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At least 109 records · Page 6Linked to original sources
PubMed2004

Prediction of outcome of advanced cervical cancer to thermoradiotherapy according to expression profiles of 35 genes selected by cDNA microarray analysis.

PURPOSE: To identify a set of genes related to thermoradiosensitivity of cervical carcinoma and to establish a predictive method. METHODS AND MATERIALS: A total of 19 patients with cervical cancer (1 with Stage IIIA, 11 with Stage IIIB, 5 with Stage IVA, and 2 with Stage IVB) who underwent definitive thermoradiotherapy between May 1995 and August 2001 were included in this study. We compared the expression profiles of 8 thermoradiosensitive and 11 thermoradioresistant tumors obtained by punch biopsy before treatment using a cDNA microarray consisting of 23,040 human genes. RESULTS: We selected 35 genes on the basis of a clustering analysis and confirmed the validity of these genes with a cross-validation test. Some of these genes were already known to be associated with apoptosis (BIK, TEGT, SSI-3), hypoxia-inducible genes (HIF1A, CA12), and tumor cell invasion and metastasis (CTSL, CTSB, PLAU, CD44). We developed a "predictive score" system that could clearly separate the thermoradiosensitive group from the thermoradioresistant group. CONCLUSION: These results from the treatment program between May 1995 and August 2001 showed that by using gene-expression profiles we can predict the outcome of thermoradiotherapy for advanced cervical carcinoma. A "predictive score" system was developed that could clearly separate the thermoradiosensitive group from the thermoradioresistant group. These results may eventually lead to the achievement of "personalized therapy" for this disease.

Adult↗
PubMed2004

Single nucleotide polymorphisms in randomly selected genes among japonica rice (Oryza sativa L.) varieties identified by PCR-RF-SSCP.

DNA polymorphism of randomly selected genes in rice cultivars was analyzed by the polymerase chain reaction-restriction fragment-single strand conformation polymorphism (PCR-RF-SSCP) technique. Single DNA fragments were amplified from genomic DNA of the Nipponbare cultivar by 671 primer pairs among the 1000 primer pairs tested. PCR-RF-SSCP analysis using the 671 primer pairs detected polymorphism in 108 DNA fragments between 17 japonica paddy-rice cultivars. An average of 36.9 DNA fragments showed polymorphism between any pair of japonica paddy-rice cultivars. The nucleotide sequences of the polymorphic DNA fragments were determined for 50 alleles of 45 genes together with Nipponbare alleles. In these genes, 142 SNPs and 32 insertions/deletions were identified. Among these 174 sequence variations, 71 were in exons, 78 in introns, and 25 in unassigned regions. There were 28 alleles which had sequence variations in the exons. One allele had a 1-bp deletion in the exon causing a frame-shift mutation, 15 alleles had missense mutations, and the other 12 alleles had synonymous changes and/or sequence variations in 3' untranslated regions. The number of genes having sequence variations between the rice cultivars and the functional implications of the identified SNPs are herein discussed.

Alleles↗
PubMed2001

Identification of conformation-dependent epitopes and V gene selection in the B cell response to type II collagen in the DA rat.

Collagen-induced arthritis (CIA) is a widely used model for rheumatoid arthritis. Induction of CIA in rats using rat type II collagen (CII) results in a chronic arthritis in which anti-CII antibodies are believed to play a pathogenic role. In this study, we analyzed the epitope selection and V gene usage in the anti-CII response in the DA rat. A panel of CII-reactive B cell hybridomas was established from the draining lymph nodes 11 days after immunization. All of the CII-specific antibodies bound cartilage in vivo, showing that these are true autoantibodies. These antibodies were all IgG and specific for several distinct triple helical epitopes on CII. Interestingly, the major epitope, recognized by four different antibodies, was identical with the major B cell epitope in the mouse CII located at position 359--369 (denoted as C1(III)). The Q52 and PC7183 V(H) gene families encoded 12 out of 14 sequenced heavy chains. There was a relatively more heterogeneous usage of V(L) genes as the antibodies were encoded by four different V(kappa) families (V(kappa)1, V(kappa)2, V(kappa)12/13 and V(kappa)RF). As in the mouse, some of the V genes used showed germline characteristics. We conclude that the immune response in the rat shares epitope specificity and a constrained V gene repertoire with the mouse. However, the V genes used for recognition of the closely related collagen structures differed considerably between mouse and rat, indicating an influence of the species-specific variation in the V gene repertoire.

Amino Acid Sequence↗
PubMed1994

Molecular analysis of mutations induced by chemical carcinogens in mammalian cells. I. The use of selectable gene loci.

Several lines of evidence indicate the important role of mutation in the process of carcinogenesis, however our understanding of the factors that influence the formation of mutation is still limited. Recent developments in the analysis of gene mutations at selectable loci in cultured mammalian cells has allowed to accumulate a significant amount of information on the type and distribution of mutations induced by a variety of chemical and physical agents. The purpose of this review is to summarize the data relative to chemical carcinogens and to discuss how their mechanism of interaction with DNA and the repair processes active on the induced lesions affect mutational spectra.

Alkylating Agents↗
PubMed1988

Association of high rate of recombination with amplification of dominant selectable gene in human cells.

The human cell line LM205, transformed with the pLR309 plasmid, contains a stably integrated selectable gene marker (neo) without a transcriptional promoter. Spontaneous tandem duplication at the integration site relocates a Simian virus 40 transcriptional promoter to a position 5' to the neo gene at a rate of 5 x 10(-8) events/cell/generation, as measured by subsequent resistance of the cells to the toxic antibiotic G418. The heterogeneity in the site of recombination observed in various G418-resistant (G418-R) subclones indicates that the sequences involved have little or no homology. The rate of tandem duplication involving the neo gene was not affected by DNA-damaging agents or by inhibitors of DNA synthesis. Although these tandem duplications were relatively stable in most G418-R subclones, others underwent further amplification of the neo gene during cloning. In one such cell line, RS-4, subclones isolated without G418 demonstrated a high degree of heterogeneity in the neo gene copy number (2-20), indicating that amplification was associated with a high rate of homologous recombination. Because LM205 was the only clone out of the 30 original clones transformed with pLR309 that demonstrated spontaneous G418-R colonies, cell DNA sequences near the integrated neo gene may promote this recombination. Inclusion of this cell DNA in the initial tandem duplication might then explain the high rate of duplication and deletion observed in the region of the neo gene in the RS-4 subclone.

Cell Line, Transformed↗
PubMed2006

Detecting and profiling tissue-selective genes.

The widespread use of DNA microarray technologies has generated large amounts of data from various tissue and/or cell types. These data set the stage to answer the question of tissue specificity of human transcriptome in a comprehensive manner. Our focus is to uncover the tissue-gene relationship by identifying genes that are preferentially expressed in a small number of tissue types. The tissue selectivity would shed light on the potential physiological functions of these genes and provides an indispensable reference to compare against disease pathophysiology and to identify or validate tissue-specific drug targets. Here we describe a systematic computational and statistical approach to profile gene expression data to identify tissue-selective genes with the use of a more extensive data set and a well-established multiple-comparison procedure with error rate control. Expression data of 35,152 probe sets in 97 normal human tissue types were analyzed, and 3,919 genes were identified to be selective to one or a few tissue types. We presented results of these tissue-selective genes and compared them to those identified by other studies.

Animals↗
PubMed2004

Extreme value distribution based gene selection criteria for discriminant microarray data analysis using logistic regression.

One important issue commonly encountered in the analysis of microarray data is to decide which and how many genes should be selected for further studies. For discriminant microarray data analyses based on statistical models, such as the logistic regression models, gene selection can be accomplished by a comparison of the maximum likelihood of the model given the real data, L(D|M), and the expected maximum likelihood of the model given an ensemble of surrogate data with randomly permuted label, L(D(0)|M). Typically, the computational burden for obtaining L(D(0)M) is immense, often exceeding the limits of available computing resources by orders of magnitude. Here, we propose an approach that circumvents such heavy computations by mapping the simulation problem to an extreme-value problem. We present the derivation of an asymptotic distribution of the extreme-value as well as its mean, median, and variance. Using this distribution, we propose two gene selection criteria, and we apply them to two microarray datasets and three classification tasks for illustration.

Chromosome Mapping↗
PubMed2003

New gene selection method for classification of cancer subtypes considering within-class variation.

In this work we propose a new method for finding gene subsets of microarray data that effectively discriminates subtypes of disease. We developed a new criterion for measuring the relevance of individual genes by using mean and standard deviation of distances from each sample to the class centroid in order to treat the well-known problem of gene selection, large within-class variation. Also this approach has the advantage that it is applicable not only to binary classification but also to multiple classification problems. We demonstrated the performance of the method by applying it to the publicly available microarray datasets, leukemia (two classes) and small round blue cell tumors (four classes). The proposed method provides a very small number of genes compared with the previous methods without loss of discriminating power and thus it can effectively facilitate further biological and clinical researches.

Acute Disease↗
PubMed2005

Altered expression of selected genes in kidney of rats with lithium-induced NDI.

Lithium treatment is associated with development of nephrogenic diabetes insipidus, caused in part by downregulation of collecting duct aquaporin-2 (AQP2) and AQP3 expression. In the present study, we carried out cDNA microarray screening of gene expression in the inner medulla (IM) of lithium-treated and control rats, and selected genes were then investigated at the protein level by immunoblotting and/or immunohistochemistry. The following genes exhibited significantly altered transcription and mRNA expression levels, and these were compatible with the changes in protein expression. 11beta-Hydroxysteroid dehydrogenase type 2 protein expression in the IM was markedly increased (198 +/- 25% of controls, n = 6), and immunocytochemistry demonstrated an increased labeling of IM collecting duct (IMCD) principal cells. This indicated altered renal mineralocorticoid/glucocorticoid responses in lithium-treated rats. The inhibitor of cyclin-dependent kinases p27 (KIP) protein expression was significantly decreased or undetectable in the IMCD cells, pointing to increased cellular proliferation and remodeling. Heat shock protein 27 protein expression was decreased in the IM (64 +/- 6% of controls, n = 6), likely to be associated with the decreased medullary osmolality in lithium-treated rats. Consistent with this, lens aldose reductase protein expression was markedly decreased in the IM (16 +/- 2% of controls, n = 6), and immunocytochemistry revealed decreased expression in the thin limb cells in the middle and terminal parts of the IM. Ezrin protein expression was upregulated in the IM (158 +/- 16% of controls, n = 6), where it was predominantly expressed in the apical and cytoplasmic domain of the IMCD cells. Increased ezrin expression indicated remodeling of the actin cytoskeleton and/or altered regulation of IMCD transporters. In conclusion, the present study demonstrates changes in gene expression not only in the collecting duct but also in the thin limb of the loop of Henle in the IM, and several of these genes are linked to altered sodium and water reabsorption, cell cycling, and changes in interstitial osmolality.

11-beta-Hydroxysteroid Dehydrogenase Type 2↗
PubMed2006

CancerGenes: a gene selection resource for cancer genome projects.

The genome sequence framework provided by the human genome project allows us to precisely map human genetic variations in order to study their association with disease and their direct effects on gene function. Since the description of tumor suppressor genes and oncogenes several decades ago, both germ-line variations and somatic mutations have been established to be important in cancer-in terms of risk, oncogenesis, prognosis and response to therapy. The Cancer Genome Atlas initiative proposed by the NIH is poised to elucidate the contribution of somatic mutations to cancer development and progression through the re-sequencing of a substantial fraction of the total collection of human genes-in hundreds of individual tumors and spanning several tumor types. We have developed the CancerGenes resource to simplify the process of gene selection and prioritization in large collaborative projects. CancerGenes combines gene lists annotated by experts with information from key public databases. Each gene is annotated with gene name(s), functional description, organism, chromosome number, location, Entrez Gene ID, GO terms, InterPro descriptions, gene structure, protein length, transcript count, and experimentally determined transcript control regions, as well as links to Entrez Gene, COSMIC, and iHOP gene pages and the UCSC and Ensembl genome browsers. The user-friendly interface provides for searching, sorting and intersection of gene lists. Users may view tabulated results through a web browser or may dynamically download them as a spreadsheet table. CancerGenes is available at http://cbio.mskcc.org/cancergenes.

Databases, Genetic↗
PubMed1983

Retrovirus transduction: generation of infectious retroviruses expressing dominant and selectable genes is associated with in vivo recombination and deletion events.

We describe the generation of infectious retroviruses containing foreign genes by an in vivo recombination-deletion mechanism. Cotransfection into mouse cells of chimeric plasmids carrying a murine retrovirus 5' long terminal repeat and either the thymidine kinase (tk) gene of herpesvirus or the dominant selectable bacterial gene for neomycin resistance (neo), along with a clone of Moloney murine leukemia virus, results in the generation of infectious thymidine kinase or neomycin-resistant viruses. Expression of the selectable marker in these viruses can be regulated by the homologous transcriptional promoter of the gene, by the promoter contained within the Friend spleen focus-forming virus long terminal repeat, or by the simian virus 40 early region promoter. In all cases, the rescued viruses appeared to arise by recombination in vivo with Moloney murine leukemia virus sequences, resulting in the acquisition of the Moloney 3' long terminal repeat and variable amounts of the 3' adjacent Moloney genome. In two of the thymidine kinase constructs where tk was inserted 200 base pairs downstream from the long terminal repeat, the rescued viruses acquired a large part of the murine leukemia virus genome, including the region involved in packaging genomic RNA into virions. The generation of infectious neomycin-resistant virus is associated with deletions of simian virus 40 splicing and polyadenylation sequences. These results demonstrate that nonhomologous recombination and deletion events can take place in animal cells, resulting in the acquisition or removal of cis-acting sequences required for, or inhibitory to, retrovirus infectivity.

Adenine Phosphoribosyltransferase↗
PubMed2006

Stomach-selective gene transfer following the administration of naked plasmid DNA onto the gastric serosal surface in mice.

The purpose of the present study was to achieve a stomach-selective gene transfer following the administration of naked plasmid DNA (pDNA) onto the gastric serosal surface in mice. Gene expression in the stomach and other tissues was evaluated by firefly luciferase activity. Six hours after gastric serosal surface instillation of naked pDNA, high gene expression in the stomach was observed. On the contrary, intravenous and intraperitoneal injection of naked pDNA exhibited no detectable gene expression. Following instillation of naked pDNA onto the gastric serosal surface, gene expression in the stomach was significantly higher than in other tissues. Gene expression in the stomach was highest 12 h after the instillation and thereafter decreased gradually. Utilizing a glass-made diffusion cell that is able to limit the contact dimension between the gastric serosal surface and the naked pDNA solution administered, site-specific gene expression in the stomach was achieved. This novel gene transfer method is expected to be a safe and effective treatment against serious stomach diseases.

Animals↗
PubMed2006

The peroxisome proliferator-activated receptor N-terminal domain controls isotype-selective gene expression and adipogenesis.

Peroxisome proliferator-activated receptors (PPARgamma, PPARalpha, and PPARdelta) are important regulators of lipid metabolism. Although they share significant structural similarity, the biological effects associated with each PPAR isotype are distinct. For example, PPARalpha and PPARdelta regulate fatty acid catabolism, whereas PPARgamma controls lipid storage and adipogenesis. The different functions of PPARs in vivo can be explained at least in part by the different tissue distributions of the three receptors. The question of whether the receptors have different intrinsic activities and regulate distinct target genes, however, has not been adequately explored. We have engineered cell lines that express comparable amounts of each receptor. Transcriptional profiling of these cells in the presence of selective agonists reveals partially overlapping but distinct patterns of gene regulation by the three PPARs. Moreover, analysis of chimeric receptors points to the N terminus of each receptor as the key determinant of isotype-selective gene expression. For example, the N terminus of PPARgamma confers the ability to promote adipocyte differentiation when fused to the PPARdelta DNA binding domain and ligand binding domain, whereas the N terminus of PPARdelta leads to the inappropriate expression of fatty acid oxidation genes in differentiated adipocytes when fused to PPARgamma. Finally, we demonstrate that the N terminus of each receptor functions in part to limit receptor activity because deletion of the N terminus leads to nonselective activation of target genes. A more detailed understanding of the mechanisms by which the individual PPARs differentially regulate gene expression should aid in the design of more effective drugs, including tissue- and target gene-selective PPAR modulators.

Adipogenesis↗
PubMed2005

Gene selection from microarray data for cancer classification--a machine learning approach.

A DNA microarray can track the expression levels of thousands of genes simultaneously. Previous research has demonstrated that this technology can be useful in the classification of cancers. Cancer microarray data normally contains a small number of samples which have a large number of gene expression levels as features. To select relevant genes involved in different types of cancer remains a challenge. In order to extract useful gene information from cancer microarray data and reduce dimensionality, feature selection algorithms were systematically investigated in this study. Using a correlation-based feature selector combined with machine learning algorithms such as decision trees, naïve Bayes and support vector machines, we show that classification performance at least as good as published results can be obtained on acute leukemia and diffuse large B-cell lymphoma microarray data sets. We also demonstrate that a combined use of different classification and feature selection approaches makes it possible to select relevant genes with high confidence. This is also the first paper which discusses both computational and biological evidence for the involvement of zyxin in leukaemogenesis.

Algorithms↗
PubMed2004

STR2: a structure to string approach for locating G-box riboswitch shapes in pre-selected genes.

Traditional sequence-based search methods such as BLAST and FASTA can be used to identify sequence similarities. Recently, there is a growing interest in performing RNA shape similarity searches inside selected genes to locate RNA structure motifs that are known to possess functionally important roles. For example, in the newly discovered RNA genetic control elements called "riboswitches", the box domain is known to be highly conserved among various bacterial species in both its nucleotide composition and shape. However, in non-bacterial species, shape conservation is likely to become more important than sequence conservation when searching for riboswitch patterns. For this purpose, we present an approach tailored for detecting RNA shape similarities. We extend the Structure to String (ST R2) method that was initially proposed to locate shape similarities in proteins to identify predicted secondary structures of RNAs. The ST R2 for RNAs is a translation of a secondary structure to a string of characters, after which known sequence-based search algorithms with an efficient implementation are being used. We validate that the ST R2 succeeds to locate G-box riboswitches in prokaryotes, as expected. Subsequently we show running examples when attempting to detect G-box riboswitch candidates in eukaryotes.

Algorithms↗
PubMed2005

[Occurrence of selected genes of the Klebsiella pneumoniae clusters waa and wb for lipolysaccharide synthesis in reference and epidemic strains].

The goal of presented study was to determine by PCR differences in existence or homology level of selected genes involved in K. pneumoniae lipopolysaccharide (LPS) synthesis and application of obtained results for genotyping. Number of 26 reference strains of K. pneumoniae belonging to serogroups O1, O2a, O2a2e, O2a2e2h, O2a2f2g, O3, O4, O5, O7, O8, and O12 was tested together with 13 epidemic strains from 5 outbreaks and 6 casual isolates for the existence of 7 (waaA, waaE, waaL, waaQ, waaZ, waaX and uge) and 4 (wbdA, wbdC, manB, wbbO) genes of the waa and wb clusters for LPS biosynthesis. Based on PCR results, 10 and 11 genotypes were distinguished in tested strains for genes from waa and wb clusters respectively. Derived dendrograms were topologically dissimilar, however observed correlation between clonal groups and O-group was marginal for both compared clusters. Since we aimed to develop genotyping method for K. pneumoniae, genes from clusters waa and wb were used together to enhance the distinguishing capacity. Twenty-one genotypes were distinguished in 45 tested strains (DI=0,46) when 11 genes were applied for typing. Although no apparent correlation between genotype and serogroup was observed, epidemic isolates from 5 outbreaks were diversified into 5 genotypes, whereas strains from the same outbreak were indistinguishable. Described here genotyping method is determinative and was found time and cost effective. This method may be applied in every clinical laboratory equipped in an ordinary PCR apparatus.

Bacterial Proteins↗
PubMedDate not supplied

Analysis of gene selection in reassortant formation between canine rotavirus K9 and human rotaviruses with different antigenic specificities.

A number of antigenic mosaic reassortants which have neutralization proteins VP4 and VP7 derived from different parental strains were analysed in order to study gene selection in reassortant formation between animal and human rotaviruses (HRV). These reassortants were isolated from mixed infection of MA-104 cells with canine rotavirus strain K9 (subgroup I and G serotype 3) and HRV strains (with subgroup I or II antigen and G serotype 1-4, 9 or 12 antigen), through repeated selections with anti-VP4 and anti-VP7 neutralizing monoclonal antibodies directed specifically at HRV and K9, respectively. By serological and genomic analyses, all the isolated clones were found to be antigenic mosaic reassortants possessing VP4 of K9 and VP7 of HRV. In the reassortants between strain K9 and one of the six strains of subgroup II HRV, a single or a few genotypes with particular constellations of RNA segments were predominant, with only a few RNA segments including gene 4 (encoding VP4) being derived from K9. In contrast, in the reassortants between strain K9 and any one of the subgroup I HRV, more than nine different genotypes were identified and various RNA segments, except for segments 8 and 10, were derived from K9. These findings indicated that the RNA segments of K9 might be reassorted more readily with those of subgroup I HRV than with those of subgroup II HRV, suggesting the possible existence of functional mechanisms which determine the extent of diversity of genome selection depending on the pairs of parent strains in the reassortant formation.

Animals↗
PubMed1995

p53 trans-dominantly suppresses tumor formation of human breast cancer cells mediated by retroviral bulk infection without marker gene selection: an expeditious in vitro protocol with implications towards gene therapy.

Studies on the molecular basis of human breast cancer have demonstrated that mutational inactivation of the p53 tumor suppressor gene may be an essential step in the development of this cancer. We and others have previously shown that transfer of the wild-type p53 gene into cultured breast cancer cells reduced their malignant potential. We report here on a p53 gene transfer protocol based on a replication-incompetent retrovirus to efficiently inhibit tumor formation of cancer cells with endogenous mutant p53. The susceptibility of the cells to retroviral infection was determined with LZRNL transducing the lacZ reporter gene. A multiplicity of infection (moi) of 2 resulted in 90% of the exposed cell population in cytochemically detectable beta-galactosidase activity. Using the p53 vector Lhp53RNL with a moi of 2 was sufficient to completely supress tumor formation by the highly tumorigenic MDAMB231 breast cancer cells carrying a point missense mutation in codon 280. Even after 12 weeks, no vital tumors were histologically detectable. For comparison, established protocols were used to infect MDAMB231 cells with low moi with the p53 virus. Clones were expanded in G418-selective media for few weeks, pooled and injected into nude mice. Tumor formation occurred already after 1 week from G418-selected cells. Long-term expression of the p53 transgene was more stable in retrovirally bulk-infected and nonselected cells resulting in an efficient suppression of tumor formation. This approach may facilitate future studies on other growth suppressive genes that potentially qualify for in vivo gene therapy.

Animals↗