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PubMed2005

Concomitant neutrophil JAK2 mutation screening and PRV-1 expression analysis in myeloproliferative disorders and secondary polycythaemia.

Polycythaemia vera (PV) is closely associated with both an acquired activating mutation of the JAK2 tyrosine kinase (JAK2(V617F)) in granulocyte-derived DNA and increased granulocyte polycythaemia rubra vera-1 (PRV-1) expression. In order to explore the correlation between these two biological markers and compare their diagnostic utility, mutation analysis for JAK2(V617F) and quantitative measurement of granulocyte PRV-1 expression were performed on the same study sample from 100 participants: 38 with PV, 22 with essential thrombocythaemia (ET), 10 with agnogenic myeloid metaplasia (AMM), 19 with secondary polycythaemia (SP) and 11 healthy volunteers. The respective overall (homozygous) JAK2(V617F) mutational frequencies were 95% (26%), 55% (0%), 30% (0%), 0% and 0%. The corresponding figures for increased PRV-1 expression were 89%, 18%, 20%, 21% and 9%. In patients with either ET or AMM, the likelihood of detecting JAK2(V617F) was significantly higher in the presence of an increased PRV-1 expression (83% vs. 38%; P = 0.05). Similarly, in patients with PV, homozygous as compared with heterozygous JAK2(V617F) correlated with higher levels of PRV-1 expression (P = 0.11). The present study suggests an allele dose-dependent effect of JAK2(V617F) on granulocyte PRV-1 expression. However, compared with the PRV-1 assay, mutation screening for JAK2(V617F) displayed greater accuracy in distinguishing PV from SP.

Adolescent↗
PubMed2004

Isolation of the gene encoding Carrot leafy cotyledon1 and expression analysis during somatic and zygotic embryogenesis.

The Arabidopsis thaliana LEC1 gene regulates embryo morphology and seed maturation. For a better understanding of its function, we isolated a carrot (Daucus carota L. cv. US-Harumakigosun) counterpart of this gene, C-LEC1, from a cDNA library of carrot somatic embryos, since carrot is a better model plant for preparing large quantities of somatic embryos at the same developmental stage. The predicted amino acid sequence of C-LEC1 is similar to that of LEC1 and contains regions that are conserved in the heme-activated protein 3 (HAP3) subunit of plants, animals and microorganisms. C-LEC1 expression was detected in embryogenic cells, somatic embryos, and developing seeds. In situ hybridization analysis revealed C-LEC1 expression in the peripheral region of the embryos but not in the endosperm. Expression of C-LEC1 driven by Arabidopsis LEC1 promoter was able to complement the defects of the Arabidopsis lec1-1 mutant. These results suggest that C-LEC1 is a functional homolog of Arabidopsis LEC1, an important regulator of zygotic and somatic embryo development.

Amino Acid Sequence↗
PubMed2004

Comparative expression analysis of two paralogous Hsp70s in rainbow trout cells exposed to heat stress.

Heat-shock protein 70 (Hsp70) is the major stress-inducible protein in vertebrates and highly conserved throughout evolution. To accurately investigate the mRNA expression profiles of multiple Hsp70s in rainbow trout Oncorhynchus mykiss, we isolated full-length cDNA clones encoding Hsp70 from the fish and investigated their mRNA expression profiles during heat stress. Consequently, two Hsp70s, Hsp70a and Hsp70b, were identified and found to have 98.1% identity in their deduced amino acid sequences. Southern blot analysis indicated that the two Hsp70s are encoded by distinct genes in the genome. Northern blot analysis showed that each of Hsp70a and Hsp70b expressed two mRNA species having different sizes by heat stress in rainbow trout RTG-2 cells. The induction levels of total Hsp70b mRNAs were consistently higher than Hsp70a counterparts during heat stress, although the expression profiles of the two genes were similar to each other in temperature shift and time course experiments. Interestingly, an mRNA species with a larger molecular size was expressed only under severe heat stress not less than 28 degrees C irrespective of Hsp70a and Hsp70b. These results suggest that the comprehensive identification of duplicated genes is a prerequisite to examining the gene expression profiles for tetraploid species such as rainbow trout.

Animals↗
PubMed2005

Expression analysis of estrogen-metabolizing enzymes in human endometrial cancer.

Estrogen-dependent endometrial cancer is related to unopposed and prolonged estrogen stimulation. We examined the expression of estrogen-metabolizing enzymes in correlation with the ERalpha and ERbeta estrogen receptors in human endometrial Ishikawa adenocarcinoma cells and in endometrial cancer specimens and adjacent normal endometrium from the same patients. Real-time PCR analysis revealed that both estrogen receptors and selected estrogen-metabolizing enzymes were expressed in the Ishikawa cells and in endometrial tissue. We detected higher expression of ERalpha than ERbeta, higher expression of sulfatase than sulfotransferase and low expression of aromatase in the Ishikawa cells and the tissue, as well as higher levels of type 2 17beta-hydroxysteroid dehydrogenase (17beta-HSD) in normal and diseased tissue than in the Ishikawa cells. When we compared the expression in endometrial cancer samples and in the adjacent normal endometrium, ERalpha and ERbeta, sulfatase and sulfotransferase were seen to be downregulated in the majority of the cancerous tissue specimens.

17-Hydroxysteroid Dehydrogenases↗
PubMed2006

Expression analysis and prognostic significance of the SRA1 gene, in ovarian cancer.

The SR-related-CTD-associated-factors (SCAFs) have the ability to interact with the C-terminal domain of the RNA polymerase II, linking this way transcription to splicing. SRA1 (SR-A1) gene, encoding for a human high-molecular weight SCAF protein, is located on chromosome 19, between the IRF3 and the R-RAS oncogene and it has been demonstrated from members of our group that SRA1 is constitutively expressed in most of the human tissues, while it is overexpressed in a subset of ovarian tumors. In this study, we examine the expression of SRA1 gene in 111 ovarian malignant tissues and in the human ovarian carcinoma cell lines OVCAR-3, TOV21-G, and ES-2, using a semi-quantitative RT-PCR method. SRA1 gene was overexpressed in 61/111 (55%) of ovarian carcinomas. This higher expression was positively associated to the size of the tumor (p<0.001), the grade and the stage of the disease (p=0.003 and p=0.006, respectively), and the debulking success (p<0.001). Kaplan-Meier survival analysis revealed that lower SRA1 expression increases the probability of both the longer overall and the progression free survival of the patients. Multivariate Cox regression analysis revealed that SRA1 may be used as an independent prognostic biomarker in ovarian cancer. Our results suggest that SRA1 is associated with cancer progression and may possibly be characterized as a new marker of unfavorable prognosis for ovarian cancer.

Adaptor Proteins, Signal Transducing↗
PubMed2002

Gene expression analysis of largemouth bass exposed to estradiol, nonylphenol, and p,p'-DDE.

The purpose of this study was to determine the specific expression profile of 132 genes, some of which are estrogen responsive, in largemouth bass (LMB) following exposure to estradiol (E(2)), or to two hormonally active agents, 4-nonylphenol (4-NP) and 1,1-dichloro-2, 2-bis (p-chlorophenyl) ethylene (p,p'-DDE), using gene array technology. The results of these experiments show that LMB exposed to E(2) and 4-NP had similar, but not identical genetic signatures for the genes examined, some of which are known to be estrogen-responsive genes. The differences suggest that 4-NP may have additional modes of action that are independent of the estrogen receptor (ER). We have also shown that exposure of male LMB to p,p'-DDE results in an increase in some estrogen-responsive genes. But in female LMB, the observed changes were a down-regulation of the normally up-regulated estrogen responsive genes. Other genes were also down-regulated. These results suggest that p,p'-DDE may affect regulation of genes differently in male and female LMB. This study further suggests that gene arrays have the potential to map out the gene activation pathways of hormonally active compounds.

Animals↗
PubMed2006

cDNA cloning, genomic structure and expression analysis of the bovine lanosterol 14alpha-demethylase (CYP51) in gonads.

Meiosis activating sterol (MAS), the intermediate of cholesterol biosynthesis, is an important substance to stimulate oocytes maturation in FSH-induced signal transduction pathway. Lanosterol 14alpha-demethylase (CYP51) converts lanosterol to MAS. Although MAS is firstly isolated from bovine testis, the information about bovine CYP51 gene and its expression is little. In present studies, the cDNA cloning, genomic structure, chromosomal mapping, and expression patterns of bovine CYP51 were demonstrated. The cDNA coding bovine CYP51 contains a 1509 bp open reading frame and a 1119 bp 3' untranslated region. And the bovine CYP51 gene includes 10 exons and spans about 17 kb. Screening the cattle RH5000 panel bovine CYP51 is mapped to chromosome 4 (0cR). The sequenced promoter region is TATA-less and contains several highly conserved regulatory elements, such as GC-box, cAMP-responsive elements (CRE), sterol regulatory element (SRE) which is important fragment for its transcription. No evidence of processed pseudogenes is found using long PCR and Southern blot. Northern blot analysis reveals that an approximately 2.7 kb mRNA is expressed in all the examined bovine tissues, while a 1.8 kb mRNA is found only in the mature bovine testis where the MAS is accumulated. Immunochemistry analysis shows that leydig cells express the highest level of the CYP51 protein in testis. Among different stages follicles it is localized primarily to the oocytes with the level varying slightly. Granulosa cells of primordial, primary and secondary follicles show background staining. While granulosa cells facing the antrum and cumulus granulosa cells of antral follicles show considerably heavier staining. The highest level is expressed in corpus lutea. These data indicate a stage- and cell type-specific expression of CYP51 protein in bovine oogenesis.

Animals↗
PubMed2003

Expression analysis of DNA methyltransferases 1, 3A, and 3B in sporadic breast carcinomas.

PURPOSE: Three genes, namely DNA methyltransferase (DNMT) 1, DNMT3A, and DNMT3B, coding for DNMTs that affect promoter methylation status are thought to play an important role in the development of cancers. Little is known of the biological and clinical significance of these genes in human breast cancer. EXPERIMENTAL DESIGN: We used real-time reverse transcription-PCR assays to quantify the mRNA expression of the three DNMT genes in a series of 130 breast cancer patients. We also sought relationships between mRNA levels of the DNMTs and those of 20 target genes involved in the DNMT pathway (subgroup of 46 breast tumors). RESULTS: The DNMT3B gene showed the highest range of expression (81.8 compared with 16.6 and 14 for DNMT1 and DNMT3A, respectively). DNMT3B was overexpressed in 30% of the patients (5.4 and 3.1% for DNMT1 and DNMT3A, respectively). DNMT3B overexpression was significantly related to Scarff, Bloom, and Richardson histopathological grade III (P = 0.002), ERalpha negativity (P = 0.0015), and strong MKI67 expression (P = 3 x 10(-6)). In univariate analysis, DNMT3B overexpression was associated with poor relapse-free survival in the subgroup of patients who received adjuvant hormone therapy (with or without chemotherapy; P = 0.0064). Although the poor prognosis associated with DNMT3B overexpression was confirmed by univariate analysis in an independent series of 98 postmenopausal women exclusively treated with adjuvant tamoxifen therapy (P = 0.0036), DNMT3B expression status did not persist as an independent prognostic factor in multivariate analysis. CONCLUSIONS: Although we failed to identify underexpression of specific target genes associated with DNMT increasing expression, the frequent overexpression of DNMT3B in this breast tumor series points to DNMT3B as a potential new therapeutic target in breast cancer.

Adult↗
PubMed2003

Identifying potential regulators of infantile hemangioma progression through large-scale expression analysis: a possible role for the immune system and indoleamine 2,3 dioxygenase (IDO) during involution.

Hemangiomas are benign endothelial tumors. Often referred to as hemangiomas of infancy (HOI), these tumors are the most common tumor of infancy. Most of these lesions proliferate rapidly in the first months of life, and subsequently slowly involute during early childhood without significant complications. However, they often develop on the head or neck, and may pose a significant cosmetic concern for families. In addition, a fraction of these tumors can grow explosively and ulcerate, bleed, or obstruct vision or airway structures. Current treatments for these tumors are associated with significant side effects, and our knowledge of the biology of hemangiomas is limited. The natural evolution of these lesions creates a unique opportunity to study the changes in gene expression that occur as the endothelium of these tumors proliferates and then subsequently regresses. Such information may also increase our understanding of the basic principals of angiogenesis in normal and abnormal tissue. We have performed large-scale genomic analysis of hemangioma gene expression using DNA microarrays. We recently identified insulin-like growth factor 2 as a potentially important regulator of hemangioma growth using this approach. However, little is known about the mechanisms involved in hemangioma involution. Here we explore the idea that hemangioma involution might be an immune-mediated process and present data to support this concept. We also demonstrate that proliferating hemangiomas express indoleamine 2,3 dioxygenase (IDO) and discuss a possible mechanism that accounts for the often slow regression of these lesions.

CD3 Complex↗
PubMed2000

Structural and expression analysis of uricase mRNA from Lotus japonicus.

Uricase (nodulin-35) cDNA, LjUr, was isolated from nodules of a model legume, Lotus japonicus. LjUr expression was most abundant in nodules, although it was detected in nonsymbiotic tissues as well, particularly in roots. Expression in nodules was detected in uninfected cells, nodule parenchyma, and, more intensely, in vascular bundles. Phylogenetic analysis of uricase sequences from various legumes indicated that uricases of amide- and ureide-transporting legumes form two distinct clades. LjUr is in the cluster of amide-transport legumes even though L. japonicus bears determinate nodules.

Amino Acid Sequence↗
PubMed2005

Global protein expression analysis in apicomplexan parasites: current status.

Members of the phylum Apicomplexa are important protozoan parasites that cause some of the most serious, and in some cases, deadly diseases in humans and animals. They include species from the genus Plasmodium, Toxoplasma, Eimeria, Neospora, Cryptosporidium, Babesia and Theileria. The medical, veterinary and economic impact of these pathogens on a global scale is enormous. Although chemo- and immuno-prophylactic strategies are available to control some of these parasites, they are inadequate. Currently, there is an urgent need to design new vaccines or chemotherapeutics for apicomplexan diseases. High-throughput global protein expression analyses using gel or non-gel based protein separation technologies coupled with mass spectrometry and bioinformatics provide a means to identify new drug and vaccine targets in these pathogens. Protein identification based proteomic projects in apicomplexan parasites is currently underway, with the most significant progress made in the malaria parasite, Plasmodium falciparum. More recently, preliminary two-dimensional gel electrophoresis maps of Toxoplasma gondii and Neospora caninum tachyzoites and Eimeria tenella sporozoites, have been produced, as well as for micronemes in E. tenella. In this review, the status of proteomics in the analysis of global protein expression in apicomplexan parasites will be compared and the challenges associated with these investigations discussed.

Animals↗
PubMed2006

Cloning and expression analysis of cadherin7 in the central nervous system of the embryonic zebrafish.

Cadherin cell adhesion molecules exhibit unique expression patterns during development of the vertebrate central nervous system. In this study, we obtained a full-length cDNA of a novel zebrafish cadherin using reverse transcriptase-polymerase chain reaction (RT-PCR) and 5' and 3' rapid amplification of cDNA ends (RACE). The deduced amino acid sequence of this molecule is most similar to the published amino acid sequences of chicken and mammalian cadherin7 (Cdh7), a member of the type II cadherin subfamily. cadherin7 message (cdh7) expression in embryonic zebrafish was studied using in situ hybridization and RT-PCR methods. cdh7 expression begins at about 12h postfertilization (hpf) in a small patch in the anterior neural keel, and along the midline of the posterior neural keel. By 24 hpf, cdh7 expression in the brain shows a distinct segmental pattern that reflects the neuromeric organization of the brain, while its expression domain in the spinal cord is continuous, but confined to the middle region of the spinal cord. As development proceeds, cdh7 expression is detected in more regions of the brain, including the major visual structures in the fore- and midbrains, while its expression domain in the hindbrain becomes more restricted, and its expression in the spinal cord becomes undetectable. cdh7 expression becomes reduced in 3-day old embryos. Our results show that cdh7 expression in the zebrafish developing central nervous system is both spatially and temporally regulated.

Amino Acid Sequence↗
PubMed1986

Isolation, physical characterization and expression analysis of the Saccharomyces cerevisiae positive regulatory gene PHO4.

The Saccharomyces cerevisiae PHO4 gene, which positively controls the expression of phosphatase genes, has been isolated by complementation of a pho4 mutation. The isolated DNA directed integration at the chromosomal PHO4 locus. The nucleotide sequence of PHO4 has a coding region of 930 nucleotides, flanked by sequences with typical transcription initiation and termination signals. The 5' region has characteristics of low-expression promoters and carries several uncommon elements, whose significance is not known. The predicted primary structure of the PHO4 protein, of 309 residues, does not show sequence elements typical of DNA-binding proteins. The transcription of PHO4 is independent of inorganic phosphate. Like other regulatory genes, PHO4 is transcribed at a very low level and the translation of its message uses preferentially several codons which are not employed for highly expressed genes.

Amino Acid Sequence↗
PubMed1993

Expression analysis of cloned chromosomal segments of Escherichia coli.

The novel transcription system of bacteriophage T7 was used to express Escherichia coli genes preferentially with a new low-copy-number plasmid vector, pFN476, to minimize toxic gene effects. Selected E. coli chromosomal fragments from an ordered genomic library (Y. Kohara, K. Ikiyama, and K. Isono, Cell 50:495-508, 1987) were recloned into this vector, and their genes were preferentially expressed in vivo utilizing its T7 promoter. The protein products were analyzed by two-dimensional gel electrophoresis. By using DNA sequence information, the gel migration was predicted for the protein products of open reading frames from these segments, and this information was used to identify gene products visualized as spots on two-dimensional gels. Even in the absence of DNA sequence information, this approach offers the opportunity to identify all gene products of E. coli and map their genes to within 10 kb on the E. coli genome; with sequence information, this approach can produce a definitive expression map of the E. coli genome.

Bacterial Proteins↗
PubMed2001

Expression analysis of Y chromosome genes in human prostate cancer.

PURPOSE: We hypothesized that alterations in Y chromosome gene expression may be associated with prostate cancer. To test this hypothesis we analyzed the expression of 19 Y chromosome genes in benign and malignant prostate tissue. MATERIALS AND METHODS: To study the expression of Y chromosome genes RNA was extracted from prostate cancer and benign prostatic hyperplasia (BPH) tissue as well as from prostate cancer cell lines. RNA was reverse transcribed and polymerase chain reaction amplified using specific primers. These primers were designed for each gene sequence obtained from the gene data bank. We analyzed 19 Y chromosome genes using 6 cell lines, 7 BPH and 7 prostate cancer tissues. Normal testis RNA served as a positive control. RESULTS: Of the 19 genes analyzed in cell lines BPH-1 cells expressed the RPS4Y, USP9Y, TMSB4Y and DBY genes; DUPro expressed RPS4Y, USP9Y, TMSB4Y, DBY and UTY; DU145 expressed DAZ, RPS4Y, USP9Y, TMSB4Y, DBY, EIAFIY, PRKY and SMCY; LNCaP expressed TSPY, SRY, BPY1, PRY, DAZ, RBMIH, RPS4Y, DBY, EIAFIY, PRKY and SMCY; ND1 expressed DAZ, RPS4Y, USP9Y, TMSB4Y, DBY, EIAFIY, PRKY and SMCY; and PC3 expressed RPS4Y, USP9Y and DBY. BPH tissue expressed the SRY, PRY, DBY, PRKY, RPS4Y, TMSB4Y, USP9Y and ZFY genes. Prostate cancer tissue expressed the PRY, TSPY, USP9Y, UTY, DBY, SMCY, ZFY, EIAFIY, TMSB4Y and RPS4Y genes. CONCLUSIONS: The differential expression of Y chromosome genes in prostate cancer, BPH tissue and prostate cancer cell lines indicates that they may have a role in prostate cancer.

Adenocarcinoma↗
PubMed2006

Expression analysis of the gastrodianin gene ga4B in an achlorophyllous plant Gastrodia elata Bl.

Gastrodia elata Bl. is an achlorophyllous orchid plant feeding on the fungus Armillaria mellea. The plant lives underground during its life cycle except for florescence. Gastrodianins, members of the superfamily of monocot mannose-binding protein (MBP), have been identified from Gastrodia elata, yet their physiological functions in the plant are rarely understood. Aspects of expression of gastrodianins in growth and development of the plant will be helpful to dissect their functional roles. Two types of cDNA clones with complete cDNA sequences matching the known gastrodianins were obtained from G. elata Bl.f.glauca S.chow (Orchidaceae) and designated gastrodianin-4A (ga4A) and gastrodianin-4B (ga4B), respectively. But only one isoform was found to be expressed in all different parts of a single plant. Based on the RNA gel blot analysis, gastrodianins were much more abundantly expressed in the fully opened flowers than the underground corms where an enhanced expression was found in the out layers of secondary corms. By RNA in situ hybridization gastrodianin transcripts were distinctly detected in the cortical cells and vascular cells of corms. Strong transcript accumulations were observed in two to eight layers of cortical cells in secondary corms. From its peripheral tissue expression pattern and level in corms and flowers, the gastrodianin may account for a possible defense against phytopathogens or insects.

Amino Acid Sequence↗
PubMed2006

Expression analysis of two Eomesodermin homologues in zebrafish lymphoid tissues and cells.

Eomesodermin (Eomes) is a T-box transcription factor that is involved in mesoderm formation in most vertebrates. Eomes is also expressed in CD8+ T cells and NK cells. No information is available on the role of Eomes in the immune system of lower vertebrates to date, although developmental studies on Eomes (Eomes1) have been performed in zebrafish. Here we report the identification of a second Eomes (Eomes2) in zebrafish and compare expression of the two Eomes genes in the immune system. Zebrafish Eomes1 and Eomes2, composed of 661 and 534 amino acids, respectively, share 49.3% amino acid identity in their coding regions and 88.7% amino acid identity in their T-box regions. Conserved synteny between regions of the human and zebrafish genomes, gene organization and phylogenetic analysis all indicate that the zebrafish Eomes2 gene is a homologue of mammalian Eomes, as previously found for zebrafish Eomes1. Eomes1 mRNA was found to be expressed in the gonad, body kidney, spleen and gill, while Eomes2 mRNA was not detected in any of these tissues. However, strong expression of both Eomes mRNAs was detected in the leukocytes from the spleen, followed by those from body kidney and peripheral blood, with expression of Eomes1 always stronger than that of Eomes2. RT-PCR analysis of body kidney cells sorted by FACS revealed that Eomes1 was expressed strongly in lymphocytes, weakly in blast cells, and was not expressed in granulocytes, while Eomes2 was expressed weakly in lymphocytes. These results suggest that both Eomes genes are involved in the zebrafish immune response, particularly in lymphocyte function as has been found in mammals.

Amino Acid Sequence↗