High-density Oligonucleotide Probe Arrays Research Articles

Design, Validation and Annotation of Transcriptome-Wide Oligonucleotide Probes for the Oligochaete Annelid Eisenia fetida

High density oligonucleotide probe arrays have increasingly become an important tool in genomics studies. In organisms with incomplete genome sequence, one strategy for oligo probe design is to reduce the number of unique probes that target every non-redundant transcript through bioinformatic analysis and experimental testing. Here we adopted this strategy in making oligo probes for the earthworm Eisenia fetida, a species for which we have sequenced transcriptome-scale expressed sequence tags (ESTs). Our objectives were to identify unique transcripts as targets, to select an optimal and non-redundant oligo probe for each of these target ESTs, and to annotate the selected target sequences. We developed a streamlined and easy-to-follow approach to the design, validation and annotation of species-specific array probes. Four 244K-formatted oligo arrays were designed using eArray and were hybridized to a pooled E. fetida cRNA sample. We identified 63,541 probes with unsaturated signal intensities consistently above the background level. Target transcripts of these probes were annotated using several sequence alignment algorithms. Significant hits were obtained for 37,439 (59%) probed targets. We validated and made publicly available 63.5K oligo probes so the earthworm research community can use them to pursue ecological, toxicological, and other functional genomics questions. Our approach is efficient, cost-effective and robust because it (1) does not require a major genomics core facility; (2) allows new probes to be easily added and old probes modified or eliminated when new sequence information becomes available, (3) is not bioinformatics-intensive upfront but does provide opportunities for more in-depth annotation of biological functions for target genes; and (4) if desired, EST orthologs to the UniGene clusters of a reference genome can be identified and selected in order to improve the target gene specificity of designed probes. This approach is particularly applicable to organisms with a wealth of EST sequences but unfinished genome.

Genome-wide screenings for circadian clock genes in Drosophila

A high-density oligonucleotide probe array (GeneChip) has been used to learn how gene expression is globally regulated by the circadian clock mechanism. Here I review five articles, including our own, describing the genome-wide identification of rhythmically expressed genes by a similar strategy using GeneChip in Drosophila under light-dark (LD) and constant dark (DD) conditions. These studies drew common conclusions in some aspects. A number of genes were cyclically expressed in fly heads and they were involved in diverse functions, suggesting the entire complexity of circadian gene expression in Drosophila. In addition, a global effect of clock mutations, ClkJrk, per0 and tim0, on gene expressions was commonly observed, implying that these clock genes are associated with the transcriptional regulation of a large number of genes.

Oscillatory Mechanisms and Functional Differentiation of Circadian Clocks

Circadian rhythms govern behavior, physiology and metabolism of living organisms. Recent studies have revealed the role of several genes in the clock mechanism both in Drosophila and mammals. The core molecular mechanism underlying circadian oscillation in Drosophila is comprised of two interlocked feedback transcriptional loops: a period (per)/ timeless (tim) loop as a negative loop, and a Clock (Clk)/cycle (cyc) loop as a positive one. The per/tim loop is initiated by CLK-CYC heterodimer which binds to the E-box sequences (CACGTG) in per and tim promoters. The per and tim gene are activated, and their products form a heterodimer (PER-TIM) in cytoplasm. The heterodimer then moves into the nucleus and inhibits CLK-CYC activity, there by repressing per/tim own transcriptions. The Clk/cyc positive loop is also initiated by CLK-CYC. CLK-CYC activates the expression of vrille (vri) and PAR domain protein 1 (Pdp1) both of which also have the E-box in the promoter region. While VRI acts as a negative regulator of Clk, Pdp1, which accumulates in a delayed fasion compared to VRI, activates the Clk transcription. Although the framework of molecular mechanism of circadian oscillation is extensively elucidated, there are many issues unsolved concerning to the basic features of circadian rhythm. For example, so far we don’t have the definitive explanation why the period of circadian rhythm is about 24 hours. Additionally, the molecular mechanism of temperature compensation of period, which is one of the most remarkable features of circadian rhythm, is still remained as absolute mystery. Also, we still don’t know the exact number of output genes whose expressions are controled by the feedback loops. To study how gene expression is globally regulated by the clock mechanism, we used a high-density oligonucleotide probe array (GeneChip) to profile gene expression patterns in Drosophila under light-dark and constant dark conditions. We found 712 genes showing a daily fluctuation in mRNA levels under light-dark conditions and among them expression of 115 genes was still cycling in constant darkness, i.e. under a free-running condition. Unexpectedly, expression of a large number of genes cycled only under constant darkness. We are now doing behavior screenings for core clock genes by RNAi method. This project is the collaborate work with Hiroki Ueda (RIKEN CDB), Ryu Ueda, Kuniaki Takahashi (NIG), Kaoru Saigo (Univ. Tokyo) and Teiichi Tanimura (Kyushu Univ.).

Rebamipide, a Gastroprotective Drug, Inhibits Indomethacin-Induced Apoptosis in Cultured Rat Gastric Mucosal Cells: Association with the Inhibition of Growth Arrest and DNA Damage-Induced 45α Expression

Rebamipide, a gastromucosal protective drug, suppresses indomethacin-induced gastropathy in humans and rodents. Effects of rebamipide on gene expression in indomethacin-treated gastric mucosal cells (RGM1) were investigated using high-density oligonucleotide arrays. Indomethacin induced apoptosis in RGM1 cells in a dose-dependent manner. Rebamipide pretreatment significantly reduced indomethacin-induced apoptosis. We used gene expression profiling on high-density oligonucleotide probe arrays to characterize the transcriptional response of RGM1 cells to indomethacin treatment for 6 hr. Of the 8,799 probes examined, 717 (8.1%) were induced (400 probes) or repressed (317 probes) at least 1.5-fold. Among the 158 genes that were induced by indomethacin at least 2.0-fold, four genes that were down-regulated by rebamipide at least 2.0-fold are listed: growth arrest and DNA-damage-inducible 45 alpha (GADD 45 alpha), golgi SNAP receptor complex member 1, iodothyronine deiodinases, and transcription factor 8. Real time-PCR confirmed GADD 45 alpha expression and its inhibition by rebamipide. Inhibition of apoptosis-related genes is possibly important for the cytoprotective effect of rebamipide against indomethacin-induced gastric mucosal cell injury.

Gene expression profiling of the preclinical scrapie-infected hippocampus

The molecular events that underlie prion disease neuropathology remain poorly defined. Within the hippocampus of the ME7/CV mouse scrapie model, profound CA1 neuronal loss occurs between 160 and 180 days post-infection (dpi). To elucidate the molecular events that may contribute to this neuronal loss, we have applied Affymetrix high-density oligonucleotide probe arrays to the study of ME7-infected hippocampal gene expression at 170 dpi. The study has identified 78 genes that are differentially expressed greater than 1.5-fold within the preclinical ME7-infected hippocampus prior to the profound late stage glial cell activation. The results indicate oxidative and endoplasmic reticulum (ER) stress, activated ER and mitochondrial apoptosis pathways, and activated cholesterol biosynthesis within the scrapie-infected hippocampus, and offer insight into the molecular events which underlie the neuropathology.

FcεRI-mediated amphiregulin production by human mast cells increases mucin gene expression in epithelial cells

Topical application of a glucocorticoid is now widely recognized as the first-line therapy for bronchial asthma. However, glucocorticoid treatment is largely ineffective in relation to overproduction of sputum and lung tissue remodeling. The purpose of the current study was to identify human mast cell (MC) products that are related to goblet cell hyperplasia. The FcepsilonRI-mediated gene expression profile of MCs was examined by using high-density oligonucleotide probe arrays and RT-PCR. Secretion of a protein, amphiregulin, by the MCs was measured by ELISA. Upregulation of mucin genes in NCI-H292 cells by amphiregulin was evaluated by real-time RT-PCR. The expression levels of amphiregulin on histological sections obtained from 40 subjects with asthma and 6 healthy control subjects were estimated by immunohistochemical staining, and the correlation with the number of goblet cells was studied. Amphiregulin was secreted by human MCs after aggregation of FcepsilonRI, and its expression was not inhibited by a glucocorticoid (dexamethasone). Amphiregulin upregulated mucin gene expression in airway epithelial cells. Upregulation of amphiregulin expression was observed in MCs of patients with asthma, but not normal control subjects. Furthermore, upregulation of amphiregulin in MCs significantly correlated with the extent of goblet cell hyperplasia in the mucosa of patients with bronchial asthma. These results suggest that after exposure to antigens, human MCs may induce sputum production via release of amphiregulin. Therefore, amphiregulin may be a new target molecule for treatment of overproduction of sputum in bronchial asthma.

Identification of granulocyte subtype–selective receptors and ion channels by using a high-density oligonucleotide probe array

Background During inflammation, neutrophils, basophils, and eosinophils release cell type–specific mediators and proteases through signaling molecules, such as G protein–coupled receptors and ion channels. As such, ion channels and receptors, including G protein–coupled receptors, are common drug targets. Objective We sought to identify, for the first time, ion channels and receptors preferentially expressed by each granulocyte subtype. Methods Using GeneChip, we compared approximately 20,000 transcripts present in 7 leukocyte types, platelets, mast cells, and fibroblasts to identify granulocyte subtype–selective transcripts for receptors and ion channels. Granulocyte subtype–selective transcripts were chosen on the basis of several conditions, such as the transcript having a 5-fold or greater expression level compared with the maximum level of other leukocytes. Results Fifty-one transcripts were chosen to be preferentially expressed by each granulocyte subtype. Seventeen of the 51 transcripts have not been previously reported as granulocyte subtype selective. Among the 17 receptors and ion channels, 6 were basophil selective, eosinophil selective, or both and were not highly expressed by other organs, indicating that they might be potential targets for antiallergy drugs. Conclusion Use of this database of potential cell type–selective drug targets should minimize the efforts required for pharmaceutical development.

Identification of granulocyte subtype-selective receptors and ion channels by high-density oligonucleotide probe array

Rationale We sought to identify, for the first time, ion channels and receptors preferentially expressed by each granulocyte subtype. Methods Using GeneChip we compared approximately 20,000 transcripts present in 7 leukocyte types, platelets, mast cells and fibroblasts to identify granulocyte subtype-selective transcripts for receptors and ion channels. Granulocyte subtype selective transcripts were chosen based on several conditions such as the transcript having 5-fold or greater expression level compared to the maximum level of other leukocytes. Results Fifty-one transcripts were chosen to be preferentially expressed by each granulocyte subtype. Seventeen out of the 51 transcripts have not been previously reported as granulocyte subtype-selective. Among the 17 receptors and ion channels, six were basophil- and/or eosinophil-selective and were not highly expressed by other organs, indicating that they may be potential targets for anti-allergic drugs. Conclusions Utilization of this database of potential cell type-selective drug targets should minimize the efforts required for pharmaceutical development.

Identification of specific gene expression profiles in human mast cells mediated by Toll-like receptor 4 and FcϵRI

AbstractRodent mast cells (MCs) are reported to play a pivotal role in both innate and adaptive immunity. However, there is so far no evidence that human MCs are involved in innate immunity. We found that a functional Toll-like receptor 4 (TLR4) was expressed on human MCs when it was up-regulated by interferon γ (IFN-γ). To systematically explore how human MCs modulate the immune system following TLR4-mediated activation and FcϵRI aggregation, we used high-density oligonucleotide probe arrays (GeneChip) to compare the lipopolysaccharide (LPS)-induced gene expression profile with the IgE/anti-IgE-mediated profile in MCs. Both a shared core response, and LPS- or anti-IgE-specific programs of gene expression were observed in MCs. Furthermore, MCs exhibited an antiviral response gene program in response to IFN-γ, and LPS sustained that expression. Compared with the LPS-stimulated gene expression profile of human peripheral blood mononuclear cells, LPS-stimulated MCs specifically induced a subset of genes that included a Th2 cytokine and chemokines that recruit Th2 cells and eosinophils. These results reveal that human MCs express tailored pathogen- and antigen-specific immune responses and that human MCs may play important roles in innate and adaptive immunity.(Blood. 2003;102:2547-2554)

Ion channel gene expression in human lung, skin, and cord blood-derived mast cells.

Immunoglobulin E (IgE)-dependent activation of human mast cells (HMC) is characterized by an influx of extracellular calcium (Ca(2+)), which is essential for subsequent release of preformed (granule-derived) mediators and newly generated autacoids and cytokines. In addition, flow of ions such as K(+) and Cl(-) is likely to play an important role in mast cell activation, proliferation, and chemotaxis through their effect on membrane potential and thus Ca(2+) influx. It is therefore important to identify these critical molecular effectors of HMC function. In this study, we have used high-density oligonucleotide probe arrays to characterize for the first time the profile of ion channel gene expression in human lung, skin, and cord blood-derived mast cells. These cells express mRNA for inwardly rectifying and Ca(2+)-activated K(+) channels, voltage-dependent Na(+) and Ca(2+) channels, purinergic P2X channels, transient receptor potential channels, and voltage-dependent and intracellular Cl(-) channels. IgE-dependent activation had little effect on ion channel expression, but distinct differences for some channels were observed between the different mast cell phenotypes, which may contribute to the mechanism of functional mast cell heterogeneity.

Interferon-α/β receptor-mediated selective induction of a gene cluster by CpG oligodeoxynucleotide 2006

BackgroundOligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN) are known to exert a strong adjuvant effect on Th1 immune responses. Although several genes have been reported, no comprehensive study of the gene expression profiles in human cells after stimulation with CpG ODN has been reported.ResultsThis study was designed to identify a CpG-inducible gene cluster that potentially predicts for the molecular mechanisms of clinical efficacy of CpG ODN, by determining mRNA expression in human PBMC after stimulation with CpG ODN. PBMCs were obtained from the peripheral blood of healthy volunteers and cultured in the presence or absence of CpG ODN 2006 for up to 24 hours. The mRNA expression profile was evaluated using a high-density oligonucleotide probe array, GeneChip®. Using hierarchical clustering-analysis, out of a total of 10,000 genes we identified a cluster containing 77 genes as having been up-regulated by CpG ODN. This cluster was further divided into two sub-clusters by means of time-kinetics. (1) Inflammatory cytokines such as IL-6 and GM-CSF were up-regulated predominantly 3 to 6 hours after stimulation with CpG ODN, presumably through activation of a transcription factor, NF-κB. (2) Interferon (IFN)-inducible anti-viral proteins, including IFIT1, OAS1 and Mx1, and Th1 chemoattractant IP-10, were up-regulated predominantly 6 to 24 hours after stimulation. Blocking with mAb against IFN-α/β receptor strongly inhibited the induction of these IFN-inducible genes by CpG ODN.ConclusionThis study provides new information regarding the possible immunomodulatory effects of CpG ODN in vivo via an IFN-α/β receptor-mediated paracrine pathway.

Marked increase in CC chemokine gene expression in both human and mouse mast cell transcriptomes following Fcε receptor I cross-linking: an interspecies comparison

Rodent mast cells (MCs) are common experimental tools but are somewhat different from their human counterparts in their responses to certain cytokines and drugs. We examined the expression of more than 10 000 distinct genes in human and mouse cultured MCs using high-density oligonucleotide probe arrays to find molecules similarly regulated and expressed by the 2 MC types. After stimulation via high-affinity Fcepsilon receptor I (FcepsilonRI), the transcriptional levels of several CC chemokines were markedly increased, and I-309 (CCL1), macrophage inflammatory protein-1alpha (MIP-1alpha) (CCL3) and MIP-1beta (CCL4) were found among the 10 most increased human and mouse transcripts from approximately 12 000 genes (including some expressed sequence tags). In addition, a costimulatory molecule that was originally found on the membrane of activated T cells, 4-1BB (CD137), was found among the 10 most increased transcripts. The FcepsilonRI-induced expression of CC chemokines and 4-1BB was also detected at the protein level in both MC types. The conservation of these responses suggests that MCs play a crucial role in recruitment of various CCR-expressing cells into the tissue in a manner dependent on immunoglobin E, and that FcepsilonRI-mediated induction of several CC chemokines and 4-1BB is highly conserved between human and mouse. Interspecies comparison studies at the whole genome expression level should be useful for the interpretation of experimental data obtained in animal models of human pathobiology.

Genome-wide Transcriptional Orchestration of Circadian Rhythms inDrosophila

Circadian rhythms govern the behavior, physiology, and metabolism of living organisms. Recent studies have revealed the role of several genes in the clock mechanism both in Drosophila and in mammals. To study how gene expression is globally regulated by the clock mechanism, we used a high density oligonucleotide probe array (GeneChip) to profile gene expression patterns in Drosophila under light-dark and constant dark conditions. We found 712 genes showing a daily fluctuation in mRNA levels under light-dark conditions, and among these the expression of 115 genes was still cycling in constant darkness, i.e. under free-running conditions. Unexpectedly the expression of a large number of genes cycled exclusively under constant darkness. We found that cycling in most of these genes was lost in the arrhythmic Clock (Clk) mutant under light-dark conditions. Expression of periodically regulated genes is coordinated locally on chromosomes where small clusters of genes are regulated jointly. Our findings reveal that many genes involved in diverse functions are under circadian control and reveal the complexity of circadian gene expression in Drosophila.

Gene expression screening of human mast cells and eosinophils using high-density oligonucleotide probe arrays: abundant expression of major basic protein in mast cells

Mast cells (MCs) and eosinophils are thought to play important roles in evoking allergic inflammation. Cell-type--specific gene expression was screened among 12,000 genes in human MCs and eosinophils with the use of high-density oligonucleotide probe arrays. In comparison with other leukocytes, MCs expressed 140 cell-type--specific transcripts, whereas eosinophils expressed only 34. Among the transcripts for expected MC-specific proteins such as tryptase, major basic protein (MBP), which had been thought to be eosinophil specific, was ranked fourth in terms of amounts of increased MC-specific messenger RNA. Mature eosinophils were almost lacking this transcript. MCs obtained from 4 different sources (ie, lung, skin, adult peripheral blood progenitor--derived and cord blood progenitor--derived MCs, and eosinophils) were found to have high protein levels of MBP in their granules with the use of flow cytometric and confocal laser scanning microscopic analyses. The present finding that MCs can produce abundant MBP is crucial because many reports regarding allergic pathogenesis have been based on earlier findings that MBP was almost unique to eosinophils and not produced by MCs. (Blood. 2001;98:1127-1134)

Toward elucidating the global gene expression patternsof developing Arabidopsis: Parallel analysis of 8 300 genesby a high-density oligonucleotide probe array

Arabidopsis thaliana has been widely used as a model system, in various aspects of biological studies, such as genomics, genetics, cellular, developmental and molecular biology. In order to reveal the molecular events and regulatory networks controlling Arabidopsis development and responses to genetic and environmental changes, we designed and used a high-density oligonucleotide probe array (GeneChip) to profile global gene expression patterns. The Arabidopsis oligonucleotide probe array consists of probes from 8 300 unique Arabidopsis genes, which covers approximately one-third of the genome. Global transcription profiles of A. thaliana in various developmental stages, and their responses to different environments were generated using this microarray, and archived. Here, we analyze data sets derived from nineteen independent experiments. Constitutively and differentially expressed genes in seedlings, roots, leaves, inflorescences, flowers and siliques at different developmental stages were identified. Functions of these genes based on homologs were determined and categorized. Our results provide insight into the coordinated transcriptional regulation of the genes during plant growth and development.

Parallel Gene Expression Monitoring using Oligonucleotide Probe Arrays of Multiple Transcripts with an Animal Model of Focal Ischemia

High density oligonucleotide arrays offer tremendous potential to study gene changes occurring in disease states. The authors described the first case of using a custom designed high density oligonucleotide probe array containing 750 genes to monitor the changes in mRNA transcript levels occurring after focal ischemia for a period of 3 hours. Permanent middle cerebral artery occlusion in the rat resulted in neuronal degeneration in the dorsolateral cortex and striatum over a time course of 24 hours. Comparing the changes in hybridization levels in the frontal and parietal cortices and the striatum, between the ipsilateral and contralateral sides of the brain using the probe arrays resulted in the up-regulation of 24 genes, which showed greater than a twofold change. Very few genes were found to be downregulated after the ischemic insult. Many of the immediate early genes (IEGs) such as c-fos, NGFI-A, NGFI-C, and Krox-20 were found to be robustly upregulated in the three different regions studied. Other genes that were up-regulated in perifocal regions included Arc, Inhibin-beta-A, and the phosphatases MKP-1 and MKP-3. The hybridization signal intensity from the probe arrays enabled quantification of many genes relative to one another, and robust changes in expression were obtained with very little interanimal variability. Furthermore, the authors were able to validate the increased expression of NGFI-C and Arc using in situ hybridization. This represented the first example of using high density oligonucleotide probe arrays in studying the expression of many genes in parallel and in discrete brain regions after focal ischemia.

Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors

Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors of the human CDK2-cyclin A kinase complex and of Saccharomyces cerevisiae Cdc28p were identified. The structural basis for the binding affinity and selectivity was determined by analysis of a three-dimensional crystal structure of a CDK2-inhibitor complex. The cellular effects of these compounds were characterized in mammalian cells and yeast. In the latter case the effects were characterized on a genome-wide scale by monitoring changes in messenger RNA levels in treated cells with high-density oligonucleotide probe arrays. Purine libraries could provide useful tools for analyzing a variety of signaling and regulatory pathways and may lead to the development of new therapeutics.

Bacterial transcript imaging by hybridization of total RNA to oligonucleotide arrays.

We have used high-density oligonucleotide probe arrays (chips) for bacterial transcript imaging. We designed a chip containing probes representing 106 Hemophilus influenzae genes and 100 Streptococcus pneumoniae genes. The apparent lack of polyadenylated transcripts excludes enrichment of mRNA by affinity purification and we thus used total, chemically biotinylated RNA as hybridization probe. We show that hybridization of Streptococcus RNA to a chip allows simultaneous quantification of the transcript levels. The sensitivity was found to be in the range of one to five transcripts per cell. The quantitative chip results were in good agreement with conventional Northern blot analysis of selected genes. This technology allows simultaneous and quantitative measurement of the transcriptional activity of entire bacterial genomes on a single oligonucleotide probe array.

Cystic fibrosis mutation detection by hybridization to light-generated DNA probe arrays.

We have combined photochemistry and photolithography with solid-phase DNA synthesis chemistry to form a new technology that makes high density oligonucleotide probe array synthesis possible. Hybridization to these two-dimensional arrays containing hundreds or thousands of oligonucleotide probes provides a powerful DNA sequence analysis tool. Two types of light-generated DNA probe arrays have been used to test for a variety of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. One array, made up of 428 probes, was designed to scan through the length of CFTR exon 11 and identify differences from the wild type reference sequence. The second type of array contained 1480 probes chosen to detect known deletions, insertions, or base substitution mutations. The validity of the probe arrays was established by hybridizing them with fluorescently labeled control oligonucleotide targets. Characterized mutant CFTR genomic DNA samples were then used to further test probe array hybridization specificity. Finally, ten unknown patient samples were genotyped using the CFTR probe array assay. The genotype assignments were identical to those obtained by PCR product restriction fragment analysis. Our results show that light-generated DNA probe arrays are highly effective in analyzing complex mutation and polymorphism patterns in a relatively large gene such as CFTR.

Cystic fibrosis mutation detection by hybridization to light‐generated DNA probe arrays

We have combined photochemistry and photolithography with solid-phase DNA synthesis chemistry to form a new technology that makes high density oligonucleotide probe array synthesis possible. Hybridization to these two-dimensional arrays containing hundreds or thousands of oligonucleotide probes provides a powerful DNA sequence analysis tool. Two types of light-generated DNA probe arrays have been used to test for a variety of mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. One array, made up of 428 probes, was designed to scan through the length of CFTR exon 11 and identify differences from the wild type reference sequence. The second type of array contained 1480 probes chosen to detect known deletions, insertions, or base substitution mutations. The validity of the probe arrays was established by hybridizing them with fluorescently labeled control oligonucleotide targets. Characterized mutant CFTR genomic DNA samples were then used to further test probe array hybridization specificity. Finally, ten unknown patient samples were genotyped using the CFTR probe array assay. The genotype assignments were identical to those obtained by PCR product restriction fragment analysis. Our results show that light-generated DNA probe arrays are highly effective in analyzing complex mutation and polymorphism patterns in a relatively large gene such as CFTR. © 1996 Wiley-Liss, Inc.