Biomedical subjects

Yusuke Nakamura

Publications and source records attributed to Yusuke Nakamura.

At least 127 records · Page 7Linked to original sources

PubMed2004

Association between genetic variation in the gene for death-associated protein-3 (DAP3) and adult asthma.

Lung epithelium plays a central role in modulation of the lung inflammatory response, and lung repair and airway epithelial cells are targets in asthma and viral infection. Activated T lymphocytes release cytokines such as interferon-gamma (IFN-gamma) that induce apoptosis, or programmed cell death, of damaged epithelial cells. Death-associated protein-3 (DAP3) is involved in mediating IFN-gamma-induced cell death. To assess the possible involvement of genetic variants of DAP3 with asthma, we searched for single-nucleotide polymorphisms (SNPs) in the gene and conducted a case-control study with 1,341 subjects. We found a strong association between bronchial asthma (BA) in adults (P=0.0051, odds ratio=1.87, 95% CI=1.20-2.92), whereas no association was found with childhood asthma. The tendency was more prominent in patients with higher serum total immunoglobulin E (IgE) (>250 IU/ml) (P=0.00061, odds ratio=2.40, 95% CI=1.44-4.00). DAP3 was expressed in normal bronchial epithelial cells, and the expression was induced by IFN-gamma. These results indicated that specific variants of the DAP3 gene might be associated with the mechanisms responsible for adult BA and contribute to airway inflammation and remodeling.

Adolescent↗

PubMed2004

Identification of 45 novel SNPs in the 83-kb region containing peptidylarginine deiminase types 1 and 3 loci on chromosomal band 1p36.13.

Peptidylarginine deiminases (PADIs) are post-translational modification enzymes that catalyze the conversion of protein-bound arginine residues into citrulline residues in the presence of calcium ions. Among PADIs, PADI4 was identified as a rheumatoid arthritis-susceptibility gene (Suzuki et al. in Nat Genet 34:395, 2003). We identified a total of 87 single nucleotide polymorphisms (SNPs) in PADI1 and PADI3 gene loci. Following a comparison of our data with SNPs in the dbSNP database in the National Center for Biotechnology Information, 45 SNPs are considered to be novel: 33 were identified in the PADI1 gene locus and 12 in the PADI3 gene locus. We also identified two insertion-deletion polymorphisms in introns of the PADI1. The high-resolution map that we constructed in this study will serve as a useful resource for analyzing gene scans of complex diseases mapped to this local segment on chromosomal band 1p36.13.

Chromosome Banding↗

PubMed2004

Functional variation in LGALS2 confers risk of myocardial infarction and regulates lymphotoxin-alpha secretion in vitro.

Myocardial infarction (MI) has become one of the leading causes of death in the world. Its pathogenesis includes chronic formation of plaque inside the vessel wall of the coronary artery and acute rupture of the artery, implicating a number of inflammation-mediating molecules, such as the cytokine lymphotoxin-alpha (LTA). Functional variations in LTA are associated with susceptibility to MI. Here we show that LTA protein binds to galectin-2, a member of the galactose-binding lectin family. Our case-control association study in a Japanese population showed that a single nucleotide polymorphism in LGALS2 encoding galectin-2 is significantly associated with susceptibility to MI. This genetic substitution affects the transcriptional level of galectin-2 in vitro, potentially leading to altered secretion of LTA, which would then affect the degree of inflammation; however, its relevance to other populations remains to be clarified. Smooth muscle cells and macrophages in the human atherosclerotic lesions expressed both galectin-2 and LTA. Our findings thus suggest a link between the LTA cascade and the pathogenesis of MI.

Case-Control Studies↗

PubMed2004

Genome-wide cDNA microarray analysis of gene expression profiles in pancreatic cancers using populations of tumor cells and normal ductal epithelial cells selected for purity by laser microdissection.

To characterize molecular mechanism involved in pancreatic carcinogenesis, we analysed gene-expression profiles of 18 pancreatic tumors using a cDNA microarray representing 23,040 genes. As pancreatic ductal adenocarcinomas usually contain a low proportion of cancer cells in the tumor mass, we prepared 95% pure populations of pancreatic cancer cells by means of laser microbeam microdissection, and compared their expression profiles to those of similarly purified, normal pancreatic ductal cells. We identified 260 genes that were commonly upregulated and 346 genes that were downregulated in pancreatic cancer cells. Because of the high degree of purity in the cell populations, a large proportion of genes that we detected as upregulated or downregulated in pancreatic cancers were different from those reported in previous studies. Comparison of clinicopathological parameters with the expression profiles indicated that altered expression of 76 genes was associated with lymph-node metastasis and that of 168 genes with liver metastasis. In addition, expression levels of 30 genes were related to the recurrence of disease. These genome-wide expression profiles should provide useful information for finding candidate genes whose products might serve as specific tumor markers and/or as molecular targets for treatment of patients with pancreatic cancer.

Epithelium↗

PubMed2004

Catalog of 300 SNPs in 23 genes encoding G-protein coupled receptors.

We previously published a series of detailed maps of single nucleotide polymorphisms (SNPs) in the genomic regions of 209 gene loci encoding drug metabolizing enzymes, transporters, receptors, and other potential drug targets. In addition to the maps reported earlier, we provide here high-resolution SNP maps of 23 genes encoding G-protein coupled receptors in the Japanese population. A total of 300 SNPs were identified through screening of these loci; 83 in four adenosine receptor family genes, 45 in three adrenergic receptor family genes, 22 in three EDG receptor family genes, 29 in three melanocortin receptor family genes, 22 in two somatostatin receptor family genes, 21 in five anonymous G protein-coupled receptor family genes, and 78 in the others (AVPR1B, OXTR, and TNFRSF1A). We also discovered a total of 33 genetic variations of other types. Of the 300 SNPs, 132 (44%) 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 association analyses.

Catalogs as Topic↗

PubMed2004

Identification of ALDH4 as a p53-inducible gene and its protective role in cellular stresses.

To identify additional targets of p53, we used a cDNA microarray system to examine gene-expression patterns in response to enforced expression of exogenous p53 in p53-deficient cancer cells, and identified the aldehyde dehydrogenase 4 ( ALDH4) gene as a direct target of p53. ALDH4 is a mitochondrial-matrix NAD+-dependent enzyme catalyzing the second step of the proline degradation pathway. Expression of ALDH4 mRNA was induced in HCT116 cells in response to DNA damage caused by adriamycin treatment, in a p53-dependent manner. ALDH4 contains a potential p53 binding sequence in intron1 and the interaction of p53 with the site was shown by EMSA and ChIP assays. We confirmed p53-dependent transcriptional activity of the binding site by means of a reporter assay. Inhibition of ALDH4 expression by antisense oligonucleotides was able to enhance cell death induced by infection with Ad-p53. H1299 cells transformed to over-express ALDH4 showed significantly lower intracellular reactive oxygen species (ROS) levels than parental or control cells after treatment with hydrogen peroxide or UV. Those cells were also resistant to cell damage caused by hydrogen peroxide. These results suggest that p53 might play a protective role against cell damage induced by generation of intracellular ROS, through transcriptional activation of ALDH4.

1-Pyrroline-5-Carboxylate Dehydrogenase↗

PubMed2004

Molecular cloning and characterization of a novel gene, EMILIN-5, and its possible involvement in skeletal development.

By analyzing expression profiles of human mesenchymal stem cells incubated in osteogenic supplements, we identified and characterized a novel human cDNA, elastin microfibril interface located protein-5 (EMILIN-5), that is likely to play a significant role in the process of osteogenesis. The deduced EMILIN-5 product consists of 766 amino acids with a cysteine-rich EMI domain at the NH(2) terminus. Western blotting detected EMILIN-5 expression in a variety of osteoblastic cell lines. Immunohistochemistry of mouse embryos 13.5 days post-coitus revealed relatively high levels of EMILIN-5 protein in perichondrium cells of developing limbs. Our findings suggest that the EMILIN-5 gene plays an important role in skeletal development.

3T3 Cells↗

PubMed2004

Analysis of single-nucleotide polymorphisms in Japanese rheumatoid arthritis patients shows additional susceptibility markers besides the classic shared epitope susceptibility sequences.

OBJECTIVE: To examine the entire HLA region for loci (other than the DRB1 locus) associated with rheumatoid arthritis (RA) susceptibility, by typing HLA-DRB1 alleles and multiple single-nucleotide polymorphisms (SNPs) in the Japanese population. METHODS: The HLA-DRB1 alleles and 88 SNPs distributed over the HLA gene complex were genotyped, for 828 patients with RA and 1,032 control subjects. The data were evaluated for linkage disequilibrium, and case-control associations were analyzed in 2 ways, in the presence or absence of the disease-susceptibility DRB1 allele, to detect loci independent of the DRB1 allele. RESULTS: HLA-DRB1 alleles *0405, *0401, *0901, *0101, *1401, *1602, *0403, and *1405 were significantly associated with RA in the Japanese population. The smallest P value (P = 1.4 x 10(-27)) was observed in association with an intronic SNP of the NOTCH4 gene, which was due to strong linkage disequilibrium with the HLA-DRB1 allele. A strong association that was independent of HLA-DRB1 shared epitope alleles was observed in 2 SNPs: one in the intron of the MICA gene, the other in the intron of the HLA-DQB2 gene. Their association with RA, independent of HLA-DRB1 shared epitope alleles, was suggestive (P = 0.0024 [corrected P (P(corr)) = 0.068, and P = 0.00037 [P(corr) = 0.012], respectively). CONCLUSION: These findings suggest that 1 or more other loci besides the HLA-DRB1 or other DRB1 (non-shared epitope, non-*0901) alleles are involved in RA susceptibility/protection.

Adult↗

PubMed2004

CD40 ligand gene and Kawasaki disease.

Kawasaki disease (KD) is an acute systemic vasculitis syndrome of infants and young children. Although its etiology is largely unknown, epidemiological findings suggest that genetic factors play a role in the pathogenesis of KD. To identify genetic factors, affected sib-pair analysis has been performed. One of the identified peaks was located on the Xq26 region. A recent report of elevated expression of CD40 ligand (CD40L), which maps to Xq26, during the acute-phase KD, and its relationship to the development of coronary artery lesions (CAL) prompted us to screen for polymorphism of CD40L and to study the association of the gene to KD. A newly identified SNP in intron 4 (IVS4+121 A>G) is marginally over-represented in KD patients as compared to controls (109/602, 18.1 vs 111/737, 15.1%). When male KD patients with CAL were analyzed as a patient group, the SNP was significantly more frequent than in controls (15/58, 25.9%, vs 111/737, 15.1%, OR=2.0, 95% CI=1.07-3.66; P=0.030). Interestingly, this variation was extremely rare in a control Caucasian population (1/145, 0.7%). Our results suggest a role of CD40L in the pathogenesis of CAL and might explain the excess of males affected with KD.

3' Untranslated Regions↗

PubMed2004

Distinct pattern of gene expression in pyothorax-associated lymphoma (PAL), a lymphoma developing in long-standing inflammation.

Pyothorax-associated lymphoma (PAL) is a unique lymphoma developing in the pleural cavity after long-standing pyothorax. They are diffuse large B-cell lymphomas (DLBCLs), frequently with immunoblastic morphology, and show a strong association with Epstein-Barr virus (EBV) infection. In this study, cDNA microarray analysis was performed in six cases with PAL and 12 with nodal DLBCL. Among 5516 informative genes, 348 displayed more than 2-fold difference (higher or lower) of expression level between PAL and nodal DLBCL (P < 0.001). These genes are known to be involved in apoptosis, interferon response, and signal transduction. One of the most differentially expressed genes, IFI27 (interferon-alpha-inducible protein 27) was subjected to quantitative RT-PCR analysis, and increased expression of IFI27 was confirmed. Overexpression of IFI27 was also found in cell lines derived from PAL, but not in other lymphoid cell lines. This study shows that PAL is a distinctive subtype of DLBCL not only in its clinical presentation, but also in its molecular profile.

Adult↗

PubMed2004

Isolation of p53-target genes and their functional analysis.

Mutations of the p53 gene are the most common genetic alterations found in human cancers, and are known to play crucial roles in tumor development and progression. The p53 gene encodes a protein functioning as a transcription factor, and the biological functions of p53 are manifested through the activities of its downstream genes. Identification of these downstream genes involved in the p53-signaling pathway should provide more detailed insight into the molecular mechanisms that mediate tumor-suppressor activities, as well as various responses to cellular stress. We have been attempting to isolate p53-target genes by means of various approaches, including differential display, cDNA microarray analysis, and direct cloning of the p53-binding sequences from human genomic DNA. Here I review our recent work on isolation of p53-target genes and their functional analysis. The physiological functions of p53-target genes include apoptosis (GML, p53AIP1, and STAG1), DNA repair (p53R2), inhibition of angiogenesis (BAI1), re-entry into the cell cycle (p53RFP), oxidative stress (CSR), and determination of cell fate (p53RDL1).

Animals↗

PubMed2004

Adenovirus-mediated p53AIP1 gene transfer as a new strategy for treatment of p53-resistant tumors.

The p53AIP1 gene, which we recently identified as a novel p53-target, mediates p53-dependent apoptosis. We evaluated the effects of adenovirus-mediated introduction of p53AIP1 (Ad-p53AIP1) on 30 human cancer-cell lines in vitro, and two cell lines in vivo, in comparison with the effects of p53 (Ad-p53). In 20 of the 30 cell lines, p53AIP1-induced apoptosis was observed, and in 12 of these p53AIP1-sensitive cancer cell lines, the apoptotic effects of p53AIP1 were greater than those of p53 itself. Cancers with wild-type p53, which were thought to be p53-resistant, were likely to be sensitive to p53AIP1-induced apoptosis. p53-resistant cancers such as LS174T (p53 +/+) and A549 (p53 +/+), in which no increase of p53AIP1 mRNA expression was observed when Ad-p53 was introduced, were killed effectively by Ad-p53AIP1. Furthermore, co-introduction of p53 and p53AIP1 had a synergistic effect on the induction of apoptosis, regardless of p53 status. Finally, adenovirus-mediated introduction of p53AIP1 suppressed tumor growth in vivo. These results suggested that p53AIP1 gene transfer might become a new strategy for the treatment of p53-resistant cancers.

Adenoviridae↗

PubMed2004

Oncogenic role of NALP7 in testicular seminomas.

To isolate novel molecular targets for treatment of testicular germ cell tumor (TGCT), we performed genome-wide expression profile analysis of testicular seminomas using a cDNA microarray. We here report identification of NACHT, leucine-rich repeat and PYD containing 7 (NALP7 ), that was significantly transactivated in testicular seminomas. Subsequent semi-quantitative RT-PCR and northern blot analyses confirmed an approximately 3.3-kb transcript that was expressed exclusively in testis, although the expression level of this gene in normal testis was much lower than in tumor cells, suggesting an important role of this gene in germ-cell proliferation. Immunohistochemical analysis using anti-NALP7 polyclonal antibody detected the endogenous NALP7 protein in the cytoplasm of embryonal carcinoma cells and testicular seminoma tissues. Transfection of small interfering RNA (siRNA) for NALP7 significantly reduced the NALP7 expression and resulted in growth suppression of testicular germ-cell tumors. These findings imply that NALP7 may play a crucial role in cell proliferation, as well as testicular tumorigenesis, and it appears to be a promising candidate for development of targeted therapy for TGCTs.

Animals↗

PubMed2004

Herpes simplex virus-induced, death receptor-dependent apoptosis and regression of transplanted human cancers.

Inoculation of a live attenuated herpes simplex virus (HSV) vector, betaH1, into human U87MG glioblastoma cells transplanted into athymic nude mice induced complete regression of tumors. The infected cells underwent histochemically confirmed apoptosis without lymphocyte infiltration after expressing CD30, CD30 ligand (CD30L), tumor necrosis factor (TNF)-alpha, TNF receptor 1 (TNF-R1), FAS, and FAS ligand (FAS-L) with activation of caspases 3 and 8. Induction of the transcripts of these receptors and ligands in inoculated tumors was confirmed by quantitative RT-PCR. To examine the specificity of apoptosis in the transplanted tumor, we inoculated betaH1 into transplanted human lung, breast, gastric, and colon cancer tumors, and similar tumor regression with apoptosis was observed in all tumors. We analyzed the roles of expression of CD30, CD30L, TNF-alpha, TNF-R1, FAS, and FAS-L in the tumors, and found that HSV-induced apoptosis was suppressed by the respective antibodies. These findings indicate that the CD30/CD30L, TNF-alpha/TNF-R1, and FAS/FAS-L interactions resulted in apoptosis and tumor regression in immunocompromised mice. In addition to the death receptor-dependent apoptosis induced by HSV, the expressed ligands and receptors might enhance the susceptibility of tumor cells to cell-mediated cyto-toxicity and augment the activation of tumor-killing lymphocytes in immunocompetent models.

Animals↗

PubMed2004

Identification of NOL8, a nucleolar protein containing an RNA recognition motif (RRM), which was overexpressed in diffuse-type gastric cancer.

In an attempt to identify novel therapeutic targets for diffuse-type gastric cancer, we had previously compared expression profiles of 20 diffuse-type gastric-cancer tissues with corresponding non-cancerous mucosae by means of a cDNA microarray consisting of 23,040 genes. Among 153 genes whose expression levels were elevated in cancers compared to non-cancerous mucosae, we focused on a gene termed NOL8 that encodes a putative 150-kDa protein with an RNA-recognition motif (RRM) domain in its amino-acid terminal region. Comparison of expression profiles between diffuse-type and intestinal-type gastric cancers showed that NOL8 was specifically up-regulated in diffuse-type cancers. Northern blot analysis revealed that NOL8 was expressed in skeletal muscle, but not expressed or hardly detectable in 22 other tissues examined. Immunocytochemical staining of NOL8 showed specific localization in the nucleolus. Subsequent protein phosphatase analysis coupled with western analysis revealed the presence of the phosphorylated form. Furthermore, transfection of short-interfering RNA (siRNA) specific to NOL8 into three diffuse-type gastric cancer cells, St-4, MKN45 and TMK-1, effectively reduced expression of this gene and induced apoptosis in these cells. These findings provide a new insight into diffuse-type gastric carcinogenesis and may contribute to the development of new therapeutic strategies for diffuse-type gastric cancer.

Carrier Proteins↗

PubMed2004

Effect of Saiko-ka-ryukotsu-borei-to on amylase activity in mice.

The effects of Saiko-ka-ryukotsu-borei-to (SRBT), a Chinese medicinal prescription, on mouse serum amylase activity were investigated in vivo. SRBT was found to not only dose- and/or time-dependently augment amylase activity, but also to increase alpha-amylase protein content and soluble starch metabolic activity. These results provide a rational basis for the clinical use of SRBT that may accompany disease therapy.

Animals↗

PubMed2004

Isolation of development and differentiation enhancing factor-like 1 (DDEFL1) as a drug target for hepatocellular carcinomas.

To disclose mechanisms of hepatocellular carcinogenesis and to identify novel diagnostic markers and/or drug targets for treatment of hepatocellular carcinomas (HCCs), we analyzed expression profiles of clinical HCCs using a genome-wide cDNA microarray. From among the transcripts that were commonly up-regulated in these tumors we identified a novel human gene at chromosomal band 1p36.13, termed DDEFL1 (development and differentiation enhancing factor-like 1), encoding a product that shared structural features with centaurin-family proteins. The deduced 903-amino acid sequence showed 46% homology to DDEF/ASAP1 (development and differentiation enhancing factor), and contained an Arf GTPase-activating protein (ArfGAP) domain and two ankyrin repeats. Gene transfer of DDEFL1 promoted proliferation of cells that lacked endogenous expression of this gene. Furthermore, reduction of DDEFL1 expression by transfection of anti-sense S-oligonucleotides inhibited the growth of SNU475 cancer cells, in which DDEFL1 expression was highly up-regulated. Our results provide novel insight into hepatocarcinogenesis and may contribute to development of new strategies for diagnosis and treatment of HCC.

Amino Acid Sequence↗

PubMed2004

Genes associated with liver metastasis of colon cancer, identified by genome-wide cDNA microarray.

To uncover mechanisms underlying progression of colorectal carcinogenesis and to identify genes associated with liver metastasis, we analyzed expression profiles of 14 primary colorectal cancers (CRCs) with liver metastases, and compared them with profiles of 11 non-metastatic carcinomas and those of 9 adenomas of the colon. A hierarchical cluster analysis using data from a cDNA microarray containing 23,040 genes indicated that the cancers with metastasis had different expression profiles from those without metastasis, although a number of genes were commonly up-regulated in primary cancers of both categories. We documented 54 genes that were frequently up-regulated and 375 that were frequently down-regulated in primary tumors with metastases to liver, but not in tumors without metastasis. Subsequent quantitative PCR experiments confirmed that PRDX4, CKS2, MAGED2, and an EST (GenBank accession number BF696304) were expressed at significantly higher levels in tumors with metastasis. These data should contribute to a better understanding of the progression of colorectal tumors, and facilitate prediction of their metastatic potential.

Cell Line, Tumor↗