Biomedical subjects

Yusuke Nakamura

Publications and source records attributed to Yusuke Nakamura.

At least 163 records · Page 9Linked to original sources

PubMed2003

Involvement of PEG10 in human hepatocellular carcinogenesis through interaction with SIAH1.

Through a genome-wide cDNA microarray, we identified that the paternally expressed gene 10 (PEG10) was highly expressed in a great majority of hepatocellular carcinomas, although its expression was absent in normal liver cells. Exogenous expression of PEG10 conferred oncogenic activity and transfection of hepatoma cells with antisense S-oligonucleotides suppressing PEG10 resulted in their growth inhibition. Additional experiments revealed that PEG10 protein associated with SIAH1, a mediator of apoptosis, and that overexpression of PEG10 decreased the cell death mediated by SIAH1. These findings suggested that development of drug(s) inhibiting PEG10 activity could be a novel approach for the treatment of hepatocellular carcinomas.

Apoptosis↗

PubMed2003

Association of single-nucleotide polymorphisms in the polymeric immunoglobulin receptor gene with immunoglobulin A nephropathy (IgAN) in Japanese patients.

Immunoglobulin A nephropathy (IgAN) is a primary glomerulonephritis of common incidence world-wide whose etiology and pathogenesis remain unresolved, although genetic factors are assumed to be involved in the development and progression of this disease. To identify genetic variations that might confer susceptibility to IgAN, we performed a case-control association study involving 389 Japanese IgAN patients and 465 controls. Genome-wide analysis of approximately 80,000 single-nucleotide polymorphisms (SNPs) identified a significant association between IgAN and six SNPs located in the PIGR (polymeric immuoglobulin receptor) gene at chromosome 1q31-q41. One of them, PIGR-17, caused an amino-acid substitution from alanine to valine at codon 580 (chi(2)=13.05, P=0.0003, odds ratio [OR] =1.59, 95% confidence interval [95% CI] =1.24-2.05); the OR of minor homozygotes to others was 2.71 (95% CI=1.31-5.61). Another SNP, PIGR-2, could affect promoter activity (chi(2)=11.95, P=0.00055, OR=1.60, 95% CI=1.22-2.08); the OR of minor homozygotes to others was 2.08 (95% CI=0.94-4.60). Pairwise analyses demonstrated that all six SNPs were in almost complete linkage disequilibrium. Biopsy specimens from IgAN patients were positively stained by antibody against the secretory component of PIGR, but corresponding tissues from non-IgAN patients were not. Our results suggest that a gene associated with susceptibility to IgAN lies within or close to the PIGR gene locus on chromosome 1q in the Japanese population.

Adult↗

PubMed2003

Catalog of 680 variations among eight cytochrome p450 ( CYP) genes, nine esterase genes, and two other genes in the Japanese population.

We screened DNAs from 48 Japanese individuals for single-nucleotide polymorphisms (SNPs) in eight cytochrome p450 ( CYP) genes, nine esterase genes, and two other genes by directly sequencing the relevant genomic regions in their entirety except for repetitive elements. This approach identified 607 SNPs and 73 insertion/deletion polymorphisms among the 19 genes examined. Of the 607 SNPs, 284 were identified in CYP genes, 302 in esterase genes, and 21 in the other two genes ( GGT1, and TGM1); overall, 37 SNPs were located in 5' flanking regions, 496 in introns, 55 in exons, and 19 in 3' flanking regions. These variants should contribute to studies designed to investigate possible correlations between genotypes and phenotypes of disease susceptibility or responsiveness to drug therapy.

Cytochrome P-450 Enzyme System↗

PubMed2003

EGR2 induces apoptosis in various cancer cell lines by direct transactivation of BNIP3L and BAK.

EGR2 plays a key role in the PTEN-induced apoptotic pathway. Using adenovirus-mediated gene transfer to 39 cancer cell lines, we found that EGR2 could induce apoptosis in a large proportion of these lines by altering the permeability of mitochondrial membranes, releasing cytochrome c and activating caspase-3, -8, and -9. Analysis by cDNA microarray and subsequent functional studies revealed that EGR2 directly transactivates expression of BNIP3L and BAK. Our results helped to clarify the molecular mechanism of the apoptotic pathway induced by PTEN-EGR2, and suggested that EGR2 may be an excellent target molecule for gene therapy to treat a variety of cancers.

Apoptosis↗

PubMed2003

Expression profiles of non-small cell lung cancers on cDNA microarrays: identification of genes for prediction of lymph-node metastasis and sensitivity to anti-cancer drugs.

To investigate genes involved in pulmonary carcinogenesis and those related to sensitivity of nonsmall cell lung cancers (NSCLCs) to therapeutic drugs, we performed cDNA microarray analysis of 37 NSCLCs after laser-capture microdissection of cancer cells from primary tumors. A clustering algorithm applied to the expression data easily distinguished two major histological types of non-small cell lung cancer, adenocarcinoma and squamous cell carcinoma. Subsequent analysis of the 18 adenocarcinomas identified 40 genes whose expression levels could separate cases with lymph-node metastasis from those without metastasis. In addition, we compared the expression data with measurements of the sensitivity of surgically dissected NSCLC specimens to six anti-cancer drugs (docetaxel, paclitaxel, irinotecan, cisplatin, gemcitabine, and vinorelbine), as measured by the CD-DST (collagen gel droplet embedded culture-drug sensitivity test) method. We found significant associations between expression levels of dozens of genes and chemosensitivity of NSCLCs. Our results provide valuable information for eventually identifying predictive markers and novel therapeutic target molecules for this type of cancer.

Adenocarcinoma↗

PubMed2003

Expression profiles of two types of human knee-joint cartilage.

We have performed a comprehensive analysis of gene-expression profiles in human articular cartilage (hyaline cartilage) and meniscus (fibrocartilage) by means of a cDNA microarray consisting of 23,040 human genes. Comparing the profiles of the two types of cartilage with those of 29 other normal human tissues identified 24 genes that were specifically expressed in both cartilaginous tissues; these genes might be involved in maintaining phenotypes common to cartilage. We also compared the cartilage profiles with gene expression in human mesenchymal stem cells (hMSC), and detected 22 genes that were differentially expressed in cells representing the two cartilaginous lineages, 11 specific to each type, which could serve as markers for predicting the direction of chondrocyte differentiation. Our data should also provide useful information about regeneration of cartilage, especially in support of efforts to identify cartilage-specific molecules as potential agents for therapeutic approaches to joint repair.

Biomarkers↗

PubMed2003

High-density SNP map of human ITR, a gene associated with vascular remodeling.

We constructed a high-density map of single-nucleotide polymorphisms (SNPs) present within a 31-kb region of human chromosome 13q31 that contains the human counterpart of the rabbit ITR gene, which encodes a rhodopsin-like G protein-coupled receptor associated with vascular remodeling. The elements of human ITR cDNA were distributed in 27,452 bp of genomic DNA; the nine exons ranged in size from 50 bp to 2271 bp, with an average size of 392 bp. We isolated a total of 22 SNPs from the ITR locus by systematically screening genomic DNA from 48 healthy Japanese individuals; three SNPs were present in the 5' flanking region, two in coding elements, 12 in introns, and five in the 3' untranslated region. By comparing our data with SNPs deposited in the dbSNP database in the National Center for Biotechnology Information, 19 of the 22 SNPs (86%) were considered to be novel. The map presented here should help in evaluating the role of human ITR in cardiovascular diseases, in other diseases mapped to this segment on chromosome 13q31, and in a variety of pharmacogenetic effects.

3' Untranslated Regions↗

PubMed2003

Inhibition of experimental intimal thickening in mice lacking a novel G-protein-coupled receptor.

BACKGROUND: Vascular restenosis attributable to intimal thickening remains a major problem after percutaneous transluminal coronary angioplasty (PTCA). METHODS AND RESULTS: Through differential-display analysis, we have identified a novel gene whose expression was increased after catheter injury of rabbit aorta. The gene that is expressed predominantly in vascular smooth muscle cells encodes a novel protein with 7 transmembrane domains, and we termed it ITR (intimal thickness-related receptor). The ITR sequence contains a motif common to the Rhodopsin-like GPCR (G-protein-coupled receptor) superfamily. In vivo analyses of this gene revealed that expression of ITR protein increased with intimal thickening induced by cuff placement around murine femoral artery. Furthermore, ITR-knockout mice were found to be resistant to this experimental intimal thickening. CONCLUSIONS: ITR thus seems to be a novel receptor that may play a role in vascular remodeling and that may represent a good target for development of drugs in the prevention of vascular restenosis.

Amino Acid Sequence↗

PubMed2003

Genetic basis of tissue specificity of vasculitis in MRL/lpr mice.

OBJECTIVE: To clarify the mode of inheritance of the tissue distribution of vasculitis in MRL/Mp-lpr/lpr (MRL/lpr) lupus-prone mice and to identify the susceptibility loci. METHODS: Vasculitis in individual MRL/lpr, C3H/HeJ-lpr/lpr (C3H/lpr), (MRL/lpr x C3H/lpr)F(1), and (MRL/lpr x C3H/lpr)F(2) intercross mice was analyzed by histopathologic grading of main branches of the aorta and of medium-sized arteries in the lower limbs. Genomic DNA samples from F(2) intercross mice were examined by simple sequence-length polymorphism analysis, and the polymorphic microsatellite markers highly associated with vasculitis in each tissue were determined as vasculitis susceptibility loci. RESULTS: A susceptibility locus with significant linkage to vasculitis of main branches of the aorta was mapped on chromosome 4 at D4Mit213 (map position 13.3cM) selectively in males, while vasculitis of medium-sized arteries in the lower limbs was mapped to different chromosomes: at D8Mit31 on chromosome 8 (map position 33.0) selectively in females and at D5Mit36 on chromosome 5 (map position 65.0). All of these were different from the previously defined loci governing susceptibility to vasculitis involving the kidneys. CONCLUSION: Systemic vasculitis in MRL/lpr mice is genetically controlled with cumulative effects of multiple gene loci, each of which has tissue specificity.

Animals↗

PubMed2003

Induction of tenascin-C by tumor-specific EWS-ETS fusion genes.

Ewing sarcoma (ES) and peripheral primitive neuroectodermal tumors (PNETs) are associated with a chromosomal translocation resulting in a fusion of the amino-terminus of EWS with the DNA-binding domain of an ETS transcription factor (most commonly FLI1 or ERG). Although previous reports suggested that these chimera proteins would act as aberrant transcription factors, their downstream targets have not been fully elucidated. To identify downstream targets of these EWS-ETS fusion proteins, we introduced EWS-ETS fusion constructs into a human fibrosarcoma cell line, HT-1080, by retroviral transduction. Here we report that Tenascin-C (TNC) is induced to a significantly higher level in cells expressing EWS-ETSs than in cells expressing normal ETSs. Furthermore, through use of an antisense cDNA expression vector we show that expression of endogenous TNC mRNA and protein were reduced coordinately with attenuation of EWS-FLI1 fusion protein expression. A chromatin immunoprecipitation assay showed direct interaction between the TNC promoter and the EWS-FLI1 fusion protein in vivo. In addition, a luciferase reporter assay revealed that EWS-ETSs upregulated the TNC gene through four ETS binding sites in the TNC promoter. High levels of TNC expression were observed in a subset of ES cell lines (3 of 6) and primary tumors (4 of 6). Together with previous studies showing that TNC expression is involved in the invasive and malignant phenotype of several tumor types, our data suggest that the oncogenic effect of EWS-ETS may be mediated in part by upregulating of TNC expression.

DNA, Antisense↗

PubMed2003

Catalog of 668 SNPs detected among 31 genes encoding potential drug targets on the cell surface.

We have been publishing a series of detailed maps of single-nucleotide polymorphisms (SNPs) detected within the genomic loci of 145 genes encoding drug-metabolizing enzymes and transporters. As an addition to the maps reported earlier, we provide here high-density SNP maps of 31 genes encoding various receptors and adhesion molecules of medical importance. By examining a total of approximately 382 kb of genomic DNA encompassing these 31 genes, we identified 668 SNPs among 48 healthy Japanese individuals: 86 in 5' flanking regions, 27 in 5' untranslated regions, 45 in coding regions, 399 in introns, 47 in 3' untranslated regions, and 64 in 3' flanking regions. We also discovered 113 variations of other types. Of the 668 SNPs, 371 (55.5%) appeared to be novel, on the basis of comparisons with the dbSNP database of the National Center for Biotechnology Information (US) or with previous publications. The maps constructed in this study will serve as an additional resource for studies of complex genetic diseases and drug-response phenotypes to be mapped by linkage-disequilibrium analyses.

Cell Adhesion Molecules↗

PubMed2003

Construction and characterization of a vestibular-specific cDNA library using T7-based RNA amplification.

Using a very small amount of inner-ear tissue, we constructed a human vestibular cDNA library by means of T7-based amplification of RNA. This library should allow us to identify genes likely to be involved in auditory and vestibular functions. Here we first report the characterization of the human vestibular cDNA library. Among 506 cDNA clones randomly selected from the vestibular cDNA library, DNA sequences of 301 cDNA clones were identical to those of genes of known function. Twenty-two cDNA clones were considered to be novel because they did not match any cDNA sequences in the public database. The information in our study will provide a valuable resource for identifying several novel genes underlying deafness disorders and vestibular dysfunction.

Bacteriophage T7↗

PubMed2003

High-resolution SNP map in the 55-kb region containing the selectin gene family on chromosome 1q24-q25.

Immunoglobulin A nephropathy (IgAN) is the most common form of glomerulonephritis characterized by predominant IgA deposits in glomerular mesangium. By means of a genome-wide case-control association study, we previously demonstrated that eight single-nucleotide polymorphisms (SNPs) within the selectin gene cluster are significantly associated with IgAN. Here we provide more detailed information of variations corresponding to selectin loci, consisting of 88 SNPs and two insertion-deletion polymorphisms in the Japanese population: 27 in 5' flanking regions, 1 in 5' untranslated regions, 6 within coding regions, 46 in introns, 4 within 3' untranslated regions, and 4 in 3' flanking regions. The SNP map presented here will be a useful resource not only for examining the relationships between selectin genotypes and susceptibility to the IgAN phenotype, but also for analyzing gene scans of complex diseases mapped to this local segment on chromosome 1.

Cell Movement↗

PubMed2003

p53RDL1 regulates p53-dependent apoptosis.

Although a number of targets for p53 have been reported, the mechanism of p53-dependent apoptosis still remains to be elucidated. Here we report a new p53 target-gene, designated p53RDL1 (p53-regulated receptor for death and life; also termed UNC5B). The p53RDL1 gene product contains a cytoplasmic carboxy-terminal death domain that is highly homologous to rat Unc5H2, a dependence receptor involved in the regulation of apoptosis, as well as in axon guidance and migration of neural cells. We found that p53RDL1 mediated p53-dependent apoptosis. Conversely, when p53RDL1 interacted with its ligand, Netrin-1, p53-dependent apoptosis was blocked. Therefore, p53RDL1 seems to be a previously un-recognized target of p53 that may define a new pathway for p53-dependent apoptosis. We suggest that p53 might regulate the survival of damaged cells by balancing the regulation of Netrin-p53RDL1 signalling, and cell death through cleavage of p53RDL1 for apoptosis.

Animals↗

PubMed2003

Functional haplotypes of PADI4, encoding citrullinating enzyme peptidylarginine deiminase 4, are associated with rheumatoid arthritis.

Individuals with rheumatoid arthritis frequently have autoantibodies to citrullinated peptides, suggesting the involvement of the peptidylarginine deiminases citrullinating enzymes (encoded by PADI genes) in rheumatoid arthritis. Previous linkage studies have shown that a susceptibility locus for rheumatoid arthritis includes four PADI genes but did not establish which PADI gene confers susceptibility to rheumatoid arthritis. We used a case-control linkage disequilibrium study to show that PADI type 4 is a susceptibility locus for rheumatoid arthritis (P = 0.000008). PADI4 was expressed in hematological and rheumatoid arthritis synovial tissues. We also identified a haplotype of PADI4 associated with susceptibility to rheumatoid arthritis that affected stability of transcripts and was associated with levels of antibody to citrullinated peptide in sera from individuals with rheumatoid arthritis. Our results imply that the PADI4 haplotype associated with susceptibility to rheumatoid arthritis increases production of citrullinated peptides acting as autoantigens, resulting in heightened risk of developing the disease.

Adult↗

PubMed2003

Impaired function of p53R2 in Rrm2b-null mice causes severe renal failure through attenuation of dNTP pools.

p53R2, which is regulated by tumor suppressor p53, is a small subunit of ribonucleotide reductase. To determine whether it is involved in DNA repair by supplying deoxyribonucleotides (dNTPs) for resting cells in vivo, we generated a strain of mice lacking Rrm2b (encoding p53R2). These mice developed normally until they were weaned but from then on had growth retardation and early mortality. Pathological examination indicated that multiple organs had failed, and all Rrm2b-null mice died from severe renal failure by the age of 14 weeks. TUNEL staining showed a greater number of apoptotic cells in kidneys of 8-week-old Rrm2b-/- mice relative to wild-type mice. p53 was activated in kidney tissues of Rrm2b-/- mice, leading to transcriptional induction of p53 target genes. Rrm2b-/- mouse embryonic fibroblasts (MEFs) became immortal much earlier than Rrm2b+/+ MEFs. dNTP pools were severely attenuated in Rrm2b-/- MEFs under oxidative stress. Rrm2b deficiency caused higher rates of spontaneous mutation in the kidneys of Rrm2b-/- mice. Our results suggest that p53R2 has a pivotal role in maintaining dNTP levels for repair of DNA in resting cells. Impairment of this pathway may enhance spontaneous mutation frequency and activate p53-dependent apoptotic pathway(s) in vivo, causing severe renal failure, growth retardation and early mortality.

Animals↗

PubMed2003

Prediction of response to imatinib by cDNA microarray analysis.

Clinical introduction of imatinib mesylate (Gleevec) (formerly STI571) has marked a major advance in the treatment of chronic myeloid leukemia (CML), inducing major cytogenetic response in 60% to 80% of patients with chronic-phase disease. Since its remarkable effect has made it difficult to decide the timing for potentially curative but life-threatening stem cell transplantation (SCT), it would be very useful to predict imatinib's effectiveness in individual patients beforehand. We analyzed gene expression profiles of peripheral leukemia cells from 18 CML patients (16 chronic phase, two blast crisis) who were treated with imatinib alone. cDNA microarrays representing 23,040 genes identified 79 genes that were expressed differentially between cytogenetically defined responders and nonresponders to imatinib. We then established a "prediction score" system using 15 or 30 of these genes that could clearly separate the responder group from the nonresponder group. Four additional patients' responses to imatinib were successfully predicted, validating the process. Thus, gene-expression profiles can predict clinical effectiveness of CML to imatinib, and may eventually lead to the achievement of "personalized therapy" for this disease.

Adult↗

PubMed2003

Identification of candidate predictive markers of anticancer drug sensitivity using a panel of human cancer cell lines.

We previously investigated the correlations between the expression of 9216 genes and various chemosensitivities in a panel of 39 human cancer cell lines(1)) and found that the expression levels of AKR1B1 and CTSH were correlated with sensitivity and resistance to multiple drugs, respectively. To validate these correlations, we investigated the expression of these two genes and the chemosensitivities in 12 additional gastric cancer cell lines. The expression of AKR1B1 in the additional cell lines exhibited significant correlations with sensitivities to 8 of the 23 drugs examined, while that of CTSH displayed a significant negative correlation with only one (MS-247) of the 27 drugs examined. Their expressions were weakly correlated with sensitivity and resistance, respectively, to the remainder of the drugs. Moreover, when the 12 cell lines were divided into high-expressing and low-expressing groups, a comparison of these groups using Mann-Whitney's U test revealed that high expression levels of AKR1B1 and CTSH were related to sensitivity to 21 of the drugs and resistance to 8 of the drugs, respectively. The present results suggest that AKR1B1 and CTSH may be good markers for prediction of sensitivity to certain drugs and that our panel of 39 cell lines has the potential to identify candidate predictive marker genes.

Aged↗