PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Tissue Array Analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,135 records · Page 63Linked to original sources

Sexually dimorphic expression of protease nexin-1 and vanin-1 in the developing mouse gonad prior to overt differentiation suggests a role in mammalian sexual development.

The mammalian sex-determining pathway is controlled by the presence or absence of SRY expression in the embryonic gonad. Expression of SRY in males is believed to initiate a pathway of gene expression resulting in testis development. In the absence of SRY, ovary development ensues. Several genes have now been placed in this pathway but our understanding of it is far from complete and several functional classes of protein appear to be absent. Sex-determining genes frequently exhibit sexually dimorphic patterns of expression in the developing gonad both before and after overt differentiation of the testis or ovary. In order to identify additional sex-determining or gonadal differentiation genes we have examined gene expression in the developing gonads of the mouse using cDNA microarrays constructed from a normalized urogenital ridge library. We screened for genes exhibiting sexually dimorphic patterns of expression in the gonad at 12.5 and 13.5 days post-coitum, after overt gonad differentiation, by comparing complex cDNA probes derived from male and female gonadal tissue at these stages on micro-arrays. Using in situ hybridization analysis we show here that two genes identified by this screen, protease nexin-1 (Pn-1) and vanin-1 (Vnn1), exhibit male-specific expression prior to overt gonadal differentiation and are detected in the somatic portion of the developing gonad, suggesting a possible direct link to the testis-determining pathway for both genes.

Amidohydrolases↗

Molecular characterization of salivary gland malignancy using the Smgb-Tag transgenic mouse model.

The molecular mechanisms underlying salivary gland tumorigenesis remain unclear. In order to identify genetic changes that occur during the development of invasive adenocarcinoma from normal salivary gland, we used the Smgb-Tag transgenic mouse model. This transgene induces the progressive development of dysplasia to invasive adenocarcinoma in the submandibular salivary gland. Gene expression patterns from 20 submandibular glands (two normal, nine dysplasia and nine adenocarcinoma samples) were assessed using a mouse 15 K cDNA array. Unsupervised hierarchical clustering was used to group gene expression based on 157 differentially expressed genes distinguishing between dysplasias and adenocarcinomas. Further analysis identified 25 significantly overexpressed and 28 underexpressed cDNA sequences in adenocarcinoma as compared to dysplasia. Differential expression of five genes (Lcn2, Ptn, Cd24a, Mapk6 and Rnps1) was validated by quantitative real-time RT-PCR in a total of 48 mouse salivary gland tissues (seven histologically normal, 13 dysplasias and 28 adenocarcinomas), including the 20 samples analyzed by cDNA arrays. Immunohistochemical analysis was used to validate the expression of Ptn and Cd24a at the protein level in a subset of 16 mouse salivary glands (four normal, five dysplasia and seven adenocarcinoma samples), as well as in 23 human submandibular gland tumors (16 pleomorphic adenomas, three adenoid cystic carcinomas, one acinic cell carcinoma, one adenocarcinoma NOS, one myoepithelial and one mucoepidermoid carcinoma). We thus demonstrated that the Smgb-Tag transgenic mouse model is a useful tool for the identification of genes that are deregulated in salivary gland adenocarcinomas. Our data suggest that Ptn and Cd24a may be genetic markers associated with salivary gland tumorigenesis and/or progression.

Adenocarcinoma↗

Decreased expression of NEFH and PCP4/PEP19 in the prefrontal cortex of alcoholics.

Patients with alcoholism exhibit behavioral adaptations to ethanol such as tolerance, dependence, and addiction. Molecular mechanisms that underlie these altered behavioral responses to ethanol are largely unclear. We have performed oligonucleotide microarray analysis in postmortem prefrontal cortices of alcoholics. Among about 12,000 genes represented on microarray, a total of 79 genes showed differential expression changes in alcoholics compared with control subjects, consisting of 54 up- and 25 down-regulated genes. Altered expressions in alcoholics were observed in genes having a wide range of biological functions. The remarkable findings were up-regulation of myelin-related genes and molecular chaperones in alcoholics. Among the genes identified, decreased expressions of NEFH and PCP4/PEP19 were further examined. NEFH encodes a component of neurofilament protein in neurons. PCP4/PEP19 encodes protein involved in calcium signaling and neuronal apoptosis. Observation of their down-regulations in alcoholics in microarray analysis was confirmed by real-time quantitative RT-PCR, and was also confirmed in the independent set of postmortem brains of alcoholics. The present results may provide some insights into understanding the mechanism of ethanol-induced altered behavioral responses at the molecular level.

Adult↗

Detection of novel gene expression in paraffin-embedded tissues by isotopic in situ hybridization in tissue microarrays.

Correlating altered gene expression patterns with particular disease states is a critical step in understanding disease processes and developing treatment strategies. Many thousands of novel gene sequences have recently been annotated in public and private databases and are now available for analysis. Tissue-specific expression patterns of these sequences can be evaluated physically on DNA arrays and other high throughput assays, or virtually by bioinformatics mining of expressed sequence tag (EST) databases. As a secondary screening tool, in situ hybridisation (ISH) not only confirms tissue specificity, but also reveals what is often valuable information about cell-type expression patterns of nov16l sequences. Due to their availability and long-term stability at room temperature, formalin-fixed paraffin-embedded clinical specimens provide an invaluable resource for evaluating expression patterns of novel human genes. We describe a high-throughput approach for identifying and quantifying the expression of novel genes in paraffin-embedded human tissues using isotopic in situ hybridisation and tissue microarrays (TMA).

Blotting, Northern↗

Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control.

Rapid rates of evolution can signify either a lack of selective constraint and the consequent accumulation of neutral alleles, or positive Darwinian selection driving the fixation of advantageous alleles. Based on a comparison of 1,350 orthologous gene pairs from human and mouse, we show that the evolution of gene expression profiles is so rapid that it is comparable to that of paralogous gene pairs or randomly paired genes. The expression divergence in the entire set of orthologous pairs neither strongly correlates with sequence divergence, nor focuses in any particular tissue. Moreover, comparing tissue expressions across the orthologous gene pairs, we observe that any human tissue is more similar to any other human tissue examined than to its corresponding mouse tissue. Collectively, these results indicate that, while some differences in expression profiles may be due to adaptive evolution, the levels of divergence are mostly compatible with a neutral mode of evolution, in which a mutation for ectopic expression may rise to fixation by random drift without significantly affecting the fitness. A disturbing corollary of these findings is that knowledge of where the gene is expressed may not carry information about its function.

Animals↗

Lymphoid tissue and emphysema in the lungs of transgenic mice inducibly expressing tumor necrosis factor-alpha.

To develop a model in which the pathogenic effects of the proinflammatory cytokine tumor necrosis factor-alpha (TNF) could be investigated, transgenic mice that express TNF in the lung under the control of a doxycycline-inducible promoter were generated. TNF transgene message was expressed at a low level in the absence of doxycycline treatment and was induced in the lung by administration of the drug. Analysis of lung lavage fluid indicated increases in neutrophils and lymphocytes in doxycycline-treated transgenic mice. Histologic analysis of lungs from adult transgenic mice treated with doxycycline revealed prominent development of lymphoid tissue and increases in airspace size. Genes upregulated in TNF transgenic mice, as identified by oligonucleotide microarray analysis, included a variety of transcripts expressed in lymphoid tissues. Immunohistochemical analysis demonstrated the presence of B lymphocytes and, to a lesser extent, T lymphocytes within lymphoid aggregates in TNF transgenic mice. CD8-positive T cells were absent from lymphocytic nodules, but in the lung parenchyma were more abundant in transgenic than in nontransgenic mice. These results indicate that induction of TNF in adult lung promotes the formation of lymphoid tissue and emphysema, and provides a model in which the pathogenic effects of TNF on the lung can be investigated.

Animals↗

Gene expression patterns and gene copy number changes in dermatofibrosarcoma protuberans.

Dermatofibrosarcoma protuberans (DFSP) is an aggressive spindle cell neoplasm. It is associated with the chromosomal translocation, t(17:22), which fuses the COL1A1 and PDGFbeta genes. We determined the characteristic gene expression profile of DFSP and characterized DNA copy number changes in DFSP by array-based comparative genomic hybridization (array CGH). Fresh frozen and formalin-fixed, paraffin-embedded samples of DFSP were analyzed by array CGH (four cases) and DNA microarray analysis of global gene expression (nine cases). The nine DFSPs were readily distinguished from 27 other diverse soft tissue tumors based on their gene expression patterns. Genes characteristically expressed in the DFSPs included PDGF beta and its receptor, PDGFRB, APOD, MEOX1, PLA2R, and PRKCA. Array CGH of DNA extracted either from frozen tumor samples or from paraffin blocks yielded equivalent results. Large areas of chromosomes 17q and 22q, bounded by COL1A1 and PDGF beta, respectively, were amplified in DFSP. Expression of genes in the amplified regions was significantly elevated. Our data shows that: 1) DFSP has a distinctive gene expression profile; 2) array CGH can be applied successfully to frozen or formalin-fixed, paraffin-embedded tumor samples; 3) a characteristic amplification of sequences from chromosomes 17q and 22q, demarcated by the COL1A1 and PDGF beta genes, respectively, was associated with elevated expression of the amplified genes.

Adult↗

Transcriptional analysis of avian embryonic tissues following infection with avian infectious bronchitis virus.

Avian infectious bronchitis virus (IBV) infection is one of the major viral respiratory diseases of chickens. Better understanding of the molecular basis of viral pathogenesis should contribute significantly towards the development of improved prophylactic, therapeutic and diagnostic reagents to control infections. In the present investigation, transcriptional profiles were analyzed by using RNA recovered from the lung tissue of IBV infected 18-day-old chicken embryos at 6, 24, 48 and 72 h post IBV infection. This microarray analysis was completed using avian cDNA arrays comprised of fragments of 1191 unique chicken and turkey gene transcripts. These arrays were generated from normalized cDNA subtraction libraries that were derived from avian pneumovirus (APV) infected chicken embryo fibroblast (CEF) cultures and tissues obtained from APV infected turkeys subtracted with their respective uninfected cultures and tissues. Of the 1191 unique genes represented on the array, the expression of a total of 327 genes (27% of total) were altered by two-fold or more from 6 through 72 h post-infection. A comparative analysis of IBV regulated genes with genes previously reported to change in expression following infection with other avian respiratory viruses revealed both conserved and unique changes. Real-time qRT-PCR was used to confirm the regulated expression of genes related to several functional classes including kinases, interferon induced genes, chemokines and adhesion molecules, vesicular trafficking and fusion protein genes, extracellular matrix protein genes, cell cycle, metabolism, cell physiology and development, translation, RNA binding, lysosomal, protein degradation and ubiquitination related genes. Microarray analysis served as an efficient tool in facilitating a comparative analysis of avian respiratory viral infections and provided insight into host transcriptional changes that were conserved as well as those which were unique to individual pathogens.

Animals↗

Gene expression profiling of the rat hippocampus one month after focal cerebral ischemia followed by enriched environment.

Functional recovery after experimental stroke in rats is enhanced by environmental enrichment by stimulating plastic changes in brain regions outside the lesion, but the molecular mechanisms are not known. We investigated the effect of environmental enrichment after focal cerebral ischemia on cognitive recovery and hippocampal gene expression using microarray analysis. Rats placed in enriched environment (EE) for 1 month after middle cerebral artery occlusion (MCAo) showed significantly improved spatial memory in the Morris water maze compared to rats housed alone after MCAo. Microarray analysis suggested several EE-induced differences in neuronal plasticity-related genes, but these changes could not be confirmed by quantitative real-time PCR. This study highlights some of the potential problems associated with gene expression profiling of brain tissues. Further studies at earlier time points and in additional subregions of the brain are of interest in the search for molecular mechanisms behind EE-induced neuronal plasticity after ischemic stroke.

Animals↗

Nucleus alignment and cell signaling in fibroblasts: response to a micro-grooved topography.

Cellular response to scaffold materials is of great importance in cellular and tissue engineering, and it is perhaps the initial cell contact with the scaffold that determines development of new tissue. Material surface morphology has strong effects on cell cytoskeleton and morphology, and it is thought that cells may react to the topography of collagen and surrounding cells during tissue embryology. A poorly understood area is, however, gene-level responses to topography. Thus, this paper used microarray to probe for consistent gene changes in response to lithographically produced topography (12.5 x 2-microm grooves) with time. The results showed many initial gene changes and also down-regulation of gene response with time. Cell and nucleus morphology were also considered, with nuclear deformation linked to cell signaling.

Cell Adhesion↗

Highly expressed genes in pancreatic ductal adenocarcinomas: a comprehensive characterization and comparison of the transcription profiles obtained from three major technologies.

When using gene expression profiling to understand human tumors, one is often confronted with long lists of genes that need to be further categorized into meaningful data. We performed a comprehensive evaluation and comparison of gene expression profiles obtained from pancreatic cancers to determine those genes most differentially expressed and thus with the most promise for translation into clinically useful targets. cDNA was prepared from 50 samples of normal pancreas or duodenal mucosal tissues, 7 samples of chronic pancreatitis, and 39 samples of pancreas cancer tissues or cancer cell lines and hybridized to the complete Affymetrix Human Genome U133 GeneChip set (arrays U133A and U133B) for simultaneous analysis of 45,000 fragments corresponding to 33,000 known genes and 6,000 expressed sequence tags. Genes expressed at levels at least 3-fold greater in the pancreatic cancers as compared with nonneoplastic tissues were identified. Three hundred seventy-seven Affymetrix fragments were identified as having > or = 3-fold expression levels in pancreas cancer specimens as compared with nonneoplastic tissues, corresponding to 234 known genes. Serial analysis of gene expression libraries (http://www.ncbi.nlm.nih.gov/SAGE/) of two normal pancreatic ductal cell cultures (HX and H126) were used to exclude 17 genes with high expression levels in the normal duct epithelium (more than five tags/library). Of the remaining 217 known genes, 75 have been previously reported as highly expressed in pancreatic cancers, while the remaining 142 genes are novel. We used principal components analysis (PCA) to identify the genes among these 217 identified as the most differentially expressed and specific to pancreatic cancer tissues or cell lines. Among the most differentially expressed genes identified by PCA were Mesothelin, Muc4, Muc5A/C, Kallikrein 10, Transglutaminase 2, Fascin, TMPRSS3 and stratifin. The differential expression identified by PCA for these genes indicates they are among the more attractive targets for novel therapeutic targets, tumor markers, or as a means of screening pancreatic cancer samples for information regarding tumor classification or potential therapeutic responses. Our findings were also compared in detail to the previously reported findings of highly expressed genes in other studies of global gene expression in pancreatic cancers. We found that robust changes in gene expression were most often identified by more than one gene expression platform. Forty genes were identified by more than one method (U133 oligonucleotide arrays, cDNA arrays or serial analysis of gene expression), and 6 of these genes were identified by all three methods. Our findings identify a novel set of genes as highly expressed in pancreatic cancer, validate the differential expression of previously reported genes, and provide additional support for those genes most differentially expressed to be translated into clinically useful targets.

Carcinoma, Pancreatic Ductal↗

Search for novel gene markers of traumatic brain injury by time differential microarray analysis.

Neuronal and glial cell death caused by axonal injury sometimes contributes to whole brain pathology after traumatic brain injury (TBI). We show that neuroprotection by 2 types of immunosuppressants, cyclosporin A (CsA) and tacrolimus (FK506), in a cryogenic brain injury model results from inhibition of calcineurin and protection from mitochondrial damage caused by formation of a mitochondrial permeability transition pore induced by cyclophilin D (CyPD), one of the prolyl cis/trans isomerase family members. We evaluated why CsA is neuroprotective by microarray analysis of gene expression in the cryogenic brain injury rat model. Analyses of expression patterns demonstrated that expression of over 14,000 genes changed between the groups with and without CsA treatment, and about 350 genes among them were extracted showing a significant difference. We learned that the differential expression of several gene targets showed specific patterns in a time-dependent manner. These results may help elucidate the mechanisms of neuronal cell death after TBI and the neuroprotective effects of CsA after TBI.

Animals↗

The effect of cooking on veterinary drug residues in food: 4. Oxytetracycline.

The heat stability of oxytetracycline (OTC) in water and vegetable oil was investigated. Results showed that the drug was unstable in water at 100 degrees C with a half-life of about 2 min, but more stable in oil at 180 degrees C where the half-life was about 8 min. The effect of a range of cooking processes including microwaving, boiling, roasting, grilling, braising and frying on OTC residues in incurred animal tissues was investigated. Substantial net reductions in OTC of 35-94% were observed, with temperature during cooking having the largest impact on the loss. Migration from the tissue into the surrounding liquid or meat juices was observed during the cooking processes. Diode-array analysis of heat-treated OTC standard solutions indicated that no individual closely related compound such as 4-epioxytetracycline, alpha- or beta-apooxytetracycline formed a significant proportion of the breakdown products. OTC was not evenly distributed throughout the tissue, but the effects of this were minimized by selecting adjacent samples for cooking and for the raw control. The findings of this investigation showed that the effect of cooking on residues of OTC should be considered before data obtained from measurements on raw tissue are used for consumer exposure estimates and dietary intake calculations.

Animals↗

A large-scale screening of the normalized mammalian mitochondrial gene expression profiles.

Mammalian mitochondrial genomes are organized in a conserved and extremely compact manner, encoding molecules that play a vital role in oxidative phosphorylation (OXPHOS) and carry out a number of other important biological functions. A large-scale screening of the normalized mitochondrial gene expression profiles generated from publicly available mammalian serial analysis of gene expression (SAGE) datasets (over 17.7 millions of tags) was performed in this study. Acquired SAGE libraries represent an extensive range of human, mouse, rat, bovine and swine cell and tissue samples (normal and pathological) in a variety of conditions. Using a straightforward in silico algorithm, variations in total mitochondrial gene expression, as well as in the expression of individual genes encoded by mitochondrial genomes are addressed, and common patterns in the species- and tissue-specific mitochondrial gene expression profiles are discussed.

Algorithms↗

A single dose of lysergic acid diethylamide influences gene expression patterns within the mammalian brain.

Hallucinogenic drugs such as lysergic acid diethylamide (LSD) have profound effects on humans including hallucinations and detachment from reality. These remarkable behavioral effects have many similarities to the debilitating symptoms of neuropsychiatric disorders such as schizophrenia. The effects of hallucinogens are thought to be mediated by serotonin receptor activation; however, how these drugs elicit the unusual behavioral effects remains largely a mystery, despite much research. We have undertaken the first comprehensive analysis of gene expression influenced by acute LSD administration in the mammalian brain. These studies represent a novel approach to elucidate the mechanism of action of this class of drugs. We have identified a number of genes that are predicted to be involved in the processes of synaptic plasticity, glutamatergic signaling and cytoskeletal architecture. Understanding these molecular events will lead to new insights into the etiology of disorders whose behavioral symptoms resemble the temporary effects of hallucinogenic drugs, and also may ultimately result in new therapies.

Animals↗

Gene expression profile analysis of lymphocytes from Alzheimer's patients.

Since the function and metabolism of peripheral lymphocytes is known to be altered in Alzheimer's disease (AD), a pilot study was carried out to examine differences in gene expression profiles of these cells in 16 AD patients and aged control probands. Using a cDNA microarray representing 3200 distinct human genes, we identified 20 candidate genes whose expression is altered in AD lymphocytes compared with the control probands. Among these were the alpha2C-adrenoreceptor gene, known to regulate blood pressure and learning, the defensin, histocompability complex enhancer-binding protein, carboxypeptidase M, and the Fc fragment of IgE known to be involved in cellular and humoral immune responses. Others, like human cell death protein, TRAIL, and galectin-4 participate in the regulation of apoptosis. Real-time quantitative reverse transcription-polymerase chain reaction analysis was performed in order to confirm the expression changes in AD lymphocytes, and it could detect down-regulation of defensin and alpha2c-adrenoceptor genes, while other genes seemed unaltered in their expression, including heat-shock protein (hsp90), cholesteryl ester transfer protein, and apolipoprotein B100 (apoB). The altered expression profile of these genes might be connected with the previously reported AD-specific lymphocyte abnormalities. It remains to be elucidated, however, how these genes are related to the pathomechanism of dementia and whether the gene expression differences of AD lymphocytes reflect disease traits or stage processes.

Aged↗

Selective induction of neuropilin-1 by vascular endothelial growth factor (VEGF): a mechanism contributing to VEGF-induced angiogenesis.

Neuropilin (NRP) 1, previously identified as a neuronal receptor that mediates repulsive growth cone guidance, has been shown recently to function also in endothelial cells as an isoform-specific receptor for vascular endothelial growth factor (VEGF)(165) and as a coreceptor in vitro of VEGF receptor 2. However, its potential role in pathologic angiogenesis remains unknown. In the present study, we first show that VEGF selectively up-regulates NRP1 but not NRP2 via the VEGF receptor 2-dependent pathway. By NRP1 binding analysis, we showed that its induction by VEGF accompanies functional receptor expression. Endothelial proliferation stimulated by VEGF(165) was inhibited significantly by antibody perturbation of NRP1. In a murine model of VEGF-dependent angioproliferative retinopathy, intense NRP1 mRNA expression was observed in the newly formed vessels. Furthermore, selective NRP1 inhibition in this model suppressed neovascular formation substantially. These results suggest that VEGF cannot only activate endothelial cells directly but also can contribute to robust angiogenesis in vivo by a mechanism that involves up-regulation of its cognate receptor expression.

Animals↗

Structural colouration of mammalian skin: convergent evolution of coherently scattering dermal collagen arrays.

For more than a century, the blue structural colours of mammalian skin have been hypothesized to be produced by incoherent, Rayleigh or Tyndall scattering. We investigated the colour, anatomy, nanostructure and biophysics of structurally coloured skin from two species of primates - mandrill (Mandrillus sphinx) and vervet monkey (Cercopithecus aethiops) - and two species of marsupials - mouse opossum (Marmosa mexicana) and wooly opossum (Caluromys derbianus). We used two-dimensional (2-D) Fourier analysis of transmission electron micrographs (TEMs) of the collagen arrays in the primate tissues to test whether these structural colours are produced by incoherent or coherent scattering (i.e. constructive interference). The structural colours in Mandrillus rump and facial skin and Cercopithecus scrotum are produced by coherent scattering by quasi-ordered arrays of parallel dermal collagen fibres. The 2-D Fourier power spectra of the collagen arrays from Mandrillus and Cercopithecus reveal ring-shaped distributions of Fourier power at intermediate spatial frequencies, demonstrating a substantial nanostructure of the appropriate spatial frequency to produce the observed blue hues by coherent scattering alone. The Fourier power spectra and the observed reflectance spectra falsify assumptions and predictions of the incoherent, Rayleigh scattering hypothesis. Samples of blue Marmosa and Caluromys scrotum conform generally to the anatomy seen in Mandrillus and Cercopithecus but were not sufficiently well preserved to conduct numerical analyses. Colour-producing collagen arrays in mammals have evolved multiple times independently within the two clades of mammals known to have trichromatic colour vision. Mammalian colour-producing collagen arrays are anatomically and mechanistically identical to structures that have evolved convergently in the dermis of many lineages of birds, the tapetum of some mammals and the cornea of some fishes. These collagen arrays constitute quasi-ordered 2-D photonic crystals.

Animals↗