Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “GEO”

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 217 records · Page 12Linked to original sources

Synergistic inhibition of human cancer cell growth by cytotoxic drugs and mixed backbone antisense oligonucleotide targeting protein kinase A.

Protein kinase A type I plays a key role in neoplastic transformation, conveying mitogenic signals of different growth factors and oncogenes. Inhibition of protein kinase A type I by antisense oligonucleotides targeting its RIalpha regulatory subunit results in cancer cell growth inhibition in vitro and in vivo. A novel mixed backbone oligonucleotide HYB 190 and its mismatched control HYB 239 were tested on soft agar growth of several human cancer cell types. HYB 190 demonstrated a dose-dependent inhibition of colony formation in all cell lines whereas the HYB 239 at the same doses caused a modest or no growth inhibition. A noninhibitory dose of each mixed backbone oligonucleotide was used in OVCAR-3 ovarian and GEO colon cancer cells to study whether any cooperative effect may occur between the antisense and a series of cytotoxic drugs acting by different mechanisms. Treatment with HYB 190 resulted in an additive growth inhibitory effect with several cytotoxic drugs when measured by soft agar colony formation. A synergistic growth inhibition, which correlated with increased apoptosis, was observed when HYB 190 was added to cancer cells treated with taxanes, platinum-based compounds, and topoisomerase II selective drugs. This synergistic effect was also observed in breast cancer cells and was obtained with other related drugs such as docetaxel and carboplatin. Combination of HYB 190 and paclitaxel resulted in an accumulation of cells in late S-G2 phases of cell cycle and marked induction of apoptosis. A cooperative effect of HYB 190 and paclitaxel was also obtained in vivo in nude mice bearing human GEO colon cancer xenografts. These results are the first report of a cooperative growth inhibitory effect obtained in a variety of human cancer cell lines by antisense mixed backbone oligonucleotide targeting protein kinase A type I-mediated mitogenic signals and specific cytotoxic drugs.

Animals↗

Transactivation of the urokinase-type plasminogen activator receptor gene through a novel promoter motif bound with an activator protein-2alpha-related factor.

The urokinase receptor overexpressed in invasive cancers promotes laminin degradation. The current study was undertaken to identify cis elements and trans-acting factors activating urokinase receptor expression through a footprinted (-148/-124) region of the promoter containing putative activator protein-2- and Sp1-binding motifs. Mobility shifting experiments using nuclear extract from a high urokinase receptor-expressing cell line (RKO) indicated that Sp1, Sp3, and a factor similar to, but distinct from, activator protein-2alpha bound to this region. Mutations preventing the binding of the activator protein 2alpha-related factor diminished urokinase receptor promoter activity. In RKO cells, the expression of a negative regulator of activator protein-2 function diminished urokinase receptor promoter activity, protein, and laminin degradation. Conversely, urokinase receptor promoter activity in low urokinase receptor-expressing GEO cells was increased by activator protein-2alphaA expression. Although using GEO nuclear extract, little activator protein-2alpha-related factor bound to the footprinted region, phorbol 12-myristate 13-acetate treatment, which induces urokinase receptor expression, increased complex formation. Mutations preventing the activator protein-2alpha-related factor and Sp1/Sp3 binding reduced urokinase receptor promoter stimulation by this agent. Thus, the constitutive and phorbol 12-myristate 13-acetate-inducible expression of the urokinase receptor is mediated partly through trans-activation of the promoter via a sequence (-152/-135) bound with an activator protein-2alpha-related factor.

Base Sequence↗

Granulation rescue and developmental marking of juxtaglomerular cells using "piggy-BAC" recombination of the mouse ren locus.

Mice lacking a functional Ren-1(d) gene exhibit a complete lack of renal juxtaglomerular cell granulation and atypical macula densa morphology. Transgenic mice carrying a 145-kilobase BAC clone encompassing the Ren-1(d) and Ren-2 loci were generated, characterized, and backcrossed with Ren-1(d-/-) mice. Homozygous Ren-1(d)-null mice expressing the BAC clone exhibited complete restoration of normal renal structure. Homologous recombination in Escherichia coli was used to generate a modified version of the BAC clone, in which an IRESbeta-geo cassette was inserted specifically into the Ren-1(d) gene. When introduced into the germline, the modified clone provided a marker for juxtaglomerular cell differentiation and beta-geo was expressed appropriately in juxtaglomerular cells throughout development. Parallel backcross experiments onto the Ren-1(d)-null background demonstrated that the juxtaglomerular cells expressed the modified Ren-1(d) locus in the absence of regranulation. These data demonstrate that the nongranulated cells constitute bona fide juxtaglomerular cells despite their altered morphology, that overexpression of renin-2 cannot compensate for the loss of renin-1(d), and that primary structural differences between the two isoforms are responsible for the differences in granulation. The use of BAC modification as part of functional complementation studies illustrates the potential for in vivo molecular dissection of key physiological mechanisms.

Animals↗

The Sox2 regulatory region 2 functions as a neural stem cell-specific enhancer in the telencephalon.

Sox2 is expressed at high levels in neuroepithelial stem cells and persists in neural stem/progenitor cells throughout adulthood. We showed previously that the Sox2 regulatory region 2 (SRR2) drives strong expression in these cells. Here we generated transgenic mouse strains with the beta-geo reporter gene under the control of the SRR2 in order to examine the spatiotemporal function of this regulatory region. We show that the SRR2 functions specifically in neural stem/progenitor cells. However, unlike Nestin 2nd intronic enhancer, the SRR2 shows strong regional specificity functioning only in restricted areas of the telencephalon but not in any other portions of the central nervous system such as the spinal cord. We also show by in vitro clonogenic assay that at least some of these SRR2-functioning cells possess the hallmark properties of neural stem cells. In adult brains, we could detect strong beta-geo expression in the subventricular zone of the lateral ventricle and along the rostral migrating stream where actively dividing cells reside. Chromatin immunoprecipitation assays reveal interactions of POU and Sox factors with SRR2 in neural stem/progenitor cells. Our data also suggest that the specific recruitment of these proteins to the SRR2 in the telencephalon defines the spatiotemporal activity of the enhancer in the developing nervous system.

Animals↗

A geographical information system (GIS) as a tool for microbial risk assessment in catchment areas of drinking water reservoirs.

The main tributaries of three drinking water reservoirs of Northrhine-Westfalia (Germany) were monitored within a 14-month period mainly for bacterial and parasitic contamination. In this context a detailed geo-ecological characterisation within the differing catchment areas was carried out to reveal a reliable informational basis for tracing back the origin of microbial loads present in the watercourses. To realise a microbial risk assessing geo-ecological information system (MRA-GIS), a Geographical Information System (GIS) has been implemented for the study areas. The results of the microbiological investigations of the watercourses showed an input of pathogens into all three of the tributaries. It could be demonstrated that the use of MRA-GIS database and some GIS-techniques substantially support the spatial analysis of the microbial contamination patterns. From the hygienic point of view, it is of the utmost importance to protect catchment areas of surface water reservoirs from microbial contamination stemming from human activities and animal sources. This constitutes essential part of the multi-barrier concept which stresses the importance of reducing diffuse and point pollution in catchment areas of water resources intended for human consumption. MRA-GIS proves to be helpful to manage multi-barrier water protection in catchment areas and ideally assists the application of the HACCP concept on drinking water production.

Environmental Monitoring↗

Mobilization and retardation of uranium DOC species at three mine piles in Schlema/Alberoda, Saxony, Germany.

The modeling of geo-chemical processes needs the detailed and comprehensive knowledge of all chemical interactions existing in the flow path of waste dumps, subsoil and aquifer. This includes the adsorption, displacement and transport of heavy metal species of fulvic and humic acids, which represent the main amount of DOC in the liquid/solid system of the flow path. Comparative measurements of DOC concentrations in the input and output flow at the three waste dumps in the district Schlema/Alberoda indicated that DOC is produced and/or supplied within the waste dumps. The speciation of heavy metal compounds of fulvic and humic acids was achieved by means of sequential chromatographic analysis SCA and isoelectric focusing IEF. Between 5% and 20% of uranium exist in the flow path in the form of stable fulvic and humic acid species. Their distribution coefficients are strongly correlated with the pH values of the geo-chemical system.

Benzopyrans↗

In silico analysis of SH3BP2 genomic alterations and expression profiles in CRC.

AIM: Colorectal cancer (CRC) is a widespread health issue that attains high mortality. The adaptor protein SH3BP2 amplification results in metabolic changes, oxidative stress, NK cell activity, and inflammation. The NK cells are capable of destroying tumor cells without prior activation, help prevent metastasis, and have prognostic value. Targeting SH3BP2 to regulate NK cell activity in the TME could enhance CRC-based immunotherapy. MATERIALS AND METHODS: The cancer hallmark tool helps in understanding SH3BP2 hallmark annotation. Utilizing the STRING tool and the KEGG pathway, protein functional enrichment and PPI networking were analyzed. TIMER 2.0 was used for immune cell infiltration correlation analysis, and UALCAN was used for CPTAC-based protein expression profiling. RESULTS AND CONCLUSIONS: The GEO (GSE9348) dataset showed SH3BP2 is upregulated in CRC (log2 fold change = 1.18). GEO, TCGA, and cBioPortal revealed SH3BP2 alterations in CRC cases, potentially aiding immune evasion. Mutations in SH3BP2 influence cancer growth, suppressing tumors or promoting them by activating NF-κB and affecting immune responses through WNT/β-catenin, PI3K, MAPK, and JAK-STAT pathways. Overall, SH3BP2 plays a key role in cancer growth and immune regulation, making it a promising target for CRC therapy. Further experimental validation is needed to demonstrate its diagnostic and therapeutic potency.

Humans↗

Large scale data mining approach for gene-specific standardization of microarray gene expression data.

MOTIVATION: The identification of the change of gene expression in multifactorial diseases, such as breast cancer is a major goal of DNA microarray experiments. Here we present a new data mining strategy to better analyze the marginal difference in gene expression between microarray samples. The idea is based on the notion that the consideration of gene's behavior in a wide variety of experiments can improve the statistical reliability on identifying genes with moderate changes between samples. RESULTS: The availability of a large collection of array samples sharing the same platform in public databases, such as NCBI GEO, enabled us to re-standardize the expression intensity of a gene using its mean and variation in the wide variety of experimental conditions. This approach was evaluated via the re-identification of breast cancer-specific gene expression. It successfully prioritized several genes associated with breast tumor, for which the expression difference between normal and breast cancer cells was marginal and thus would have been difficult to recognize using conventional analysis methods. Maximizing the utility of microarray data in the public database, it provides a valuable tool particularly for the identification of previously unrecognized disease-related genes. AVAILABILITY: A user friendly web-interface (http://compbio.sookmyung.ac.kr/~lage/) was constructed to provide the present large-scale approach for the analysis of GEO microarray data (GS-LAGE server).

Algorithms↗

Integrative multi-omics quantitative trait loci prioritize CASP7 as a candidate protective gene for cataract.

Cataracts are the leading cause of vision loss worldwide. Despite surgery being the only effective treatment, its economic burden highlights the necessity of exploring the pathogenesis of cataracts. In this study, we analyzed 4 large-scale GWAS (genome-wide association study) datasets for cataracts and performed SMR analysis along with heterogeneity in dependent instruments (HEIDI) testing to explore the effects of methylation, expression, and protein QTLs on cataracts. We further validated shared genetic variants through COLOC analysis. Additionally, we searched datasets related to cataracts from the Gene Expression Omnibus (GEO) database for differentially expressed genes (DEGs) and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses. By integrating summary-based Mendelian randomization (SMR) results with bioinformatics findings, CASP7 showed a consistent protective-direction association with cataract risk (mQTL: OR [95% CI] = 0.959 [0.941-0.977], FDR-adjusted P = .039; eQTL: OR [95% CI] = 0.897 [0.860-0.937], FDR-adjusted P = .0046; pQTL: OR [95% CI] = 0.597 [0.483-0.738], FDR-adjusted P = .00083). GEO-based analyses provided transcriptomic support for CASP7 involvement in cataract-related lens biology. These findings prioritize CASP7 as a genetically supported candidate protective gene associated with cataract risk. Because this study is based on public summary-level and transcriptomic datasets, the results should be interpreted cautiously and require functional validation in human lens-relevant systems.

Quantitative Trait Loci↗

Transcriptional enhancers act in cis to suppress position-effect variegation.

We have examined the basis of enhancer effects on gene expression by altering the action of enhancers on expression of a stably integrated reporter gene. We used two distinct experimental approaches: recombinase-mediated deletion of an enhancer and modulation of the activity of another enhancer composed of downstream metal response elements (MREs). The flp recombinase was used to delete the 5'HS2 globin enhancer from a site downstream of beta-geo at nine separate integration sites in K562 erythroleukemia cells. In no case does deletion of 5'HS2 have a significant effect on the level of expression; however, the deletion does increase dramatically the rate at which expression of beta-geo is silenced. Zinc stimulation of a metallothionein enhancer has no effect on the level of reporter expression, but slows the rate of silencing. Silencing in both cases is highly site dependent, and resembles position-effect variegation (PEV). These results strongly support a binary mode of enhancer action, as in both cases the enhancer maintains reporter expression without a strong effect on the level of expression. Taken together, these findings suggest that transcriptional activators have a direct interaction with repressive chromatin structures, which is independent of an effect on the rate of transcription. We propose that cis-acting transcriptional control elements may act primarily through this mechanism.

Enhancer Elements, Genetic↗

Dysregulated Sheddase Signalling as a Molecular Driver of Plaque Instability Revealed by Integrative Transcriptomics.

Atherosclerosis is a major cause of mortality due to chronic and progressive low-grade inflammation and fibroproliferative remodelling of the intima of arteries. Comprehensive understanding of the interplay between plaque biology and the mechanisms underlying plaque vulnerability and rupture is essential. Here, we aimed to investigate the transcriptomic profiles of stable and unstable atherosclerotic plaques using RNA sequencing data from human carotid atherosclerotic plaque samples based on next-generation knowledge discovery (NGKD) methods. High-throughput RNA-seq data from plaques dissected in stable and unstable regions of four patients were obtained from the Gene Expression Omnibus (GEO) database. GEO RNA-seq Experiments Interactive Navigator (GREIN) software was used to obtain raw gene-level counts and filtered metadata for this dataset. The data were further filtered and normalized using Express analyst to derive differentially expressed genes (DEGs) in unstable plaques compared to stable plaques. The DEGs were further analysed using WebGestalt, STRING DB, preranked gene set enrichment analysis (GSEA), and Ingenuity Pathway Analysis (IPA) software. We identified 4792 DEGs in unstable plaques based on a p-value cutoff of <&#x2009;0.05. NGKD analysis revealed that the sheddase pathway, collagen degradation, activation of matrix metalloproteinases (MMPs), and extracellular matrix (ECM) degradation ranked among the top five upregulated pathways, whereas the inhibition of MMPs and smooth muscle contraction pathways were identified as the most prominent downregulated pathways in unstable plaques. We found that the sheddase pathway was one of the most significantly upregulated canonical pathways in unstable plaques and this finding opens new avenues for potential therapeutic interventions in patients with atherosclerosis.

Humans↗

An evaluation of the accuracy of shallow water matched field inversion results.

In this article the accuracy of geo-acoustic and geometric parameter estimates obtained through matched field inversion (MFI) was assessed. Multi-frequency MFI was applied to multi-tone data (200-600 Hz) received at a 2-km source/receiver range. The acoustic source was fixed and the signals were received at a vertical array. Simultaneously with the acoustic transmissions, a CTD (conductivity, temperature and depth)-chain was towed along the acoustic track. A genetic algorithm was used for the global optimization, whereas a normal mode model was applied for the forward acoustic calculations. Acoustic data received at consecutive times were inverted and the stability of the inverted parameters was determined. Also, the parameter estimates were compared with independent measurements, such as multi-channel seismic surveys (for geo-acoustic parameters). The obtained uncertainty in the inversion results was assumed to have two distinct origins. The first origin is the inversion method itself, since each optimization will come up with some solution close to the exact optimum. Parameter coupling and the fact that some parameters hardly influence the acoustic propagation further contribute to this uncertainty. The second is due to oceanographic variability. Both contributions were evaluated through simulation. The contribution of oceanographic variability was evaluated through synthetic inversions that account for the actual sound speed variations as measured by the towed CTD-chain.

Journal Article↗

Binding of Germanium to Pseudomonas putida Cells.

The binding of germanium to Pseudomonas putida ATCC 33015 was investigated by using whole intact cells grown in a medium supplemented with GeO(2) and catechol or acetate. Electron-microscopic examination of the control and metal-loaded samples revealed that germanium was bound within the cell envelope. A certain number of small electron-dense deposits of the bound element were found in the cytoplasm when the cells were grown in the presence of GeO(2) and catechol. The study of germanium distribution in cellular fractions revealed that catechol facilitated the intracellular accumulation of this element.

Journal Article↗

Adeno-associated virus vectors transduce primary cells much less efficiently than immortalized cells.

Immortalized cell lines have been used to study infection and replication of adeno-associated virus (AAV) in culture, but primary cells presumably provide a better model for AAV behavior in animals. Here, we have evaluated the ability of AAV vectors to transduce primary and immortalized strains of human epithelial cells and fibroblasts. Two AAV vectors were used, one that transduced an alkaline phosphatase gene (AAV-LAPSN), and one that transduced a beta-galactosidase/neomycin phosphotransferase fusion gene (AAV-L beta geo). The transduction efficiency of the AAV-LAPSN vector, quantitated by measurement of alkaline phosphatase-positive cell foci following infection, was 10 to 60 times greater in immortalized human cells than in primary cells, and total alkaline phosphatase activity in cell lysates was 40 to 50 times greater in immortalized cells. The AAV-L beta geo vector gave similar results. In contrast, the transduction efficiency of a retrovirus vector encoding alkaline phosphatase was equivalent in primary and immortalized cells. Analysis of the quantity and state of the AAV vector genomes in cells showed that primary and immortalized cells contained comparable numbers of vector copies per cell and that the vast majority of vector DNA was not integrated into the cell genome. Additionally, the level of AAV vector-derived message paralleled the transduction efficiency. These results indicate that the block to functional transduction in primary cells occurred after virus entry and limited the abundance of vector-derived message. Data from AAV transduction in cultures of human cells containing immortalizing genes suggest that cellular changes secondary to the introduction of immortalizing genes increased permissiveness for transduction by AAV vectors. In summary, our data demonstrate that AAV vectors transduce primary human cells much less efficiently than immortalized cells and indicate the importance of using primary cells to evaluate AAV vectors for gene therapy applications.

Cells, Cultured↗

Peri-implantation lethality in mice lacking the Sm motif-containing protein Lsm4.

Small nuclear ribonucleoproteins (snRNPs) are particles present only in eukaryotic cells. They are involved in a large variety of RNA maturation processes, most notably in pre-mRNA splicing. Several of the proteins typically found in snRNPs contain a sequence signature, the Sm domain, conserved from yeast to mammals. By using a promoter trap strategy to target actively transcribed loci in murine embryonic stem cells, a new murine gene encoding an Sm motif-containing protein was identified. Database searches revealed that it is the mouse orthologue of Lsm4p, a protein found in yeast and human cells and putatively associated with U6 snRNA. Introduction of the geo reporter gene cassette under the control of the murine Lsm4 (mLsm4) endogenous promoter showed that the gene was ubiquitously transcribed in embryonic and adult tissues. The insertion of the geo cassette disrupted the mLsm4 allele, and homozygosity for the mutation led to a recessive embryonic lethal phenotype. mLsm4-null zygotes survived to the blastocyst stages, implanted into the uterus, but died shortly thereafter. The early death of mLsm4p-null mice suggests that the role of mLsm4p in splicing is essential and cannot be compensated by other Lsm proteins.

Amino Acid Sequence↗

Public health, GIS, and spatial analytic tools.

We review literature that uses spatial analytic tools in contexts where Geographic Information Systems (GIS) is the organizing system for health data or where the methods discussed will likely be incorporated in GIS-based analyses in the future. We conclude the review with the point of view that this literature is moving toward the development and use of systems of analysis that integrate the information geo-coding and data base functions of GISystems with the geo-information processing functions of GIScience. The rapidity of this projected development will depend on the perceived needs of the public health community for spatial analysis methods to provide decision support. Recent advances in the analysis of disease maps have been influenced by and benefited from the adoption of new practices for georeferencing health data and new ways of linking such data geographically to potential sources of environmental exposures, the locations of health resources and the geodemographic characteristics of populations. This review focuses on these advances.

Cluster Analysis↗

Therapeutic synergy of oral taxane BMS-275183 and cetuximab versus human tumor xenografts.

PURPOSE: Combination therapy consisting of an oral taxane, BMS-275183, and the anti-epidermal growth factor receptor monoclonal antibody, cetuximab, was assessed for enhanced therapeutic benefit in preclinical tumor models. EXPERIMENTAL DESIGN: Mice bearing human tumor xenografts, either L2987 lung or GEO colon carcinoma, were administered the aforementioned treatments singly or in combination regimens. Delays in tumor growth and tumor-free status were evaluated and combination treatments were assessed relative to optimal solo treatments. RESULTS: Combination therapies with the oral taxane plus cetuximab were tolerated and therapeutic synergistic outcomes obtained. The therapeutic enhancements were >1 log cell kill greater than the antitumor effect caused by either solo agent applied optimally. For example, at the maximum-tolerated dose of BMS-275183, 60 mg/kg/administration, given p.o. once every 3 days for a total of six administrations (q3dx6), 1.0 gross log cell kill was achieved in mice bearing well established (100 to 200 mg) s.c. implanted L2987 tumors. Cetuximab, at an optimal dose of 1 mg/mouse, given i.p. q3dx6, produced 1.3 log cell kill. When cetuximab, 1 mg/mouse, i.p., plus BMS-275183, 25 mg/kg/administration, p.o., were both given q3dx6, the result was 2.6 log cell kill with three of eight mice cured (P < 0.01). Similar efficacy benefits were obtained in the GEO tumor model. CONCLUSIONS: The combination of oral taxane BMS-275183 plus cetuximab provided therapeutically synergistic antitumor activity in two different human tumor xenograft models. Clinical evaluation of this combination is recommended.

Animals↗

Synergistic antitumor effects of combined epidermal growth factor receptor and vascular endothelial growth factor receptor-2 targeted therapy.

PURPOSE: Combination therapies that target the epidermal growth factor receptor (EGFR) and vascular endothelial growth factor receptor (VEGFR) pathways, are being actively tested for the treatment of cancer. In evaluating combination strategies, the ideal combination would be one in which the treatments interact in a way that is synergistic with regard to antitumor effects. Here, we have evaluated the interaction between anti-EGFR antibody Erbitux (cetuximab) and anti-VEGFR2 antibody, DC101, in preclinical models of pancreatic (BxPC-3) and colon (GEO) cancer. EXPERIMENTAL DESIGN: Analysis of the interaction between cetuximab and DC101 in vivo used a novel method for establishing the upper 95% confidence limits for the combination index (CI) of isobologram analyses, where CI < 1 indicates synergy. Assessment of tumor cell proliferation, apoptosis, VEGF production, and hypoxia, as well as tumor vascularization, was performed to gain insights into the mechanistic basis for synergy between agents targeting different tumor compartments. RESULTS: Monotherapy ED(50) values for tumor growth inhibition ranged from 1.8 to 2.3 mg/kg and 10.5 to 16.6 mg/kg for cetuximab and DC101, respectively. From the dose response of the combination treatment, it was determined that cetuximab and DC101 are synergistic in the BxPC-3 (CI = 0.1, P < 0.01) and GEO (CI = 0.1, P < 0.01) models. Overlapping effects on the tumor cell and vascular compartments form a basis for the interaction, with VEGF production and hypoxia-inducible factor 1alpha potentially acting as molecular links between EGFR and VEGFR2 inhibition. CONCLUSIONS: Results show antitumor synergy for combined EGFR and VEGFR2 targeted therapy, supporting the significant therapeutic potential of this combination strategy.

Adenocarcinoma↗