Na+/myoinositol symporter) and chemotropism of the pollen tube (peptide transporter) during pollination.

Cell Division↗
PubMed2006

Gene expression profiles of hepatic cell-type specific marker genes in progression of liver fibrosis.

AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis. METHODS: Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells), and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells. RESULTS: The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSC-specific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis, suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocyte-specific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis. CONCLUSION: Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibrogenesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis.

Alanine Transaminase↗
PubMed2004

Stratification of acute myeloid leukemia based on gene expression profiles.

Acute myeloid leukemia (AML) is characterized by clonal growth of immature leukemic blasts and develops either de novo or secondarily to anticancer treatment or to other hematologic disorders. Given that the current classification of AML, which is based on blast karyotype and morphology, is not sufficiently robust to predict the prognosis of each affected individual, new stratification schemes that are of better prognostic value are needed. Global profiling of gene expression in AML blasts has the potential both to identify a small number of genes whose expression is associated with clinical outcome and to provide insight into the molecular pathogenesis of this condition. Emerging genomics tools, especially DNA microarray analysis, have been applied in attempts to isolate new molecular markers for the differential diagnosis of AML and to identify genes that contribute to leukemogenesis. Progress in bioinformatics has also yielded means with which to classify patients according to clinical parameters such as long-term prognosis. The application of such analysis to large sets of gene expression data has begun to provide the basis for a new AML classification that is more powerful with regard to prediction of prognosis.

Biomarkers, Tumor↗
PubMed2006

GOurmet: a tool for quantitative comparison and visualization of gene expression profiles based on gene ontology (GO) distributions.

BACKGROUND: The ever-expanding population of gene expression profiles (EPs) from specified cells and tissues under a variety of experimental conditions is an important but difficult resource for investigators to utilize effectively. Software tools have been recently developed to use the distribution of gene ontology (GO) terms associated with the genes in an EP to identify specific biological functions or processes that are over- or under-represented in that EP relative to other EPs. Additionally, it is possible to use the distribution of GO terms inherent to each EP to relate that EP as a whole to other EPs. Because GO term annotation is organized in a tree-like cascade of variable granularity, this approach allows the user to relate (e.g., by hierarchical clustering) EPs of varying length and from different platforms (e.g., GeneChip, SAGE, EST library). RESULTS: Here we present GOurmet, a software package that calculates the distribution of GO terms represented by the genes in an individual expression profile (EP), clusters multiple EPs based on these integrated GO term distributions, and provides users several tools to visualize and compare EPs. GOurmet is particularly useful in meta-analysis to examine EPs of specified cell types (e.g., tissue-specific stem cells) that are obtained through different experimental procedures. GOurmet also introduces a new tool, the Targetoid plot, which allows users to dynamically render the multi-dimensional relationships among individual elements in any clustering analysis. The Targetoid plotting tool allows users to select any element as the center of the plot, and the program will then represent all other elements in the cluster as a function of similarity to the selected central element. CONCLUSION: GOurmet is a user-friendly, GUI-based software package that greatly facilitates analysis of results generated by multiple EPs. The clustering analysis features a dynamic targetoid plot that is generalizable for use with any clustering application.

Artificial Intelligence↗
PubMed2005

Discovery of glpC, an organic solvent tolerance-related gene in Escherichia coli, using gene expression profiles from DNA microarrays.

Gene expression profiles were collected from Escherichia coli strains (OST3410, TK33, and TK31) before and after exposure to organic solvents, and the six genes that showed higher gene expression were selected. Among these genes, glpC encoding the anaerobic glycerol-3-phosphate dehydrogenase subunit C remarkably increased the organic solvent tolerance.

Cyclohexanes↗
PubMed2004

Gene expression profiling of potential PPARgamma target genes in mouse aorta.

Diminished activity of peroxisome proliferator-activated receptor-gamma (PPARgamma) may play a role in the pathogenesis of hypertension and vascular dysfunction. To better understand what genes are regulated by PPARgamma, an experimental data set was generated by microarray analysis, in duplicate, of pooled aortic mRNA isolated from mice treated for 21 days with a PPARgamma agonist (rosiglitazone) or vehicle. Of the 12,488 probe sets present on the array (Affymetrix MG-U74Av2), 181 were differentially expressed between groups according to a statistical metric generated using Affymetrix software. A significant correlation was observed between the microarray results and real-time RT-PCR analysis of 39 of these genes. Cluster analysis revealed 3 expression patterns, 29 transcripts of moderate abundance that were decreased (-93%) to very low levels, 106 transcripts that were downregulated (-42%), and 46 transcripts that were upregulated (+70%). Functional groups that were decreased included inflammatory response (-93%, n = 6), immune response (-86%, n = 7), and cytokines (-82%, n = 7). There was an overall upregulation in the oxidoreductase activity group (+47%, n = 9). Individually, six transcripts in this group were increased (+72%), and three were decreased (-34%). Fourteen of the genes map to regions in the rat genome that have been linked to increased blood pressure, and of 142 upstream regions analyzed, sequences resembling the DNA binding site for PPARgamma were identified in 101 of the differentially expressed genes.

Animals↗
PubMed2002

Gene expression profiling of embryo-derived stem cells reveals candidate genes associated with pluripotency and lineage specificity.

Large-scale gene expression profiling was performed on embryo-derived stem cell lines to identify molecular signatures of pluripotency and lineage specificity. Analysis of pluripotent embryonic stem (ES) cells, extraembryonic-restricted trophoblast stem (TS) cells, and terminally-differentiated mouse embryo fibroblast (MEF) cells identified expression profiles unique to each cell type, as well as genes common only to ES and TS cells. Whereas most of the MEF-specific genes had been characterized previously, the majority (67%) of the ES-specific genes were novel and did not include known differentiated cell markers. Comparison with microarray data from embryonic material demonstrated that ES-specific genes were underrepresented in all stages sampled, whereas TS-specific genes included known placental markers. Investigation of four novel TS-specific genes showed trophoblast-restricted expression in cell lines and in vivo, whereas one uncharacterized ES-specific gene, Esg-1, was found to be exclusively associated with pluripotency. We suggest that pluripotency requires a set of genes not expressed in other cell types, whereas lineage-restricted stem cells, like TS cells, express genes predictive of their differentiated lineage.

Animals↗
PubMed2002

[Preliminary analysis on the gene expression profiles of different types of gliomas with cDNA array].

BACKGROUND & OBJECTIVE: There is great signification to classify the molecular pathogenesis of gliomas. Gene chip is able to profile the gene expression of tumors, which may become a new method for studying molecular pathology of tumors. The cDNA was used in order to detect the differences in gene expression profiles of different types of gliomas. METHODS: cDNA probes tagged with 32P were converted from total RNA extracted from 4 samples of 3 different pathological types, including oligodendrogliomas, anaplastic astrocytomas and ependymomas, and one sample of normal human brain tissue as well, which were then hybridized to the Atlas array. After autoradiography, the gene expression profiles were analyzed with the special software and by the cluster analysis. RESULTS: As compared to the normal brain tissue, the number of differential expressed genes in these tumor samples ranging from 11 to 118 was found. These 4 samples could be divided into 3 kinds of types when 107 differential expressed genes were selected to be as the cluster analysis index. This result was in accordance with the neuropathological diagnosis. CONCLUSION: cDNA array is able to profile gene expression in different types of gliomas. Combined with the bioinformational method, we may further obtain useful information about molecular pathology of gliomas.

Gene Expression Profiling↗
PubMed2005

Gene expression profiling analysis of Mycobacterium tuberculosis genes in response to salicylate.

Salicylate stimulates the oxygen consumption and also induces multiple drug resistance in Mycobacterium tuberculosis. To gain insight into the mechanisms involved in the above observations, a microarray analysis of M. tuberculosis genes in response to salicylate was performed. Salicylate, besides highly inducing the 27 kD gene (Rv0560c) previously identified as highly salicylate-inducible, also caused increased transcription of a range of genes including an open reading frame (Rv0559c) that is located immediately downstream of the 27 kD gene, and some membrane/transmembrane proteins that may serve as potential efflux pumps or porins. Salicylate also caused a general shutdown of transcription and translation and energy production by down-regulating a range of genes involved in RNA and protein synthesis and ATP synthesis. The role of the salicylate-regulated genes in salicylate induced drug resistance and its unique effect on stimulating oxygen consumption in tubercle bacillus is discussed.

Adaptation, Physiological↗
PubMed2004

Gene expression profiles in human nasal polyp tissues studied by means of DNA microarray.

BACKGROUND: Nasal polyposis (NP) is a chronic inflammatory disease of the sinuses. Its pathogenesis is unknown. DNA microarray analysis allows simultaneous measurement of expression of thousands of genes in the same tissue sample and might help to identify gene alterations in various disorders. OBJECTIVE: We sought to screen for disease-related genes in NP by using DNA microarrays and to validate the altered expression of selected genes at the mRNA and protein level. METHODS: Expression microarrays containing approximately 10,500 genes were used to compare individual gene profiles of NP samples (n=10) and normal mucosal samples obtained from sphenoid sinuses in patients undergoing pituitary surgery (n=4). Four of the 5 most upregulated, and the single most downregulated, genes were retested by means of quantitative RT-PCR and immunohistochemistry in a different set of NP and normal mucosal samples obtained from the ethmoid and sphenoid sinuses. RESULTS: Compared with normal sinus tissue, 192 genes were upregulated at least 2-fold, and 156 genes were downregulated by at least 50% in NP samples (approximately 3% of genes evaluated). Four of the top 5 overexpressed genes (statherin, 48.0-fold; prolactin-induced protein [PIP] , 24.9-fold; lactoferrin, 26.6-fold; and deleted in malignant brain tumor 1 [DMBT1] , 30.3-fold) and the most underexpressed gene (Clara cell 10-kd protein [CC10] , -20.1-fold) were selected and retested by means of quantitative RT-PCR and immunohistochemical staining. Quantitative RT-PCR and immunohistochemical staining confirmed the differential expression of all except statherin in NP tissue. CONCLUSION: DNA microarrays can provide new insight into the possible pathophysiologic processes involved in NP.

Adult↗
PubMed2000

Gene expression profiling of mouse postnatal cerebellar development.

Expression patterns of 1,869 genes were determined using adapter-tagged competitive PCR (ATAC-PCR) at 6 time points during mouse postnatal cerebellar development. The expression patterns were classified into 12 clusters that were further assembled into 3 groups by hierarchical cluster analysis. Among the 1,869 genes, 1,053 known genes were assigned to 90 functional categories. Statistically significant correlation between the clusters or groups of gene expression and the functional categories was ascertained. Genes involved in oncogenesis or protein synthesis were highly expressed during the earlier stages of development. Those responsible for brain functions such as neurotransmitter receptor and synapse components were more active during the later stages of development. Many other genes also showed expression patterns in accordance with literature information. The gene expression patterns and the inferred functions were in good agreement with anatomical as well as physiological observations made during the developmental process.

Animals↗
PubMed2005

[Differentially expressed gene profiles of cochlea in rats induced by acute and chronic sodium salicylate injection].

OBJECTIVE: To study the mechanism of electrophysiologic changes caused by different type of sodium salicylate injection. METHODS: Decapitated three group rats ( acute injected, chronic injected and normal rats ) separately, dissected the temporal bones to collect cochlea, and the otic capsules were removed. Then the cochlear materials from each groups were pooled and homogenized respectively, extracted the total RNA, obtained cDNA from purified total RNA by reversed transcription, cDNA were transcripted to cRNA probes in vitro. Hybridized the cRNA probes with tester chip to evaluate the quality of probes, if good, hybridized the probes with real chip. Obtained three gene expression profiles of different groups of cochlea Analyzed the differentially expressed genes among three groups by SOM. Analogized the SOM result to electrophysiologic changes. Then analyzed the genes in clusters of analog results by Gene Ontology. Then the genes in clusters of analog results were analyzed by Gene Ontology. Hsp27 was chosen to validate the result of gene chip using real time quantitative reverse transcription PCR ( RTQ RT-PCR). RESULTS: The probes was good, and the chip hybridization results was credible. We obtained 6 clusters genes by SOM analysis, in which we choose cluster 3 and cluster 4 as candidate cluster. There were 46 genes in cluster 3 and 30 genes in cluster 4 employing GO analysis, which involved in cell communication, cell motility, metabolism, immune response and nerve ensheathment, et al. The result of RTQ RT-PCR showed high concordance with that of gene chip. CONCLUSION: It's a new method to study the mechanism of electrophysiologic changes caused by sodium salicylate by gene chip and SOM analysis.

Animals↗
PubMed2005

Acute myeloid leukemia bearing cytoplasmic nucleophosmin (NPMc+ AML) shows a distinct gene expression profile characterized by up-regulation of genes involved in stem-cell maintenance.

Approximately one third of acute myeloid leukemias (AMLs) are characterized by aberrant cytoplasmic localization of nucleophosmin (NPMc+ AML), consequent to mutations in the NPM putative nucleolar localization signal. These events are mutually exclusive with the major AML-associated chromosomal rearrangements, and are frequently associated with normal karyotype, FLT3 mutations, and multilineage involvement. We report the gene expression profiles of 78 de novo AMLs (72 with normal karyotype; 6 without major chromosomal abnormalities) that were characterized for the subcellular localization and mutation status of NPM. Unsupervised clustering clearly separated NPMc+ from NPMc- AMLs, regardless of the presence of FLT3 mutations or non-major chromosomal rearrangements, supporting the concept that NPMc+ AML represents a distinct entity. The molecular signature of NPMc+ AML includes up-regulation of several genes putatively involved in the maintenance of a stem-cell phenotype, suggesting that NPMc+ AML may derive from a multipotent hematopoietic progenitor.

Acute Disease↗
PubMed2006

Gene expression profile and overexpression of apoptosis-related genes (NGFI-B and Gadd 45 gamma) in early phase of Thy-1 nephritis model.

Mesangioproliferative glomerulonephritis (MPGN) is a disease of high incidence in humans. Rat Thy-1 nephritis (Thy-1 N), namely, anti-thymocyte serum (ATS)-induced nephritis, is considered to be an animal model for studying MPGN. Although previous studies have demonstrated that glomerular mesangial cell (GMCs) injury might be a feature of Thy-1 N, the mechanism of the disease (i.e., GMC apoptosis) remains unclear. We have examined the pathologic changes of GMCs and the gene expression profile of renal tissues in Thy-1 N. The pathologic changes of Thy-1 N include three phages: GMC apoptosis (40 min), necrosis (2 h), and proliferation (5 days). Many TUNEL-positive cells are found 40 min after administration of ATS. Concomitantly, 341 genes are up-regulated, whereas 392 genes are down-regulated, as shown by microarrays analysis. The mRNA and protein of two of the up-regulated genes (nerve growth factor induced protein I-B, NGFI-B; growth arrest- and DNA-damage-inducible protein 45 gamma, Gadd 45 gamma) in the GMC apoptotic phase of Thy-1 N are markedly elevated, as observed by real-time polymerase chain reaction and immunohistochemistry. Our data indicate that pathologic changes of Thy-1 N are involved in the abnormal gene profile. The overexpression of the NGFI-B and Gadd 45 gamma genes may be associated with GMC apoptosis of Thy-1 N.

Animals↗