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PubMed1989

Induction of tumor promotor-inducible genes in murine 3T3 cell lines and tetradecanoyl phorbol acetate-nonproliferative 3T3 variants can occur through protein kinase C-dependent and -independent pathways.

We isolated a group of genes that are rapidly and transiently induced in 3T3 cells by tetradecanoyl phorbol acetate (TPA). These genes are called TIS genes (for TPA-inducible sequences). Epidermal growth factor (EGF), fibroblast growth factor (FGF), and TPA activated TIS gene expression with similar induction kinetics. TPA pretreatment to deplete protein kinase C activity did not abolish the subsequent induction of TIS gene expression by epidermal growth factor or fibroblast growth factor; both peptide mitogens can activate TIS genes through a protein kinase C-independent pathway(s). We also analyzed TIS gene expression in three TPA-nonproliferative variants (3T3-TNR2, 3T3-TNR9, and A31T6E12A). The results indicate that (i) modulation of a TPA-responsive sodium-potassium-chloride transport system is not necessary for TIS gene induction either by TPA or by other mitogens and (ii) TIS gene induction is not sufficient to guarantee a proliferative response to mitogenic stimulation.

Animals↗
PubMed1984

Alpha-amanitin-insensitive transcription of variant surface glycoprotein genes provides further evidence for discontinuous transcription in trypanosomes.

Many, if not all, mRNAs in T.brucei start with the same sequence of 35 nucleotides, separately encoded in clustered so-called mini-exon repeats. From these mini-exon repeats a 141-nt precursor RNA with the 35-nt sequence at its 5' end is transcribed. Indirect evidence suggests that this RNA is linked in a second step to pre-mRNA transcripts. We have studied the sensitivity of RNA synthesis to alpha-amanitin in isolated trypanosome nuclei. Transcription of several protein coding genes is almost completely inhibited by a concentration of 5 micrograms alpha-amanitin per ml, whereas strong inhibition of mini-exon transcription is achieved with 200 micrograms alpha-amanitin per ml. In contrast, transcription of genes for variant surface glycoproteins (VSGs) is not inhibited by 1000 micrograms alpha-amanitin per ml, as is transcription of the genes for the major rRNAs. Since the mature VSG mRNAs start with the 35-nt sequence, our results provide additional evidence that the 35-nt sequence and the main part of VSG mRNA are produced from independent transcription units, these are transcribed by (partly) different RNA polymerases.

Amanitins↗
PubMed2001

A PCR-ELISA assay for the detection of disseminated osteosarcoma cells in a mouse metastatic model.

Circulating tumor cells in the blood play a central role in the metastatic process. There have been no reports describing the relationship between lung metastasis and circulating osteosarcoma cells. We developed a system with a polymerase chain reaction assay based on an enzyme-linked immunosorbent assay (PCR-ELISA) to detect circulating osteosarcoma cells in a mouse metastatic model. Osf2/Cbfa1, hereafter called Osf2, a member of the runt family of transcription factors, was used as a target gene. One splicing variant of Osf2 mRNA was identified and its expression was restricted to the bones and osteosarcomas. The amount of the splicing variant of Osf2 mRNA was significantly higher in the blood of mice with metastasis than in the blood of the control group. The PCR-ELISA using Osf2 mRNA is a potential method to detect circulating osteosarcoma cells in peripheral blood.

Alternative Splicing↗
PubMed2006

Association of VKORC1 and CYP2C9 polymorphisms with warfarin dose requirements in Japanese patients.

Warfarin is the most commonly used oral anticoagulant for treatment of thromboembolism, but adjustment of the dose appropriate to each patient is not so easy because of the large inter-individual variation in dose requirement. We analyzed single nucleotide polymorphism (SNP) genotypes of the VKORC1 and CYP2C9 genes using DNA from 828 Japanese patients treated with warfarin, and investigated association between SNP genotype and warfarin-maintenance dose. Five SNPs in VKORC1, 5' flanking-1413A > G, intron 1-136T > C, intron 2+124C > G, intron 2+837T > C and exon 3 343G > A, were in absolute linkage disequilibrium, and showed a significant association with daily warfarin dose of these patients. The median warfarin dose of patients with homozygosity for the minor allele was 4.0 mg/day, which is significantly higher than those heterozygous for the minor allele (3.5 mg/day) or those homozygous for the major allele (2.5 mg/day; P = 5.1 x 10(-11) in the case of intron 1-136T > C SNP). We then genotyped the CYP2C9 gene for the Japanese common genetic variant, CYP2C9*3 and, based on the genotype of these two genes, classified patients into three categories, which we call "warfarin-responsive index." The median warfarin daily dose varied significantly in this classification according to the warfarin-responsive index (2.0 mg/day for index 0 group, 2.5 mg/day for index 1 group, and 3.5 mg/day for index 2 group; P = 4.4 x 10(-13)). Thus, analysis of the combination of VKORC1 and CYP2C9 genotypes should identify warfarin-sensitive patients who require a lower dose of drug, allowing personalized warfarin treatment.

Anticoagulants↗
PubMed2006

The intracellular localisation and mobility of Type Igamma phosphatidylinositol 4P 5-kinase splice variants.

There are three known splice variants of Type Igamma phosphatidylinositol 4-phosphate 5-kinase (PIPkin Igamma): PIPkins Igamma87, Igamma90, and the most recently cloned (Giudici, M.L., Emson, P.C. and Irvine, R.F. (2004) A novel neuronal-specific splice variant of Type I phosphatidylinositol 4-phosphate 5-kinase isoform gamma. Biochem. J. 379, 489-496) PIPkin IgammaC (here called PIPkin Igamma93). Here, we have explored the subcellular localisation and mobility of Type I PIPkins in transfected cells by confocal microscopy and flourescence recovery after photobleaching. The unique behaviour shown by PIPkin Igamma93 is consistent with its suggested distinct function. Moreover, the markedly different localisation and mobility of active versus inactive PIPkin Igamma93 provide insights into the factors that dictate cellular targeting of Type Igamma PIPkins.

Animals↗
PubMed2004

Mathematical models of diffusion-constrained polymerase chain reactions: basis of high-throughput nucleic acid assays and simple self-organizing systems.

DNA templates amplified by polymerase chain reaction in thin polyacrylamide gels form diffusion-constrained amplicons called "polonies" (polymerase colonies) that have been used to phase DNA haplotypes over long distances, to analyse RNA splice variants, and to assay other phenomena of biological interest. We present two sets of mathematical models, one for single polony growth (SPGM) and one for two polony interaction (TPIM), that will be used to optimize polony technology. The models provide detailed predictions of polony yield, concentration profiles, growth of isolated polonies, and the interaction of neighboring polonies. The TPIM explains an experimental observation that nearby polonies deform against each other rather than interpenetrate, an effect important for optimizing polony protocols. However, the TPIM also predicts that polonies may invade each other with a complex geometry when sufficiently close. Polonies are also of interest as simple abiotic systems that exhibit lifelike properties of self-organization, growth, and development, and the models may also apply to biological phenomena involving propagation through tethering and diffusion. Our polony modeling software is available at our web site.

Algorithms↗
PubMed1998

Oxidation of guanines in the iron-responsive element RNA: similar structures from chemical modification and recent NMR studies.

BACKGROUND: The translation or stability of the mRNAs from ferritin, maconitase, erythroid aminoevulinate synthase and the transferrin receptor is controlled by the binding of two iron regulatory proteins to a family of hairpin-forming RNA sequences called iron-responsive elements (IREs). The determination of high-resolution nuclear magnetic resonance (NMR) structures of IRE variants suggests an unusual hexaloop structure, leading to an intra-loop G-C base pair and a highly exposed loop guanine, and a special internal loop/bulge in the ferritin IRE involving a shift in base pairing not predicted with standard algorithms. RESULTS: Cleavage of synthetic 55- and 30-mer RNA oligonucleotides corresponding to the ferritin IRE with complexes based on oxoruthenium(IV) shows enhanced reactivity at a hexaloop guanine and at a guanine adjacent to the internal loop/bulge with strong protection at a guanine in the internal loop/bulge. These results are consistent with the recent NMR structures. The synthetic 55-mer RNA binds the iron-regulatory protein from rabbit reticulocyte lysates. The DNA analogs of the 55- and 30-mers do not show the same reactivity pattern. CONCLUSIONS: The chemical reactivity of the guanines in the ferritin IRE towards oxoruthenium(IV) supports the published NMR structures and the known oxidation chemistry of the metal complexes. The results constitute progress towards developing stand-alone chemical nucleases that reveal significant structural properties and provide results that can ultimately be used to constrain molecular modeling.

Animals↗
PubMed2000

Severe chromosomal aberrations in pleural mesotheliomas with unusual mesodermal features. Comparative genomic hybridization evidence for a mesothelioma subgroup.

Malignant mesotheliomas are tumors known for their extensive heterogeneity. Apart from the three classical patterns, predominantly epithelioid, sarcomatoid, and biphasic, some rare variants do exist. In some cases, one can find uncommon additional mesodermal tumor components. These tumors have previously been called "mesodermomas" and, like regular mesotheliomas, are usually associated with a previous asbestos exposure. We examined eight cases of mesodermomas by light microscopy, immunohistochemistry and comparative genomic hybridization (CGH). Besides biphasic and epithelioid areas, unusual epithelial, chondroid, osseous, or even angioblastic elements may be found to varying degrees. Immunohistochemical analysis shows similar staining results as with regular mesotheliomas. CGH reveals a high number of chromosomal imbalances (16.5 per case; range, 11-27). In 10 classical biphasic mesotheliomas that served as a control, defects of comparable number and severity could not be detected (8 per case; range, 2-16). The most frequent defects of mesodermomas (losses on 1p, 4pq, 9p, 13q, 14q, and gains on 1q and 15q), however, could also be found in mesotheliomas of the classical type. Thus, our results support the classification of the so-called mesodermomas as a separate tumor subgroup while maintaining the relationship to the classical mesotheliomas. Therefore, we propose to use the term mesodermoma for this subgroup.

Aged↗
PubMed2000

Effect of amphotericin B on wild-type and mutated prion proteins in cultured cells: putative mechanism of action in transmissible spongiform encephalopathies.

Transmissible spongiform encephalopathies form a group of fatal neurodegenerative disorders that have the unique property of being infectious, sporadic, or genetic in origin. Although some doubts remain on the nature of the responsible agent of these diseases, it is clear that a protein called PrP(Sc) [the scrapie isoform of prion protein (PrP)] plays a central role. PrP(Sc) represents a conformational variant of PrP(C) (the cellular isoform of PrP), the normal host protein. Polyene antibiotics, such as amphotericin B, have been shown to delay the accumulation of PrP(Sc) and to increase the incubation time of the disease after experimental transmission in laboratory animals. Unlike agents such as Congo red, the inhibitory effect of amphotericin B on PrP(Sc) generation has not been observed in infected cultures. Using transfected cells expressing wild-type or mutated mouse PrPs, we show here that amphotericin B is able to interfere with the generation of abnormal PrP isoforms in culture. Its action seems related to a modification of PrP trafficking through the association of this glycosylphosphatidylinositol-anchored protein with detergent-resistant microdomains. These results represent a first step toward the comprehension of the mechanism of action of amphotericin B in transmissible spongiform encephalopathies.

Amphotericin B↗
PubMed1991

Papillary carcinoma of thyroid with exuberant nodular fasciitis-like stroma. Report of three cases.

Three examples of an unusual morphologic variant of papillary thyroid carcinoma (PTC) are reported. The presence of a prominent stromal component resulted in low-power microscopic appearances resembling fibroadenoma, phyllodes tumor, or fibrocystic disease of the breast in two cases. The carcinomatous component grew in the form of anastomosing narrow tubules, clustered glands, solid sheets with or without squamous differentiation, and/or papillae, and exhibited the typical nuclear features of PTC. The abundant stroma had a nodular fasciitis-like quality and was composed of short fascicles of spindle cells separated by varying amounts of mucoid matrix, collagen, and extravasated red blood cells; this was interpreted as an exuberant mesenchymal reaction to the carcinoma. The importance of recognizing this variant of PTC is that, when one encounters a fibroproliferative lesion of the thyroid, a diligent search should be made for papillary carcinoma. This variant also must be distinguished from the vastly more aggressive papillary carcinomas with anaplastic transformation and the so-called carcinosarcomas.

Adult↗
PubMed2006

MDM2 gene promoter polymorphisms and risk of lung cancer: a case-control analysis.

The MDM2 protein negatively regulates p53 expression level in modulating DNA repair, cell-cycle control, cell growth and apoptosis. Polymorphisms in the promoter region of the MDM2 gene have been shown to alter protein expression and may, thus, play a role in carcinogenesis. To test our hypothesis that the MDM2 promoter polymorphisms are associated with risk of lung cancer, we conducted a hospital-based, case-control study of 1026 non-Hispanic white patients newly diagnosed with lung cancer and 1145 cancer-free controls who were frequency-matched by age (+/-5 years), sex, ethnicity and smoking status. We genotyped for the MDM2 promoter G2580T (also called SNP309) and G2164A polymorphisms that have a minor allele frequency >0.05. The distributions of the MDM2-2580G variant allele and genotypes were significantly less common among the cases than among the controls (P = 0.038 and 0.045, respectively), but this was not evident for MDM2-2164G (P = 0.865 and 0.614, respectively). Compared with the MDM2-2580TT genotype, the MDM2-2580G variant genotypes were associated with a decreased risk of lung cancer [odds ratio = 0.81 and 95% confidence interval = 0.67-0.98 for GT, 0.83 (0.63-1.08) for GG, and 0.81 (0.68-0.97) for the combined GT/GG genotype]. However, no significant association was observed between the MDM2-2164G variant genotypes and lung cancer risk. Our results suggest that the MDM2-2580G allele may be a marker of reduced genetic susceptibility to lung cancer in the non-Hispanic white population, a finding that seems to contradict previous reports.

Adult↗
PubMed1991

Immunocytochemical analysis of estrogen and progesterone receptors in benign stromal lesions of the breast. Evidence for hormonal etiology in pseudoangiomatous hyperplasia of mammary stroma.

Five cases of pseudoangiomatous hyperplasia of mammary stroma, together with seven examples of mammary hamartoma, were probed with monoclonal antibodies H222 and KD68 to investigate the possible role of estrogen and progesterone receptor expression in the pathogenesis of these benign stromal proliferations. All five cases of pseudoangiomatous hyperplasia showed patchy, intense labelling of the stromal cells with progesterone receptor antibodies, a pattern contrasting markedly with the absence of immunoreactivity in normal (nongestational) mammary stroma or the stromal component of common juvenile mammary hyperplasia. The stroma of the hamartoma group labeled inconsistently, with the notable exception of three myoid hamartomas. Stromal immunoreactivity was diffuse and intense in two of these, and patchy and distinct in the remaining case. These findings (a) support the contention that pseudoangiomatous hyperplasia represents a localized form of stromal overgrowth with a hormonal (primarily progestagenic) etiology and (b) further highlight the heterogeneity of so-called mammary hamartomas by demonstrating dramatically different progesterone receptor immunoreactivity patterns in myoid lesions as compared with other hamartoma variants.

Adult↗
PubMed2007

Genomic screen for substance dependence and body mass index in southwest California Indians.

Substance abuse and obesity are health disparities that may afflict Native Americans more than some other ethnic groups. One theoretical assumption concerning Native people is that the long history of dependence on foraging and subsistence agriculture may have led to selective enrichment of traits that improve genetic fitness, so called 'thrifty' or 'fat sparing' genes. We have speculated that this same selective pressure may have enriched for genetic variants that increase the risk for consumption of alcohol and drugs of abuse. Here, we report the results of a genome scan that compared findings for two consumption phenotypes: 'any drug dependence and/or regular tobacco use' and body mass index (BMI) in southwest California (SWC) Indian families. Variance component analyses from SOLAR were used to generate log of the odds ratio (LOD) scores. Evidence for linkage was found on chromosome 6 for both the 'any drug' (LOD score = 3.3) and BMI (LOD score = 2.3) phenotypes. Bivariate analyses of the two phenotypes revealed a combined LOD score of 4.1 at that location. Additional loci on chromosomes 6, 15, 16 and 21 were found for the 'any drug' phenotype, and on chromosomes 8, 16 and 18 for BMI (LOD scores ranged between 1.2 and 2.3). These results provide suggestive evidence for linkage for substance abuse and BMI in this Mission Indian population and, furthermore, provide preliminary data suggesting that 'consumption phenotypes' may share some genetic determinants.

Adolescent↗
PubMed1998

ASAP1, a phospholipid-dependent arf GTPase-activating protein that associates with and is phosphorylated by Src.

Membrane trafficking is regulated in part by small GTP-binding proteins of the ADP-ribosylation factor (Arf) family. Arf function depends on the controlled exchange and hydrolysis of GTP. We have purified and cloned two variants of a 130-kDa phosphatidylinositol 4, 5-biphosphate (PIP2)-dependent Arf1 GTPase-activating protein (GAP), which we call ASAP1a and ASAP1b. Both contain a pleckstrin homology (PH) domain, a zinc finger similar to that found in another Arf GAP, three ankyrin (ANK) repeats, a proline-rich region with alternative splicing and SH3 binding motifs, eight repeats of the sequence E/DLPPKP, and an SH3 domain. Together, the PH, zinc finger, and ANK repeat regions possess PIP2-dependent GAP activity on Arf1 and Arf5, less activity on Arf6, and no detectable activity on Arl2 in vitro. The cDNA for ASAP1 was independently identified in a screen for proteins that interact with the SH3 domain of the tyrosine kinase Src. ASAP1 associates in vitro with the SH3 domains of Src family members and with the Crk adapter protein. ASAP1 coprecipitates with Src from cell lysates and is phosphorylated on tyrosine residues in cells expressing activated Src. Both coimmunoprecipitation and tyrosine phosphorylation depend on the same proline-rich class II Src SH3 binding site required for in vitro association. By directly interacting with both Arfs and tyrosine kinases involved in regulating cell growth and cytoskeletal organization, ASAP1 could coordinate membrane remodeling events with these processes.

ADP-Ribosylation Factor 1↗
PubMed2001

The new World Health Organization classification of lung tumours.

Tumour classification systems provide the foundation for tumour diagnosis and patient therapy and a critical basis for epidemiological and clinical studies. This updated classification was developed with the aim to adhere to the principles of reproducibility, clinical significance, and simplicity in order to minimize the number of unclassifiable lesions. Major changes in the revised classification as compared to the previous one (WHO 1981) include the addition of two pre-invasive lesions to squamous dysplasia and carcinoma in situ; atypical adenomatous hyperplasia and diffuse idiopathic pulmonary neuroendocrine cell hyperplasia. Another change is the subclassification of adenocarcinoma: the definition of bronchioalveolar carcinoma has been restricted to noninvasive tumours. There has been substantial evolution of concepts in neuroendocrine lung tumour classification. Large cell neuroendocrine carcinoma (LCNEC) is now recognized as a histologically high grade non small cell carcinoma showing histopathological features of neuroendocrine differentiation as well as immunohistochemical neuroendocrine markers. The large cell carcinoma class has been enriched with several variants, including the LCNEC and the basaloid carcinoma, both with a dismal prognosis. Finally, a new class was defined called carcinoma with pleomorphic, sarcomatoid, or sarcomatous elements, which brings together a number of proliferations characterized by a spectrum of epithelial to mesenchymal differentiation. Immunohistochemistry and electron microscopy are invaluable techniques for diagnosis and subclassification, but our intention was to render the classification simple and practical to every surgical laboratory, so that most lung tumours could be classified by light microscopic criteria.

Adenocarcinoma↗
PubMed2006

The C-terminal T peptide of cholinesterases: structure, interactions, and influence on protein folding and secretion.

Mammalian cholinergic tissues mostly express the T splice variant of acetylcholinesterase, in which the catalytic domain is associated with a C-terminal peptide of 40 residues, called the t peptide (Massoulié, 2002). Homologous t peptides exist in all vertebrate cholinesterases, acetylcholinesterases (AChEs), and butyrylcholinesterases (BChEs): they contain a series of seven conserved aromatic residues, including three tryptophans, and a cysteine at position-4 of their C-terminus. The major AChE isozyme of the nematode Caenorhabditis elegans also contains a similar peptide. Although the C-terminal t peptides do not seem to affect the catalytic activity of cholinesterases, they determine their physiological function, because they allow cholinesterase subunits of type T to form oligomers and to associate with structural anchoring proteins. When reduced to their catalytic domain, AChE subunits without a t peptide are active but remain monomeric and soluble.

Amino Acid Sequence↗
PubMed1999

[Acquired forms of Creutzfeldt-Jakob disease].

AIM: To establish the recent neuropathological data concerning the acquired forms of human prions diseases at the exception of the new variant. RESULTS: Kuru transmitted by cannibalism involved mainly the cerebellum with cerebellar tracts degeneration and presence of amyloid plaques called "kuru plaques" labeled by anti PrP antibodies. To day the disease has disappeared. Iatrogenic forms have been found after corneal graft or more frequently dura-mater graft. In these later cases, neuronal loss, spongiosis and gliosis are diffuse in cerebral and cerebellar cortex with the same intensity. The cases associated with pituitary-derived human growth hormone administration are observed in young patients. Histologic lesions, in 16 cases, are present in basal ganglia, thalamus, brain stem and predominantly in the cerebellum especially in the granule cell layer. Cortical involvement is moderate. Plaques have not been always looked for. CONCLUSION: The diversity of acquired forms is in favor of the hypothesis of selection of specific strains.

Brain↗
PubMed1999

[New knowledge of the molecular biology of enterohemorrhagic Escherichia coli (EHEC) O157].

Since 1982, enterohaemorrhagic Escherichia coli (EHEC) have been identified as a cause of diarrhoea and haemorrhagic colitis. The most serious complication of the infection is the haemolytic-uraemic syndrome (HUS) that develops in 5 to 10% of children with diarrhoea. Shiga toxins (Stx) are the most important presently known virulence factors of EHEC. After reaching the bloodstream, the toxins cause damage of endothelial cells but also of tubular cells in the kidneys which may result in renal failure. In EHEC O157 isolates from patients, we were able to identify seven different combinations of stx genes that occurred with different frequency. The genes encoding Stx are located in the genomes of prophages that are integrated in EHEC chromosomes. In addition, EHEC O157 strains possess a chromosomally located pathogenicity island (pais) termed LEE that contains numerous pathogenicity genes including the eae gene encoding intimin. Moreover, EHEC O157 strains possess a 93-kb plasmid harbouring genes encoding the EHEC-hemolysin (EHEC-HlyA), a serin protease (EspP) that cleaves factor V and a protein called ToxB that shows homology with the toxin B of Clostridium difficile. The EHEC O157 strains exist in two variants, namely non-sorbitol-fermenting (NSF) O157:H7 and sorbitol-fermenting (SF) O157:H- strains that are evolutionary older. Our results obtained up to now demonstrate marked differences in epidemiology of the infection caused by the respective EHEC O157 variants. EHEC O157:H7 strains occur worldwide, whereas SF strains have been hitherto found only in Germany and recently also in the Czech Republic. While the EHEC O157:H7 strains occur mainly during warm months, the SF strains are more frequent during the cold season of the year. In addition, differences exist with regard to the resistance to heavy metals, the plasmid structure, and the reservoir. We postulate that SF O157:H- strains occur only in the human intestine, whereas NSF O157:H7 strains have become adapted to other hosts, such as cattle, promoting a more rapid spread of the strains.

Animals↗