Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Oligonucleotide Array Sequence Analysis”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 361 records · Page 20Linked to original sources

Antisense abrogation of DENN expression induces apoptosis of leukemia cells in vitro, causes tumor regression in vivo and alters the transcription of genes involved in apoptosis and the cell cycle.

We previously reported that messenger RNA expression of DENN (differentially expressed in normal and neoplastic cells) is considerably higher in cancer cell lines than in normal cells. In our present study, we established that certain cancer cell lines express conspicuously higher levels of the 2 DENN isoforms in contrast to the 2 pro-apoptotic IG20 isoforms. Antisense DENN oligodeoxynucleotide treatment of K36 cells in vitro induced extensive apoptosis, while antisense DENN silencing of K36 tumor-bearing mice caused significant tumor regression in vivo. Compared to wild-type murine embryonic fibroblasts, antisense treatment of NFkappaB and TNFR1 KO cells resulted in markedly more pronounced cell death, whereas antisense-treated TNFalpha and TNFR2 knockouts exhibited less prominent apoptosis. Cell viability and apoptosis were authenticated by flow cytometry, membrane integrity, TUNEL, annexin V assays, histology and electron microscopy. Antisense abrogation of DENN expression culminated in upregulated expression of TNFR2, TRAIL and Fas, but downregulation of TNFalpha, TNFR1 and cyclin D3. Conversely, DENN overexpression stimulated cell proliferation and led to upregulated TRPM2 and cyclin B1, but diminished expression of Fas, TNFR2, TRAIL and Egr-1. The participation of TNFalpha, TNFR1, TNFR2 and Fas in the inhibition of DENN expression was also demonstrated. These data support the anti-apoptotic and cell survival role of DENN, especially in malignant cells, and its interaction with specific genes and proteins involved in the apoptotic and cell cycle pathways.

Animals↗

Identification of c-Jun as a critical mediator for the intracrine 24 kDa FGF-2 isoform-induced cell proliferation.

Tumor cells frequently synthesize an N-terminally extended the FGF-2 isoform of 24 kDa devoid of signal peptide but that contains a functional nuclear localization sequence (NLS). Although the signaling pathways elicited by secreted FGF-2 are well described, the molecular mechanisms involved in the growth promoting action of nuclearized 24 kDa FGF-2 remain unknown. The cancer cell line AR4-2J was engineered to stably express only the 24 kDa FGF-2 isoform and cDNA microarrays were used to identify targets implicated in the intracrine-induced cell proliferation. Levels of 27 transcripts were found either upregulated or downregulated compared to control cells. Among the 18 upregulated genes was c-jun, which is often involved in cell proliferation. Real-time PCR and Western blot analyses confirmed c-jun induction at both mRNA and protein levels. The c-jun antisense oligonucleotide strategy pointed out the involvement of c-Jun in the 24 kDa FGF-2-induced cell proliferation. The mitogenic effect was found to depend on ERK pathway and not on phosphoinositide 3-kinase, p38 MAPK, c-Jun NH2-terminal kinase signal transducers. In addition, the MEK inhibitor PD98059 reduced the 24 kDa FGF-2-dependent c-Jun level. These data show that intracrine FGF-2-mediated regulation of cell growth involves ERK activation and consequent c-Jun expression. Thus, despite its incapacity to be secreted, the intracellular-localized 24 kDa FGF-2 can activate a growth-related signaling pathway normally elicited by cell surface receptors.

Animals↗

Immunosurveillance is active in colorectal cancer as downregulation but not complete loss of MHC class I expression correlates with a poor prognosis.

Many colorectal tumors lose or downregulate cell surface expression of MHC class I molecules conferring resistance to T-cell-mediated attack. It has been suggested that this phenomenon is due to in vivo immune-tumor interactions. However, evidence of the impact of MHC class I loss on outcomes from colorectal cancer is scarce. In our study of more than 450 colorectal cancers in tissue microarray format, we have shown that both high levels of MHC class I expression and absent MHC class I expression are associated with similar disease-specific survival times, possibly due to natural killer cell-mediated clearance of MHC class I-negative tumor cells. However, tumors with low level expression of MHC class I were found to confer a significantly poorer prognosis, retaining independent significance on multivariate analysis. The existence of these poor prognosis tumors, which may avoid both NK- and T-cell-mediated immune surveillance, has important implications for the design of immunotherapeutic strategies in colorectal cancer.

Aged↗

Microarray analyses in bladder cancer cells: inhibition of hTERT expression down-regulates EGFR.

The human telomerase reverse transcriptase (hTERT) contributes to the immortal phenotype of the majority of cancers. Targeting hTERT by transfection with antisense oligonucleotides (AS-ODNs) induced immediate growth inhibition in human bladder cancer (BCa) cells. The molecular basis of the antiproliferative capacity of hTERT AS-ODNs was investigated by oligonucleotide microarray analyses and was compared to effects caused by siRNA-mediated knock-down of hTERT in EJ28 BCa cells. Two different AS-ODNs -- both down-regulated the expression of hTERT -- changed the expression of different genes mainly involved in stress response (including EGR1, ATF3 and GDF15), but without an association to telomerase function. This indicates that the immediate growth inhibition was caused, at least in part, by off-target effects. In comparison to that the blockade of the expression of hTERT using 2 different siRNAs was accompanied by the down-regulation of the oncogenes FOS-like antigen 1 (FOSL1) and epidermal growth factor receptor (EGFR), known to be overexpressed in BCa. We show here for the first time that repression of the hTERT transcript number decreased the expression of EGFR both at the mRNA and protein levels, suggesting a potential new function of hTERT in the regulation of EGFR-stimulated proliferation. Furthermore, the suppression of hTERT by siRNAs caused an enhancement of the antiproliferative capacity of the chemotherapeutics mitomycin C and cisplatin. The results presented herein may support the hypothesis that hTERT promotes the growth of tumor cells by mechanisms independent from telomere lengthening. The detailed clarification of these processes will shed light on the question, whether telomerase inhibitors might constitute suitable anticancer tools.

DNA-Binding Proteins↗

Microarray assay for detection and discrimination of Orthopoxvirus species.

A microarray method was developed for simultaneous detection and identification of six species of Orthopoxvirus (OPV) including Variola, Monkeypox, Cowpox, Camelpox, Vaccinia, and Ectromelia viruses. The method allowed us to discriminate OPV species from varicella-zoster virus (VZV), Herpes Simplex 1 virus (HSV-1), and Herpes Simplex 2 virus (HSV-2) that cause infections with clinical manifestations similar to OPV infections. The nucleotide sequences of the C23L/B29R and the B19R genes identified for 86 and 72 different OPV strains, respectively, were used to design species-specific microarray oligonucleotide probes (oligoprobes). The microarray also contained several oligoprobes selected from the ORF31, US4, and US5 genes of VZV, HSV-1, and HSV-2, respectively. The samples (from HSVs or OPVs) of ssDNAs for analyses were prepared by using asymmetric PCR followed by chemical labeling of ssDNA with Cy3 dye. DNA from 52 samples of various OPV species, two isolates of VZV, two of HSV-1, and three of HSV-2 were tested using the developed microarray assay; all tested viruses were accurately identified. To ensure the robustness of the microarray assay, three additional unrelated variola virus strains with unknown sequences of the C23L/B29R and the B19R genes were tested. In each instance the microarray unambiguously identified them as Variola virus species. The results obtained in this study demonstrated that this new microarray method is a valuable tool for the rapid and accurate detection and differentiation of these important viral pathogens.

Carbocyanines↗

Survey of microarray technologies suitable to elucidate transcriptional networks as exemplified by studying KRAB zinc finger gene families.

Current microarray systems are suitable to monitor genome-wide expression patterns, to detect single-nucleotide polymorphisms (SNP), to identify target genes of transcription factors and DNA-protein interaction sites thereof as well as to determine genomic sites that are modified by methylation of CpG islands. In this review, advantages and limitations of individual microarray technologies are presented as well as experiences from ongoing studies on KRAB zinc finger gene families are taken to exemplify how different microarray approaches are applicable to elucidate complex transcriptional networks of gene regulation. However, bioinformaticians should be aware that each microarray technology has limitations in its sensitivity and selectivity that has to be taken into account once data mining on comprehensive genome-wide microarray data is conducted. In many cases, microarray results are the initial step to identify target genes of interest and to study the molecular regulation of biological processes thereof followed and validated by complementary proteome, metabolome or toponome analysis. Thus, microarray technologies can be considered a reliable approach for determining gene functions that might be modulated by electromagnetic fields.

Gene Expression Profiling↗

Immobilization of oligonucleotides onto a glass support via disulfide bonds: A method for preparation of DNA microarrays.

The covalent attachment of disulfide-modified oligonucleotides to a mercaptosilane-modified glass surface is described. This method provides an efficient and specific covalent attachment chemistry for immobilization of DNA probes onto a solid support. Glass slides were derivatized with 3-mercaptopropyl silane for attachment of 5-prime disulfide-modified oligonucleotides via disulfide bonds. An attachment density of approximately 3 x 10(5) oligonucleotides/microm2 was observed. Oligonucleotides attached by this method provided a highly efficient substrate for nucleic acid hybridization and primer extension assays. In addition, we have demonstrated patterning of multiple DNA probes on a glass surface utilizing this attachment chemistry, which allows for array densities of at least 20,000 spots/cm2.

DNA Probes↗

Nearly instantaneous, cation-independent, high selectivity nucleic acid hybridization to DNA microarrays.

Hybridization rate enhancement has been demonstrated for high molecular weight DNA target binding to a microarray. Microarrays were fabricated using biotin-modified oligonucleotides complexed with streptavidin (SA), which serves as an attachment to the underlying surface. It is shown that at low salt and pH 5, where SA develops a positive charge, duplex formation becomes at least 80-fold faster than seen under standard conditions, where SA is neutral or anionic. Duplex formation becomes independent of solution state cation concentration in the low pH state, under conditions where specificity remains high. The utility of such applied surface science is discussed.

Biotin↗

Inhibition of Smad5 in human hematopoietic progenitors blocks erythroid differentiation induced by BMP4.

Patients with secondary myelodysplasias and acute myeloid leukemias (MDS/AML) frequently exhibit interstitial deletions of the chromosome-5q resulting in hemizygous loss of the transcription transactivator Smad5. Smad5 is a member of the signal transducer family conveying the pleiotropic TGF-gb/BMP cytokine signals with roles in development, cell growth control, and tumor progression. Here we present a study of the Smad5 expression and its functional role in leukemia cell lines as well as in primary CD34+ progenitors of MDS/AML patients and healthy individuals. Consistent Smad5 gene expression in these cell types and the gradual increase in its mRNA and protein levels in a model of induced erythroid differentiation of murine erythroleukemia (MEL) cells suggest a role of the gene in hematopoiesis. We show that bone morphogenetic protein 4 (BMP4) directs Smad5 activation in human hematopoietic cells, as monitored at the levels of protein phosphorylation, nuclear translocation, and specific transcription response. In vitro induction of normal human CD34+ cells by BMP4 results in significantly increased proliferation of erythroid progenitors (BFU-E) and formation of glycophorin-A+ cells, whereas perturbation of Smad5 expression by antisense oligonucleotides causes significantly decreased rates of BMP4-induced erythroid differentiation. We have not detected any effects of Smad5 inhibition on BMP4-stimulated progenitors of the granulocyteNmacrophage lineage. We propose that the BMP4/Smad5 signal transduction pathway activates hematopoietic differentiation programs that may be impaired in anemia manifestations in MDS and AML patients with Smad5 haploinsufficiency.

Active Transport, Cell Nucleus↗

Oligonucleotide scanning arrays: application to high-throughput screening for effective antisense reagents and the study of nucleic acid interactions.

Oligonudeotide scanning arrays are useful tools in the study of nucleic acid interaction. Such arrays of oligonucleotides, corresponding to a full set of complements of a known sequence, can be readily made in a single series of coupling reactions, adding each nudeotide in the complement of the target sequence in turn. The synthesis is carried out on the surface of a solid substrate such as glass or polypropylene that has been modified to allow nucleotide coupling. A mask is used to apply the DNA synthesis reagents in a defined area and is moved by a fixed step size after each coupling reaction so that consecutive couplings overlap a portion of the previous one. The size of the mask and the displacement at each coupling determine the length of the oligonucleotides. A radiolabeled or fluorescently tagged target sequence is hybridised to a scanning array and its interaction with the complementary oligonudeotides is displayed as a hybridisation signal. It is thus possible to determine the exact sequence and lengths of large numbers of interacting sequences in a single hybridisation experiment. The array image is analysed using a computer program (xvseq) that calculates quantitative measurements of the binding strengths. We have found scanning arrays a useful tool not only to find effective antisense reagents, but also to study RNA folding and the mechanisms of heteroduplex formation. In this article, we discuss the format of these arrays, the technology used to fabricate and to read them, and their applications.

Algorithms↗

Detection of multiple human herpes viruses by DNA microarray technology.

BACKGROUND: The detailed characterization of virus DNA is a challenge, and the genotyping that has been achieved to date has only been possible because researchers have sent a great deal of time and effort to do so. Instead of the simultaneous detection of hundreds of viruses on a single high-density DNA-chip at very high costs per chip, we present here an alternative approach using a well-designed and tailored microarray which can establish whether or not a handful of viral genes are present in a clinical sample. METHODS: In this study we applied a new concept of microarray-based, optimized and robust biochemistry for molecular diagnostics of the herpesviruses. For comparison, all samples were genotyped using standard procedures. RESULTS: The biochemical procedure of a knowledge-based, low-density microarray was established based on the molecular diagnostics of human herpes viruses: herpes simplex virus (HSV) HSV-1, HSV-2, varicella zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), and HHV-6. The study attempted to optimize parameters of microarray design, surface chemistry, oligonucleotide probe spotting, sample labeling and DNA hybridization to the developed DNA microarray. The results of 12 900 hybridization reactions on about 150 configured herpes virus microarrays showed that the established microarray-based typing procedure was reproducible, virus-specific and sufficiently sensitive with a lower limit of 100 viral copies per mL sample. CONCLUSIONS: The developed method utilizes low-fluorescence background coverslips, epoxy surface chemistry, standardized oligonucleotide probe spotting, PCR-labeling with Cy3 of isolated DNA, array hybridization, and detecting of specific spot fluorescence by an automatic microarray reader. We expect the configured microarray approach to be the method for high-throughput associated studies on human herpes viruses.

Carbocyanines↗

Oligonucleotide microarray with RD-PCR labeling technique for detection and typing of human papillomavirus.

Currently, screening for high-risk human papillomavirus (HPV) infection remains an important health concern throughout the world, because of the close association between certain types of HPV and cervical cancer. In this study, we explore the possibility of using approximately 70mer oligonucleotide microarray for detection and genotyping of HPV. The approximately 70mer type-specific oligonucleotide probes of four different types HPV were designed by using biological software Array designer 2.0, which analyzed the whole genome sequences of HPV and selected optimal probes. These probes were synthesized and printed onto the surface of glass slides in order to prepare a low-density microarray. HPV samples were labeled with fluorescence dyes Cy3 using a method of restriction display polymerase chain reaction (RD-PCR). HPV plasmid DNA was restricted with Sau3A I to produce multiple fragments that were ligated to adaptors subsequently and used as PCR template. PCR labeling was performed with the fluorescently labeled universal primer (Cy3-UP) whose sequence is designed according to the adaptor of the RD-PCR approaches. The labeled samples were hybridized with the oligonucleotide microarray. The scanning results showed that HPV DNA hybridized specifically with multiple spots correspondingly to show positive signals, whereas no signals were detected of all the negative and blank controls. These results demonstrated that approximately 70mer oligonucleotide microarray can be applied to HPV detection and genotyping. The application of RD-PCR in the sample labeling can increase significantly the sensitivity of the assay and will be especially useful for the discriminate diagnosis of multiple pathogens.

Carbocyanines↗

Tissue microarrays: applications in urological cancer research.

Tissue microarrays (TMAs) are used to simultaneously study the expression of proteins in hundreds of tissue samples, offering the important advantage to screen large tissue banks for biomarker expression and to simultaneously examine serial sections obtained from the same tumor specimen by a time- and cost-effective analytical approach. This review article presents an overview of the importance and the impact of this technique in cancer research with increasing number of investigations using TMAs in its eighth anniversary. Its application, limitations, and selected previous study results regarding urologic malignancies are presented and discussed.

Biomarkers, Tumor↗

The Bradyrhizobium japonicum Fur protein is an iron-responsive regulator in vivo.

The Fur protein is a global regulator of iron metabolism in many bacterial species. However, Fur homologs from some rhizobia appear not to mediate iron-dependent gene expression in vivo. Here, transcriptional profiling analysis showed that more than one-fourth of the genes within the iron stimulon of Bradyrhizobium japonicum were aberrantly controlled by iron in a fur mutant. However, Fur has only a modest role in regulating iron transport genes. Quantitative real time reverse transcriptase PCR measurements confirmed abnormal gene expression in iron-limited cells of the fur strain, thereby demonstrating that Fur must function under those conditions. The findings show that B. japonicum Fur is involved in iron-dependent gene expression, and support the conclusion that rhizobial Fur proteins have novel functions compared with well studied model systems.

Bacterial Proteins↗

Identification of ALDH4 as a p53-inducible gene and its protective role in cellular stresses.

To identify additional targets of p53, we used a cDNA microarray system to examine gene-expression patterns in response to enforced expression of exogenous p53 in p53-deficient cancer cells, and identified the aldehyde dehydrogenase 4 ( ALDH4) gene as a direct target of p53. ALDH4 is a mitochondrial-matrix NAD+-dependent enzyme catalyzing the second step of the proline degradation pathway. Expression of ALDH4 mRNA was induced in HCT116 cells in response to DNA damage caused by adriamycin treatment, in a p53-dependent manner. ALDH4 contains a potential p53 binding sequence in intron1 and the interaction of p53 with the site was shown by EMSA and ChIP assays. We confirmed p53-dependent transcriptional activity of the binding site by means of a reporter assay. Inhibition of ALDH4 expression by antisense oligonucleotides was able to enhance cell death induced by infection with Ad-p53. H1299 cells transformed to over-express ALDH4 showed significantly lower intracellular reactive oxygen species (ROS) levels than parental or control cells after treatment with hydrogen peroxide or UV. Those cells were also resistant to cell damage caused by hydrogen peroxide. These results suggest that p53 might play a protective role against cell damage induced by generation of intracellular ROS, through transcriptional activation of ALDH4.

1-Pyrroline-5-Carboxylate Dehydrogenase↗

Evaluation of the rpoB macroarray assay to detect rifampin resistance in Mycobacterium tuberculosis in Beijing, China.

The aim of this study was to evaluate the modified rifampin oligonucleotide (RIFO) macroarray method to detect mutations in the hot-spot region of the rpoB gene, associated with rifampin (RIF) resistance in Mycobacterium tuberculosis. The study sample included 123 strains of M. tuberculosis isolated in the Beijing, China, area in 2002-2005, including 73 RIF-resistant and 40 pansusceptible strains. The genotypic assay successfully identified 91.8% of the RIF-resistant strains, whereas no mutations were found in RIF-susceptible strains. The most frequently detected rpoB mutations were in the codons 516, 526, and 531, together accounting for 74% of RIF-resistant strains. Spoligotyping subdivided all strains into 11 unique profiles and 3 profiles shared by 3, 4, and 103 strains, respectively. The 113 strains belonged to the Beijing family genotypes, defined by the specific spoligotype signature (absence of signals 1-34) and deletion of the RD105 region. The rpoB S531L (TCG-->TTG) mutation was found in 57.4% of the RIF-resistant strains of the Beijing genotype. A mutation in the rpoB hot-spot region was found in 51 of the 55 (92.7%) multidrug-resistant strains (i.e., resistant to at least RIF and isoniazid), thus demonstrating the added utility of the modified RIFO method to predict multidrug resistance. The RIFO method is relatively simple to perform and allows straightforward interpretation of results; consequently, it can be used in clinical diagnostic laboratories as a fast complement to phenotypic methods.

Antibiotics, Antitubercular↗

Monitoring expression profiles of Arabidopsis genes during cold acclimation and deacclimation using DNA microarrays.

A comparative analysis of gene expression profiles during cold acclimation and deacclimation is necessary to elucidate the molecular mechanisms of cold stress responses in higher plants. We analyzed gene expression profiles in the process of cold acclimation and deacclimation (recovery from cold stress) using two microarray systems, the 7K RAFL cDNA microarray and the Agilent 22K oligonucleotide array. By both microarray analyses, we identified 292 genes up-regulated and 320 genes down-regulated during deacclimation, and 445 cold up-regulated genes and 341 cold down-regulated genes during cold acclimation. Many genes up-regulated during deacclimation were found to be down-regulated during cold acclimation, and vice versa. The genes up-regulated during deacclimation were classified into (1) regulatory proteins involved in further regulation of signal transduction and gene expression and (2) functional proteins involved in the recovery process from cold-stress-induced damages and plant growth. We also applied expression profiling studies to identify the key genes involved in the biosynthesis of carbohydrates and amino acids that are known to play important roles in cold acclimation. We compared genes that are regulated during deacclimation with those regulated during rehydration after dehydration to discuss the similarity and difference of each recovery process.

Acclimatization↗

Comparison of cryopreservation and standard needle biopsy for gene expression profiling of human breast cancer specimens.

Given the growing importance of molecular profiling of breast cancer, we initiated a small study to test whether human breast biopsies obtained via cryopreservation large core needle biopsy (C-LCNB) provided similar gene expression profiles compared with 'optimally handled' standard large core needle biopsy (S-LCNB) specimens. Five matched pairs of C-LCNB versus S-LCNB were obtained at the same visit, and subjected to gene array expression analysis using the Affymetrix system with U133A chips. No significant changes in gene expression were identified comparing the C-LCNB versus the matched S-LCNB from individual patients. This was corroborated by a paired t-test analysis, which supported the hypothesis that the S/C biopsies measured equivalent samples. A small number of genes (17) showed decreased expression when second biopsies were compared with first biopsies, suggesting a slight patient response to the first biopsy. A scatter plot analysis comparing first biopsy versus second biopsy values disclosed a slope of 0.859, further indicating that the first biopsy affects the second biopsy measurement. It therefore appears that conventional biopsies, when handled appropriately, provide RNA which is equivalent to RNA from biopsies which are frozen immediately, but that multiple biopsy protocols may introduce additional complexities.

Biopsy, Needle↗