Laser capture microdissection and its applications in genomics and proteomics.
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Breast Neoplasms↗
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Results for “Tissue Array Analysis”
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Transcriptional profile of aging in C. elegans.
BACKGROUND: Numerous gerontogene mutants leading to dramatic life extensions have been identified in the nematode Caenorhabditis elegans over the last 20 years. Analysis of these mutants has provided a basis for understanding the mechanisms driving the aging process(es). Several distinct mechanisms including an altered rate of aging, increased resistance to stress, decreased metabolic rate, or alterations in a program causing organismic aging and death have been proposed to underlie these mutants. RESULTS: Whole-genome analysis of gene expression during chronological aging of the worm provides a rich database of age-specific changes in gene expression and represents one way to distinguish among these models. Using a rigorous statistical model with multiple replicates, we find that a relatively small number of genes (only 164) show statistically significant changes in transcript levels as aging occurs (<1% of the genome). Expression of heat shock proteins decreases, while expression of certain transposases increases in older worms, and these findings are consistent with a higher mortality risk due to a failure in homeostenosis and destabilization of the genome in older animals. Finally, a specific subset of genes is coordinately altered both during chronological aging and in the transition from the reproductive form to the dauer, demonstrating a mechanistic overlap in aging between these two processes. CONCLUSIONS: We have performed a whole-genome analysis of changes in gene expression during aging in C. elegans that provides a molecular description of C. elegans senescence.
Aging↗
Micro patterning of cell and protein non-adhesive plasma polymerized coatings for biochip applications.
Micro scale patterning of bioactive surfaces is desirable for numerous biochip applications. Polyethyleneoxide-like (PEO-like) coating with non-fouling functionality has been deposited using low frequency AC plasma polymerization. The non-fouling properties of the coating were tested with human cells (HeLa) and fluorescence labeled proteins (isothiocyanate-labeled bovine serum albumin, i.e. FITC-BSA). The PEO-like coatings were fabricated by plasma polymerization of 12-crown-4 (ppCrown) with plasma polymerized hexene (ppHexene) as adhesion layer. The coatings were micro patterned using conventional cleanroom photolithography and lift-off. Single cell arrays showed sharp contrast in cell adhesion between the untreated glass surface and the ppCrown layer. Similarly, proteins adsorbed selectively to untreated glass but not to ppCrown. The simplicity of the lift-off technique and the sturdiness and versatility of the plasma-polymerized coatings, make this technology highly suitable for bio-MEMS and biochip applications, where patterned high contrast non-fouling surfaces are needed.
Adsorption↗
Expression signature of the mouse prostate.
Genetically engineered mice are being used increasingly for delineating the molecular mechanisms of prostate cancer development. Epithelium-stroma interactions play a critical role in prostate development and tumorigenesis. To better understand gene expression patterns in the normal sexually mature mouse prostate, epithelium and stroma were laser-capture microdissected from ventral, dorsolateral, and anterior prostate lobes. Genome-wide expression was measured by DNA microarrays. Our analysis indicated that the gene expression pattern in the mouse dorsolateral lobe was closest to that of the human prostate peripheral zone, supporting the hypothesis that these prostate compartments are functionally equivalent. Stroma from a given lobe had closer gene expression patterns with stroma from other lobes than epithelium from the same lobe. Stroma appeared to have higher expression complexity than epithelium. Specifically, stromal cells had higher expression levels of genes implicated in cell adhesion, muscle development, and contraction, in structural constituents of cytoskeleton and actin binding, and in components such as sarcomere and extracellular matrix collagen. Among the genes that were enriched in the epithelium were secretory proteins, including seminal vesicle protein secretion 2 and 5. Surprisingly, prostate stroma expressed many osteogenic molecules, as confirmed by immunohistochemistry. A "bone-like" environment in the prostate may predispose prostate cells for survival in the bone. Chemokine Cxcl12 but not its receptor, Cxcr4, was expressed in normal prostate. In prostate tumors, interestingly, Cxcl12 was up-regulated in epithelial cells with a concomitant expression of Cxcr4. Expression of both the receptor and ligand may provide an autocrine mechanism for tumor cell migration and invasion.
Actins↗
Rapid and diverse changes of gene expression in the kidneys of protein-overload proteinuria mice detected by microarray analysis.
BACKGROUND: Microarray is a method that allows the analysis of a large number of genes at the same time. We applied this method to show the difference of gene expression in the kidney caused by proteinuria. METHODS: An experimental mouse model of protein overload was prepared by bovine serum albumin injection. The mRNAs of kidneys isolated after 0, 1, 2, 3 and 4 weeks loading were analysed by Northern blotting. We analysed about 18000 genes by microarray. The expression patterns of the microarray were displayed on control, 1 and 3 weeks of protein overload using the clustering procedure. A clone showing the greatest changes of up-regulation in the kidney was cloned and analysed by in situ hybridization and immunohistochemistry. RESULTS: Over 1600 kinds of gene expression were confirmed in control kidneys. Proteinuria caused systematic changes of gene expression demonstrated by the cluster analysis. The up-regulation of osteopontin mRNA was shown and confirmed by Northern blot analysis. One of the clones showing the largest changes, AA275245, was isolated and characterized. It revealed that AA275245 was an unreported 3' non-coding region of vinculin mRNA which was associated with cytoskeleton proteins (e.g. alpha-actinin, talin, F-actin). Immunohistochemistry and in situ hybridization showed that this clone was identified in glomeruli as a mesangial pattern. The detected signal intensity using both methods, however, was virtually identical in control and disease kidney models. All data including images and analysed signal intensities are accessible on the web site. CONCLUSION: The microarray analysis revealed that the renal gene expression pattern was changed dynamically in mice with experimentally induced proteinuria within a few weeks.
Actins↗
Molecular techniques for identifying HCC origin and biology after orthotopic liver transplantation.
Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. Liver transplantation represents the potentially curative treatment for small HCC. Recurrence after surgical resection and liver transplantation remains one of the major obstacles in further prolonging survival of patients with HCC. In the new liver, HCC might be of recipient or donor origin. One approach for investigating this question is by performing human identification and/or engraftment analysis. Distinction between recurrent and de novo HCC after orthotopic liver transplantation could allow for the development of important clinical and therapeutic strategies. Polymerase chain reaction amplification of highly polymorphic short tandem repeat DNA sequences, gene expression profiling, and fluorescence in situ hybridization were applied in a patient who developed a second HCC after orthotopic liver transplantation from an opposite gender donor. These techniques provided consistent evidence that the second HCC was a recurrence of the primary tumor.
Amelogenin↗
Brain lipid binding protein in axon-Schwann cell interactions and peripheral nerve tumorigenesis.
Loss of axonal contact characterizes Schwann cells in benign and malignant peripheral nerve sheath tumors (MPNST) from neurofibromatosis type 1 (NF1) patients. Tumor Schwann cells demonstrate NF1 mutations, elevated Ras activity, and aberrant epidermal growth factor receptor (EGFR) expression. Using cDNA microarrays, we found that brain lipid binding protein (BLBP) is elevated in an EGFR-positive subpopulation of Nf1 mutant mouse Schwann cells (Nf1(-/-) TXF) that grows away from axons; BLBP expression was not affected by farnesyltransferase inhibitor, an inhibitor of H-Ras. BLBP was also detected in EGFR-positive cell lines derived from Nf1:p53 double mutant mice and human MPNST. BLBP expression was induced in normal Schwann cells following transfection with EGFR but not H-Ras12V. Furthermore, EGFR-mediated BLBP expression was not inhibited by dominant-negative H-Ras, indicating that BLBP expression is downstream of Ras-independent EGFR signaling. BLBP-blocking antibodies enabled process outgrowth from Nf1(-/-) TXF cells and restored interaction with axons, without affecting cell proliferation or migration. Following injury, BLBP expression was induced in normal sciatic nerves when nonmyelinating Schwann cells remodeled their processes. These data suggest that BLBP, stimulated by Ras-independent pathways, regulates Schwann cell-axon interactions in normal peripheral nerve and peripheral nerve tumors.
Animals↗
Rad is temporally regulated within myogenic progenitor cells during skeletal muscle regeneration.
The successful use of myogenic progenitor cells for therapeutic applications requires an understanding of the intrinsic and extrinsic cues involved in their regulation. Herein we demonstrate the expression pattern and transcriptional regulation of Rad, a prototypical member of a family of novel Ras-related GTPases, during mammalian development and skeletal muscle regeneration. Rad was identified using microarray analysis, which revealed robust upregulation of its expression during skeletal muscle regeneration. Our current findings demonstrate negligible Rad expression with resting adult skeletal muscle; however, after muscle injury, Rad is expressed within the myogenic progenitor cell population. Rad expression is significantly increased and localized to the myogenic progenitor cell population during the early phases of regeneration and within the newly regenerated myofibers during the later phases of regeneration. Immunohistochemical analysis demonstrated that Rad and MyoD are coexpressed within the myogenic progenitor cell population of regenerating skeletal muscle. This expression profile of Rad during skeletal muscle regeneration is consistent with the proposed roles for Rad in the inhibition of L-type Ca(2+) channel activity and the inhibition of Rho/RhoA kinase activity. We also have demonstrated that known myogenic transcription factors (MEF2, MyoD, and Myf-5) can increase the transcriptional activity of the Rad promoter and that this ability is significantly enhanced by the presence of the Ca(2+)-dependent phosphatase calcineurin. Furthermore, this enhanced transcriptional activity appears to be dependent on the presence of a conserved NFAT binding motif within the Rad promoter. Taken together, these data define Rad as a novel factor within the myogenic progenitor cells of skeletal muscle and identify key regulators of its transcriptional activity.
Animals↗
Characterization of differential gene expression in quiescent and invasive human arterial smooth muscle cells.
Proliferation, migration and invasion of smooth muscle cells (SMCs) are essential pathogenic processes in the development of a broad spectrum of cardiovascular disorders, like arteriosclerosis, restenosis after percutaneous transluminal angioplasty and stent implantation as well as transplant vessel disease. As an in vitro model mimicking these processes, the Boyden chamber was employed to characterize the diverging migratory and invasive potentials of proliferating and nonproliferating human arterial SMCs (haSMCs). Using this model, differential gene expression of both phenotypes was analyzed by a cDNA array system (Clontech human cardiovascular array). With these arrays, 558 cardiovascular-associated genes could be compared. Further, gene expression was exactly quantified by real-time RT-PCR. Protein expression was analyzed by ELISA and Western blotting. In total, 47 genes were differentially expressed more than 1.5 times. Most of the differentially regulated genes in this study were associated with the extracellular matrix (ECM) and cell motility. In detail, the respective groups were matrix-organizing proteins, ECM proteins, cell adhesion proteins, extracellular communication and cytoskeleton motility proteins. Genes known to be differentially regulated during haSMC migration and invasion, like TIMP 2, TIMP 3, and MMP 3, were confirmed by the array data. Reduced expression of several cytoskeletal proteins, like vimentin, fibronectin, cytokeratins and beta1 integrin, was shown in the invasive phenotype. Further, angio-associated protein, alpha E-catenin and atrial brain natriuretic peptide receptor were downregulated whereas TFPI 2 was strongly upregulated in invasive haSMCs. In conclusion, several relevant potential candidate genes for the quiescent and the invasive SMC phenotype were identified and genes already known to be differentially regulated by previous analysis were confirmed.
Arteriosclerosis↗
A rigorous method for multigenic families' functional annotation: the peptidyl arginine deiminase (PADs) proteins family example.
BACKGROUND: large scale and reliable proteins' functional annotation is a major challenge in modern biology. Phylogenetic analyses have been shown to be important for such tasks. However, up to now, phylogenetic annotation did not take into account expression data (i.e. ESTs, Microarrays, SAGE, ...). Therefore, integrating such data, like ESTs in phylogenetic annotation could be a major advance in post genomic analyses. We developed an approach enabling the combination of expression data and phylogenetic analysis. To illustrate our method, we used an example protein family, the peptidyl arginine deiminases (PADs), probably implied in Rheumatoid Arthritis. RESULTS: the analysis was performed as follows: we built a phylogeny of PAD proteins from the NCBI's NR protein database. We completed the phylogenetic reconstruction of PADs using an enlarged sequence database containing translations of ESTs contigs. We then extracted all corresponding expression data contained in EST database This analysis allowed us 1/To extend the spectrum of homologs-containing species and to improve the reconstruction of genes' evolutionary history. 2/To deduce an accurate gene expression pattern for each member of this protein family. 3/To show a correlation between paralogous sequences' evolution rate and pattern of tissular expression. CONCLUSION: coupling phylogenetic reconstruction and expression data is a promising way of analysis that could be applied to all multigenic families to investigate the relationship between molecular and transcriptional evolution and to improve functional annotation.
Animals↗
Assessing prognosis in non-small-cell lung cancer: avenues to a more complete picture?
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Antineoplastic Agents↗
A novel function of OLIG2 to suppress human glial tumor cell growth via p27Kip1 transactivation.
The basic helix-loop-helix transcription factor OLIG2 is specifically expressed in cells of the oligodendrocyte lineage. It is also expressed in various tumors originating from glial cells; however, the expression of OLIG2 is rare or weak in glioblastomas, the most malignant gliomas. The role of OLIG2 in glioma remains unclear. To investigate the function of OLIG2 in glial tumor cells, we have established a glioblastoma cell line, U12-1, in which the expression of OLIG2 is induced by the Tet-off system. Induction of OLIG2 resulted in suppression of both the proliferation and anchorage-independent growth of U12-1. It also resulted in an increase in the expression of p27(Kip1). A luciferase assay revealed that the CTF site of the p27(Kip1) gene promoter was essential for OLIG2-dependent activation of p27(Kip1) gene transcription. Electrophoretic mobility shift assays confirmed that a nuclear extract of OLIG2-expressing U12-1 cells contained a protein complex that binds to the CTF site of the p27(Kip1) gene promoter. Furthermore, siRNA against p27(Kip1) rescued the OLIG2-mediated growth and DNA synthesis inhibition of U12-1 cells. These results indicate that OLIG2 suppresses the proliferation of U12-1 and that this effect is mediated by transactivation of the p27(Kip1) gene, and low expression of OLIG2 may be related to the malignant behavior of human glioblastoma.
Basic Helix-Loop-Helix Proteins↗
Diagnostic plots for detecting outlying slides in a cDNA microarray experiment.
Different sources of systematic and random error variations are often observed in cDNA microarray experiments. A simple scatter plot is commonly used to examine outlying slides that have unusual expression patterns or larger variability than other slides. These outlying slides tend to have large impacts on the subsequent analyses, such as identification of differentially expressed genes and clustering analysis. However, it is difficult to select outlying slides rigorously and consistently based on subjective human pattern recognition on their scatter plots. A graphical method and a rigorous diagnostic measure are proposed to detect outlying slides. The proposed graphical method is easy to implement and shown to be quite effective in detecting outlying slides in real microarray data sets. This diagnostic measure is also informative to compare variability among slides. Two cDNA microarray data sets are carefully examined to illustrate the proposed approach. A 3840-gene microarray experiment for neuronal differentiation of cortical stem cells and a 2076-gene microarray experiment for anticancer compound time-course expression of the NCI-60 cancer cell lines.
Algorithms↗
Transcriptional silencing of zinc finger protein 185 identified by expression profiling is associated with prostate cancer progression.
We profiled the expression of genes in benign and untreated human prostate cancer tissues using oligonucleotide microarrays. We report here 50 genes with distinct expression patterns in metastatic and confined tumors (Gleason score 6 and 9; lymph node invasive and noninvasive). Validation of expression profiles of 6 genes by quantitative PCR revealed a strong inverse correlation in the expression of zinc finger protein 185 (ZNF185), bullous pemphigoid antigen gene (BPAG1), and prostate secretory protein (PSP94) with progression of prostate cancer. Treatment of prostate cancer cell lines with 5-aza-2'-deoxycytidine (5-Aza-CdR), an inhibitor of DNA methylation, restored ZNF185 expression levels. Moreover, methylation-specific PCR confirmed methylation of the 5'CpG islands of the ZNF185 gene in all of the metastatic tissues and 44% of the localized tumor tissues, as well as in the prostate cancer cell lines tested. Thus, transcriptional silencing of ZNF185 by methylation in prostate tumor tissues implicates the ZNF185 gene in prostate tumorigenesis.
Aged↗
Gene profiling approach in the analysis of lymphotoxin and TNF deficiencies.
Mice with combined lymphotoxin-alpha (LTalpha) and tumor necrosis factor (TNF) deficiencies show defects in the structure of peripheral lymphoid organs such as spleen, lymph nodes, and gut-associated lymphoid tissues. To identify genes associated with this defective phenotype in spleen, we applied a gene profiling approach, including subtractive cloning and gene array hybridizations, to mice with combined TNF/LT deficiency. The differentially expressed genes identified by these techniques was then evaluated by Northern blot analysis for splenic expression in knockout mice with single LTalpha or single TNF deficiency. Most of the genes detected in this analysis are directly or indirectly associated with disrupted LT and not TNF signaling.
Animals↗
eXPRESSION: an in silico tool to predict patterns of gene expression.
In embryological studies, expression pattern analyses are of special importance since genes that have temporally and spatially restricted expression are not only essential as lineage markers but are often causative in formation of specific fates. Further, where a molecule is expressed can be quite revealing in regard to its endogenous function. We present a gene discovery tool, termed eXPRESSION, that utilizes the public EST databases to identify genes matching desired transcriptional profiles. We first tested and validated the ability of eXPRESSION to discover tissue-specific genes in the adult mouse; empirically as well as with DNA microarrays and RT-PCRs. These studies showed that eXPRESSION predictions could identify genes that are specifically expressed in adult mouse tissues. Next, we developed a novel search strategy to find genes that are expressed in specific regions or tissues of the developing mouse embryo. With these tools, we identified several novel genes that exhibited a neural-specific or neural-enriched expression pattern during murine development. The data show that eXPRESSION is widely applicable and may be used to identify both adult and embryonic tissue- or organ-specific genes with minimal cost and effort.
Algorithms↗
Gene expression analysis of the critical period in the visual cortex.
The development of the primary visual cortex in animals possessing binocular vision is a classical paradigm for the study of activity-dependent neuronal plasticity. To elucidate the genetic determinants of this period of substantial plasticity, we conducted an unbiased and comprehensive transcript profiling analysis with differential display and DNA array techniques. We characterized the transcripts that change significantly between the critical and postcritical periods in the rat binocular visual cortex. We determined if these changes are specific for the visual cortex by simultaneously profiling the hippocampus and examined the impact of sensory experience on the accumulation of the identified transcripts. Our results uncover visual cortex-specific and unspecific transcription programs. Transcripts for protein kinases and phosphatases are particularly regulated. The identified transcripts support the notion that the critical period provides a permissive state for plasticity.
Animals↗
Gene expression in giant-cell tumors.
Malignant transformation is thought to be associated with changes in the expression of a number of genes, and this alteration in gene expression is considered critical to the development of the malignant phenotype. In this study, gene expression in 8 samples of giant-cell tumor (GCT) of bone, as well as in bone at the site of osteoarthritis and in a variety of normal tissues, was determined at Gene Logic Inc (Gaithersburg, Md) with the use of Affymetrix GeneChip U_133 arrays containing approximately 40,000 genes/expressed sequence tags (ESTs). Gene-expression analysis was performed with the use of the Gene Logic GeneExpress Software System. Differences in gene expression between GCTs and bone were observed. In addition, genes expressed uniquely in GCTs among these and 519 samples from 20 other tissue types were identified. Some of the genes that were found to be overexpressed in GCTs, such as tartrate-resistant acid phosphatase and the lysosomal H + -transporting ATPase, are also expressed by osteoclasts. Osteoprotegrin ligand (OPGL) was also selectively overexpressed in GCTs. The genes found to be overexpressed in GCTs appear to reflect the genetic profile of osteoclast-lineage cells and also the genetic profile of an osteoclastogenic environment. The genes identified in this study may play a role in the pathogenesis of GCTs, confirm the likely importance of OPGL in GCT pathogenesis, and may indicate other possible targets to which antitumor therapy could be directed.
Adolescent↗