Biomedical subjects

Masahiro Okamoto

Publications and source records attributed to Masahiro Okamoto.

17 recordsLinked to original sources

PubMed2006

Specific gene-expression profiles of noncancerous liver tissue predict the risk for multicentric occurrence of hepatocellular carcinoma in hepatitis C virus-positive patients.

BACKGROUND: Hepatitis C virus (HCV) infection produces chronic hepatitis, cirrhosis, and, ultimately, hepatocellular carcinoma (HCC). A molecular analysis of the damaged liver tissues infected with HCV may identify specific gene-expression profiles associated with a risk for liver carcinogenesis. METHODS: Forty patients with HCV-positive HCC were classified into two groups: single nodular HCC group (n = 28) and multicentric HCC group (n = 12). Using a complementary DNA microarray, we compared the gene-expression patterns of the noncancerous liver tissue specimens between the two groups. We also identified the differentially expressed genes related to multicentric recurrence in the liver remnant. We then evaluated whether a specific gene-expression profile can accurately estimate the risk for multicentric hepatocarcinogenesis. RESULTS: We selected the 230 differentially expressed genes in the multicentric HCC group. A hierarchical clustering analysis identified a cluster that might be closely associated with the multicentric occurrence of HCC. On the basis of the gene-expression profiling of the 36 genes commonly associated with both multicentric HCC and multicentric recurrence, we created a scoring system to estimate the risk for multicentric hepatocarcinogenesis. The prediction score of patients in the multicentric HCC group with multicentric recurrence (19.9 +/- 9.2) was significantly higher (P < .05) than that in the single nodular HCC group without multicentric recurrence (-1.8 +/- 12.7). CONCLUSIONS: Specific gene-expression signatures in noncancerous liver tissue may help to accurately predict the risk for developing HCC.

Aged↗

PubMed2006

Novel technique for preprocessing high dimensional time-course data from DNA microarray: mathematical model-based clustering.

MOTIVATION: Classifying genes into clusters depending on their expression profiles is one of the most important analysis techniques for microarray data. Because temporal gene expression profiles are indicative of the dynamic functional properties of genes, the application of clustering analysis to time-course data allows the more precise division of genes into functional classes. Conventional clustering methods treat the sampling data at each time point as data obtained under different experimental conditions without considering the continuity of time-course data between time periods t and t+1. Here, we propose a method designated mathematical model-based clustering (MMBC). RESULTS: The proposed method, designated MMBC, was applied to artificial data and time-course data obtained using Saccharomyces cerevisiae. Our method is able to divide data into clusters more accurately and coherently than conventional clustering methods. Furthermore, MMBC is more tolerant to noise than conventional clustering methods. AVAILABILITY: Software is available upon request. CONTACT: taizo@brs.kyushu-u.ac.jp.

Algorithms↗

PubMed2006

WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways.

We have implemented an efficient, user-friendly biochemical reaction simulator called Web-based BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing large-scale nonlinear networks such as metabolic pathways. Users can easily design and analyze an arbitrary reaction scheme through the Internet and an efficient graphical user interface without considering the mathematical equations. The reaction scheme can include several reaction types, which are represented by both the mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state, such as Michaelis-Menten, Hill cooperative, Competitive inhibition. However, since all modules in Web-based BEST-KIT have been developed in Java applet style, users cannot optionally make use of original mathematical equations in addition to the prepared equations. In the present study, we have developed a new version of BEST-KIT (for Microsoft Windows called WinBEST-KIT) to allow users to define original mathematical equations and to customize these equations very easily as user-defined reaction symbols. The following powerful system-analytical methods are prepared for system analysis: time-course calculation, parameter scanning, estimation of the values of unknown kinetic parameters based on experimentally observed time-course data of reactants, dynamic response of reactants against virtual external perturbations, and real-time simulation (Virtual Dry Lab).

Computational Biology↗

PubMed2006

Application of bioinformatics for DNA microarray data to bioscience, bioengineering and medical fields.

In the 1990s, DNA microarray or DNA chip as a novel biological experimental technology was developed, which enables the comprehensive measurement of the expression levels of hundreds of genes, simultaneously. Using this technique, a comprehensive understanding of the cell can be achieved. However, because even simple life forms, such as microorganisms, have more than a thousand kinds of genes, the data from a DNA chip cannot be analyzed without statistical and informational technology. Bioinformatics is the interdisciplinary research field integrating molecular biology with informatics, and it is expected to have a huge impact on the bioscientific, bioengineering and medical fields. There are many techniques in bioinformatics for the analysis of DNA microarray data; however, these are mainly divided into fold-change analysis, clustering, classification, genetic network analysis, and simulation. In this review, these techniques are briefly explained by using some examples.

Animals↗

PubMed2005

Global analysis of altered gene expressions during the process of esophageal squamous cell carcinogenesis in the rat: a study combined with a laser microdissection and a cDNA microarray.

The genetic alterations that occur during esophageal tumorigenesis have yet to be determined. We previously established a Wister rat carcinogenesis model of esophageal squamous cell carcinoma. To understand more about the molecular mechanisms during carcinogenesis, we produced esophageal neoplastic lesions by administering N-amyl-N-methylnitrosamine and 12-O-tetradecanoylphorbol-13-acetate to rats. We used laser microdissection to specifically isolate the cells from the normal epithelium, papilloma, dysplasia, and invasive carcinoma. Using a cDNA microarray representing 14,815 clones, we then analyzed the gene expression profiles for each esophageal lesion. The number of differentially expressed genes compared with the normal control dramatically increased in a step-by-step fashion from normal epithelium (1,151 +/- 119 genes) to papilloma (1,899 +/- 543 genes), dysplasia (1,991 +/- 193 genes), and invasive carcinoma (2,756 +/- 87 genes). A hierarchical clustering analysis showed that the three stages of normal epithelium, dysplasia (papilloma), and invasive carcinoma could be clearly classified, whereas the gene expression patterns of papilloma and dysplasia were indistinguishable. Using the Fisher criterion, we also identified 50 genes whose expression level had either significantly increased or decreased in a step-by-step manner from the normal epithelium to dysplasia and then finally to invasive carcinoma. Many of these genes were not previously known to be associated with esophageal carcinogenesis. The present findings in our rat model thus seem to provide us with a better understanding of the molecular alterations that occur during esophageal carcinogenesis and hopefully will also help lead to the development of novel diagnostic and therapeutic targets.

Animals↗

PubMed2005

Dioptric changes in eyes with reversed intraocular lenses.

PURPOSE: To theoretically calculate refractive changes in eyes with reversed intraocular lenses (IOLs). SETTING: Nara Medical University, Nara, Japan. METHODS: With the ray-tracing method, the refractive changes in a theoretical eye model with a reversed IOL in the capsular bag were calculated. Data for 3 models, anterior biconvex (MA60AC, Alcon), posterior biconvex (MA60BM, Alcon), and convex plano (UV2565T, Menicon), were provided by the manufacturer and used in the analysis. RESULTS: Using the assumption that the axial length varied from 22 to 27 mm, the anterior-biconvex IOLs elicited small refractive changes when reversed. The posterior-biconvex IOLs elicited a significant myopic shift (up to 0.90 diopter [D]) when reversed. The convex-plano IOLs elicited a significant hyperopic shift (up to 2.01 D) when reversed. CONCLUSIONS: Anterior-biconvex IOLs with similar anterior and posterior radii of curvature will not cause large diopter surprises when reversed. High-power posterior-convex IOLs will cause significant myopic diopter surprises when reversed. Both these changes shift toward myopic if the postoperative anterior chamber depth (ACD) becomes shallow. Medium- to high-power convex-plano IOLs will cause a large hyperopic shift when reversed. This hyperopic shift decreases if the postoperative ACD becomes shallower.

Humans↗

PubMed2005

Genomic screens for genes upregulated by demethylation in colorectal cancer: possible usefulness for clinical application.

Inactivation of tumor suppressor genes may result in clinically aggressive tumors and poor prognoses for cancer patients. This study was conducted to investigate the clinical significance of genomic screens for genes upregulated by demethylation in colorectal cancer. We performed a comprehensive survey of commonly inactivated genes in colorectal cancer through the functional reactivation of epigenetically silenced genes by 5-Azacytidine, using cDNA microarrays containing 12,814 genes. We then investigated the clinical significance of the identified gene in colorectal cancer patients. Among 41 candidate genes identified by this microarray analysis, 31 (76%) harbored CpG islands, and many of the genes were associated with cancer-testis antigens, Wnt inhibitors, growth factors, and cell cycle regulators. Subsequent analysis by quantitative RT-PCR confirmed the reliability of our microarray strategy. In order to elucidate the potential clinical significance of these identified genes, we selected one of these genes, apolipoprotein D (apo D), and investigated its mRNA expression in 63 colorectal cancer patients using quantitative real-time RT-PCR. The mean expression level of Apo D mRNA was significantly lower in cancerous tissues than in non-cancerous tissues (p < 0.01), and a lower expression of Apo D was significantly correlated with lymph node metastasis (p < 0.05), advanced stages (p < 0.05) and poorer overall survival (p < 0.05). These results indicated that a genomic screen for genes upregulated by demethylation may be a useful approach for the identification of genes that are of clinical significance in colorectal cancer patients.

Aged↗

PubMed2004

Development of a computer-aided diagnosis system for a new modality of renal replacement therapy: an integrated approach combining both peritoneal dialysis and hemodialysis.

The authors developed a computer-aided diagnosis system that includes a simple clinical test for the chronic renal disease patient who needs an integrated approach that combines both peritoneal dialysis and hemodialysis (PD-HD therapy). In this case study, the system simulated and estimated the dialysis outcome, the ultrafiltration volume and nutritional analysis by employing a pharmacokinetic model, and assessed the peritoneal permeable enhancement that can be a grave complication with peritoneal dialysis. This system requires only a minimum amount of nursing time and may be able to predict the optimal treatment schedule for PD-HD therapy and provide therapeutic monitoring in long-term peritoneal dialysis.

Computer Simulation↗

PubMed2004

Induction of vascular endothelial growth factor and matrix metalloproteinase-3 (stromelysin) by interleukin-1 in human articular chondrocytes and synoviocytes.

We investigated the effects of interleukin (IL)-1 on vascular endothelial growth factor (VEGF) and matrix metalloproteinase-3 (MMP-3) (stromelysin) secretion from chondrocytes and synoviocytes in different clinical conditions. Specifically, cells obtained from osteoarthritic (OA) (n = 7), rheumatoid arthritic (RA) (n = 5), and post-traumatic (PT) (n = 5) patients were stimulated in vitro with IL-1beta in the presence or absence of an IL-1 receptor antagonist (IL-1ra) (anakinra). Levels of secreted MMP-3 and VEGF were measured by enzyme-linked immunosorbent assay. The VEGF mRNA expression was analyzed quantitatively. Interleukin-1 induced both VEGF and MMP-3 secretion from all of the samples tested, and VEGF mRNA expression was also upregulated. Interleukin-1ra significantly suppressed the enhancing effect of IL-1 on MMP-3 and VEGF in both cell types. In conclusion, IL-1 simultaneously induces MMP-3 and VEGF production from chondrocytes and synoviocytes in inflammatory, degenerative, and post-traumatic joints. Therefore, IL-1ra might be beneficial for protection from VEGF-mediated alterations of cartilage metabolism in pathologic and physiologic conditions.

Aged↗

PubMed2004

Long-term observation of the refraction with a reversed-optic posterior chamber intraocular lens.

A 73-year-old man had phacoemulsification and implantation of a posterior chamber intraocular lens (PC IOL) in both eyes. In the right eye, the optic was unintentionally reversed in the bag. In the left eye, the posterior capsule was ruptured and the IOL haptics were fixated in the ciliary sulcus. The refraction in the sulcus-fixated left eye was stable from 1 month to 4 years. The right eye had a myopic shift at 1 month, with a regression of 1.50 diopters that continued for 2 years. The final IOL position in the right eye was 0.25 mm anterior to the position predicted by the SRK/T formula. It took 2 years for the refraction in the eye with the reversed-optic PC IOL to become stable. A large myopic shift and gradual regression in refraction may stem from a different wound-healing reaction than that of properly fixated IOLs.

Aged↗

PubMed2004

A gene-expression signature can quantify the degree of hepatic fibrosis in the rat.

BACKGROUNDS/AIMS: A more accurate and objective quantification of hepatic fibrosis would provide clinically useful information for the monitoring of chronic liver disease progression and therapy recommendation. METHODS: Using a cDNA microarray of 14,814 clones, we analyzed the gene-expression profiles of fibrotic livers in a rat model. RESULTS: We identified 750 up- and 345 down-regulated genes by combining a signal-to-noise score and a random permutation test (P<0.01). The functions of these genes provided insight into the underlying molecular mechanisms of both structural remodeling and functional deficits in cirrhosis. To quantify the extent of liver fibrosis, we have generated for the first time a 'genetic fibrosis index' based on gene-expression profiling of 95 genes by combining a Pearson correlation coefficient and a 'leave-one-out' cross-validation procedure. This technique based on a supervised learning analysis correctly quantified the various degrees of fibrosis in both 20 training samples (R(2)=0.829, P<0.001) and 6 test samples (R(2)=0.822, P<0.05). CONCLUSIONS: Our method will assist researchers in identifying rational targets for intervention and might help clinicians to objectively monitor the severity of liver fibrosis.

Animals↗

PubMed2004

An integrated comprehensive workbench for inferring genetic networks: voyagene.

We propose an integrated, comprehensive network-inferring system for genetic interactions, named VoyaGene, which can analyze experimentally observed expression profiles by using and combining the following five independent inferring models: Clustering, Threshold-Test, Bayesian, multi-level digraph and S-system models. Since VoyaGene also has effective tools for visualizing the inferred results, researchers may evaluate the combination of appropriate inferring models, and can construct a genetic network to an accuracy that is beyond the reach of a single inferring model. Through the use of VoyaGene, the present study demonstrates the effectiveness of combining different inferring models.

Algorithms↗

PubMed2004

Expression of cancer-testis antigen (CTA) genes in intrahepatic cholangiocarcinoma.

BACKGROUND: Cancer-testis antigens (CTA), such as MAGE, are selectively expressed in various types of human neoplasms but not in normal tissues other than testis. This characteristic feature of CTA makes them promising antigens for cancer-specific immunotherapy. METHODS: We investigated the expression of five genes, including MAGE-1, MAGE-3, NY-ESO-1, SCP-1, and SSX-4, in 20 surgical samples of intrahepatic cholangiocarcinomas (IHCC) using reverse transcription-polymerase chain reaction. To visualize the localization of MAGE proteins, we performed immunohistochemical studies. Furthermore, the correlation between the CTA expression and DNA methylation status was studied in three bile duct cancer cell lines. RESULTS: Expression of MAGE-1, MAGE-3, NY-ESO-1, SCP-1, and SSX-4 was recognized in 4, 4, 2, 6, and 3 of all 20 cases, respectively. In contrast, the expressions of five genes were not recognized at all in the corresponding normal tissues. In 10 cases (50%), the tumors expressed at least one of the five CTA. An immunohistochemical analysis of MAGE proteins demonstrated homogenous or focal distributions in cytoplasm of the IHCC. Using a demethylating agent, MAGE-1, NY-ESO-1, SCP-1, and SSX-4 were induced in two of three cell lines, whereas MAGE-3 was not. CONCLUSIONS: Half of the tumor tissues of IHCC expressed at least one of the CTA. Some of the patients with IHCC, therefore, should be candidates for potentially useful cancer-specific immunotherapy.

Aged↗

PubMed2003

Downregulation of Cap43 gene by von Hippel-Lindau tumor suppressor protein in human renal cancer cells.

We previously identified 9 genes (i.e., thymosin beta4, secreted protein acidic and rich in cysteine, Cap43, ceruloplasmin, serum amyloid A, heat shock protein 90, LOT1, osteopontin and casein kinase Igamma) that are more highly expressed in cancerous regions than in noncancerous regions in human renal cancers. In our study, we considered the possibility that the von Hippel-Lindau (VHL) tumor suppressor gene might be able to affect the expression of these 9 genes in renal cancer cells. We first established 2 VHL-positive cell lines, 786/VHL-1 and 786/VHL-2, after the introduction of wild-type VHL into VHL-negative renal cancer 786-O cells. Of these 9 genes, expression of the Cap43 gene was specifically downregulated by VHL. Expression of Cap43 was also much lower in 4 other VHL-positive renal cancer cell lines than in VHL-negative 786-O cells. Cap43 promoter assays with several deletion or mutation constructs demonstrated that the Sp1 site in the element from -286 base pairs (bp) to -62 bp was partly responsible for VHL-induced suppression of the Cap43 gene. Immunostaining analysis with human specimens of renal cancers demonstrated that the Cap43 protein was expressed in most cancer cells and macrophages. We also observed a marked and specific increase of Cap43 mRNA levels in response to hypoxia or nickel in all VHL-positive cell lines. Cellular expression of Cap43 mRNA in response to hypoxia or nickel thus is closely associated with VHL gene expression in renal cancer cells. Although the function of the Cap43 protein remains unclear, the expression of Cap43 protein could be a molecular marker closely associated with VHL in renal cancer.

Carcinoma, Renal Cell↗

PubMed2002

Suppression of thymidine phosphorylase-mediated angiogenesis and tumor growth by 2-deoxy-L-ribose.

Thymidine phosphorylase (TP), an enzyme involved in the reversible conversion of thymidine to thymine, is identical to an angiogenic factor, platelet-derived endothelial cell growth factor (PD-ECGF). Both TP and one of the TP-degradation products of thymidine 2-deoxy-D-ribose (dRib) display endothelial cell chemotactic activity in vitro and angiogenic activity in vivo. Recently, we demonstrated that 2-deoxy-L-ribose (lRib) could abolish the inhibitory effect of dRib on hypoxia-induced apoptosis. This suggested that lRib may be a useful inhibitor of dRib and thereby of TP functions. Therefore, we investigated the ability of lRib to inhibit the range of biological activities of TP and dRib. lRib suppressed both dRib-induced endothelial cell migration in a chemotaxis assay and endothelial tube formation induced by dRib in a collagen gel. lRib could also suppress the biological effects of TP in vivo assays of angiogenesis and tumor growth. Thus, in a corneal assay of angiogenesis, lRib inhibited angiogenesis induced by the implantation of recombinant TP. In a dorsal air sac assay of angiogenesis, lRib inhibited angiogenesis induced by the implantation of KB cells overexpressing TP (KB/TP). In a tumor growth assay, lRib treatment considerably decreased the growth rate of KB/TP cells xenografted into nude mice and also resulted in an increase in the proportion of apoptotic cells in KB/TP tumors. These findings demonstrate that TP and dRib play an important role in angiogenesis and tumor growth, and that these effects can be inhibited by lRib. Thus, lRib is a potentially useful agent for the suppression of TP-dependent angiogenesis and tumor growth.

Animals↗

PubMed2002

Up-regulation of thrombospondin-1 gene by epidermal growth factor and transforming growth factor beta in human cancer cells--transcriptional activation and messenger RNA stabilization.

Thrombospondin-1 (TSP-1), a multifunctional matrix protein, affects tumor growth through modulation of angiogenesis and other stromal biological functions. In several of nine human cancer cell lines derived from liver, brain, pancreas, and bone, expression of TSP-1 was up-regulated in response to the two most representative growth factors, epidermal growth factor (EGF) and transforming growth factor beta1 (TGFbeta1). Expression of TSP-1 was markedly enhanced in hepatic HuH-7 cells by EGF but not by TGFbeta1. In contrast, expression of TSP-1 was markedly enhanced by TGFbeta1, but not by EGF, in osteosarcoma MG63 cells. EGF induced activation of TSP-1 promoter-driven luciferase activity in HuH-7 cells, and the elements between -267 and -71 on the 5' region of TSP-1 gene containing two GC boxes to which Sp1 bound, were found to be responsible for the promoter activation by EGF. However, EGF did not alter TSP-1 mRNA stability in hepatic cells. On the other hand, no such enhancement of the TSP-1 promoter activity by TGFbeta1 appeared in MG63 cells. Enhanced expression of TSP-1 by TGFbeta1 in MG63 cells was partially blocked by exogenous addition of SB203580, an inhibitor of p38 mitogen-activated protein kinase. TGFbeta was found to induce marked elongation of TSP-1 mRNA longevity in osteosarcoma cells when mRNA degradation was assayed in the presence of alpha-amanitin. The up-regulation of TSP-1 by EGF and TGFbeta might play a critical role in modulation of angiogenesis and formation of matrices in tumor stroma.

Bone Neoplasms↗

PubMedDate not supplied

Biocompatibility of polyvinylalcohol gel as a vitreous substitute.

Polyvinylalcohol (PVA) hydrogel cross-linked by gamma irradiation was assessed as a possible vitreous substitute. From a series of experiments, rise of intraocular pressure and inflammatory changes in the vitreous cavity after operation were observed in some cases. Crab-eating macaques were used for this experiment. PVA gels were injected into vitreous cavity after vitrectomy and followed clinically by opthalmoscopy, tonometry, fundus photography, electroretinogram (ERG), chemotaxis, and flare cell meter. Histopathologic examination by light and electron microscopy was performed after 3 months. As a result, there were no significant changes in ophthalmoscopic findings. No abnormal rising of intraocular pressure (IOP) was recognized. ERG did not show meaningful amplitude weakness. From the photon counting of flare cell meter, significant break of blood-aqueous barrier and blood-retinal barrier was not observed. Histopathologic examination revealed that all layers of the retina were intact and no loss of tissue was evident. However, in PVA gel-injected eyes, some vacuolations of the inner retina were found in some specimens. To conclude, PVA gel was well tolerated in these experiments. The gel with a network similar to the vitreous body showed the best biocompatibility, though it is necessary to investigate the biocompatibility for the long-term. PVA gel is a good candidate for a vitreous substitute.

Animals↗