Biomedical subjects

Kazuhide Imai

Publications and source records attributed to Kazuhide Imai.

10 recordsLinked to original sources

PubMed2006

A new method for gene discovery in large-scale microarray data.

Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure to discover whole sets of genes related to a quantitative trait of interest, which is generally controlled by several loci that make various contributions. Here, we describe a high-throughput gene discovery method based on correspondence analysis with a new index for expression ratios [arctan (1/ratio)] and three artificial marker genes. This method allows us to quickly analyze the whole microarray dataset and discover up-/down-regulated genes related to a trait of interest. We employed an example dataset to show the theoretical advantage of this method. We then used the method to identify 88 cancer-related genes from a published microarray data from patients with breast cancer. This method also allows us to predict the phenotype of a given sample from the gene expression profile. This method can be easily performed and the result is also visible in 3D viewing software that we have developed.

Breast Neoplasms↗

PubMed2006

Altered gene expression in the subdivisions of the amygdala of Fyn-deficient mice as revealed by laser capture microdissection and mKIAA cDNA array analysis.

Fyn-tyrosine-kinase-deficient mice exhibit increased fearfulness and display enhanced excitability in the amygdala. To gain insight into the molecular changes associated with the increased excitability of the amygdala, we used a newly developed cDNA array system comprising mouse KIAA cDNA clones to identify novel genes differentially expressed in the amygdala of fyn(-/-) and fyn(+/-) mice following administration of N-methyl-D-aspartate (NMDA). Laser capture microdissection in combination with PCR-based cDNA amplification allowed us to analyze gene expression in each amygdalar subdivision. The statistical significance of the differential expressions was tested by one-way analysis of variance (ANOVA) by the false discovery rate controlling approach. Among the 805 mKIAA cDNA clones tested, only the expression level of mKIAA1577 (Zinc finger SWIM domain containing protein 6; gene name, Zswim6) showed statistically significant change in regard to the genotype and amygdalar subdivision. Namely, only the lowered expression of mKIAA1577 in the central nucleus of fyn(-/-) mice 1 h after NMDA administration (2.1-fold lower relative to fyn(+/-) mice) was statistically significant. In situ hybridization analysis confirmed the downregulation of the mRNA in the central nucleus of the fyn(-/-) mice 1 h after NMDA administration (3.2-fold lower relative to fyn(+/-) mice). The NMDA-induced change in gene expression was partially blocked by the NMDA antagonist D-AP-5. These results suggest that Fyn deficiency was responsible for the NMDA-induced downregulation of a specific gene in the amygdalar central nucleus.

2-Amino-5-phosphonovalerate↗

PubMed2006

Repeated methamphetamine administration alters expression of the NMDA receptor channel epsilon2 subunit and kinesins in the mouse brain.

Repeated amphetamine administration results in behavioral sensitization. Behavioral sensitization related to abuse and/or relapse may be associated with stable changes in gene expression. To explore the participating genes, we examined the changes in gene expression levels 24 h or 21 days (long-term withdrawal period) after chronic methamphetamine (METH) treatment for 2 weeks. The expression of several genes related to glutamatergic neural transmission was altered, although changes in the corresponding protein expression were not always consistent with the results for mRNA expression. Of interest, in the frontal cortex of mice treated with METH for 2 weeks, protein expression levels of KIF17 and the N-methyl-D-asparate (NMDA) receptor channel epsilon2 subunit (NRepsilon2) were concomitantly increased. The alteration in expression of these proteins, KIF17 and NRepsilon2, might be a part of the molecular basis of the behavioral sensitization to METH.

Animals↗

PubMed2005

Temporal change in mKIAA gene expression during the early stage of retinoic acid-induced neurite outgrowth.

mKIAA genes are mouse counterparts of human KIAA genes, which were isolated in our cDNA project and were functionally unknown at the time they were sequenced. Because KIAA/mKIAA genes were isolated mainly from cDNA libraries derived from brain tissues, they are thought to be important for the organization and function of the brain. To investigate the participation of mKIAA genes in neuronal phenomena, we analyzed retinoic acid-induced neurite outgrowth using an mKIAA oligonucleotide microarray. Focusing on the early stage of this outgrowth phenomenon, we analyzed temporal gene expression changes 1-24 h after treatment with retinoic acid and found several change patterns in 38 mKIAA genes. Among them, six were upregulated at 3 h and subsequently returned to the steady state. Supposing that these genes had important roles, we performed semi-quantitative RT-PCR analysis and confirmed the existence of temporal expression patterns in two genes (mKIAA0182 and mKIAA1039). Further computational analysis of the 38 genes enabled us to find the cellular pathway associated with 6 of them with high confidence. These results indicate that some mKIAA genes are apparently relevant to retinoic acid-induced neurite outgrowth.

Animals↗

PubMed2005

Congenital neuromuscular disease with uniform type-1 fibers, presenting early stage dystrophic muscle pathology.

We report two male siblings presenting with severe hypotonia, generalized muscle atrophy, multiple joint contractures and respiratory failure. The serum creatine kinase levels were within normal limits, 75 IU/l in the younger boy and 123 IU/l in the older one. Muscle biopsies at the age of 28 days in the younger boy and 48 days in the older one revealed dystrophic pathology with increased interstitial fibrous tissue, scattered basophilic fibers and an increased number of undeveloped type-2C fibers. Although the elder brother died from respiratory failure at 4 months of age, the younger child has been sustained with mechanical ventilation, and has been exhibiting non-progressive muscle symptoms. Upon re-biopsy of the younger sibling at the age of 3 years, neither basophilic regenerating fibers nor degenerating fibers were found. All muscle fibers were found to be extremely atrophic and behaved mostly like type-1 fibers, displaying the features of congenital neuromuscular disease with uniform type-1 fibers. Since early biopsies in congenital myopathies reveal numerous undifferentiated immature muscle fibers, it is difficult to make a definite diagnosis, unless we recognize disease-specific cytoplastic abnormalities of nemaline body formation and abnormalities of core structure.

Child, Preschool↗

PubMed2005

Methamphetamine modulation of gene expression in the brain: analysis using customized cDNA microarray system with the mouse homologues of KIAA genes.

Amphetamine abuse may be associated with adaptive changes in gene expression. In the present study, we used a newly developed cDNA array system comprising mouse KIAA (mKIAA) cDNA clones to examine changes in gene expression after chronic methamphetamine (MAP) treatment. Mice were daily treated with saline or MAP (2 mg/kg, ip) for 2 weeks. Approximately 800 mKIAA clones were blotted onto a nylon membrane and hybridized with 33P-labeled DNA derived from mRNAs from mouse whole brain. MAP-induced changes were found in several clones by using whole brain mRNA. Since gene expression of Per2, one of the period protein-related proteins, was the most affected by MAP treatment, its expression was further analyzed in pooled hippocampi from 20 mice that had been treated with saline or MAP (2 mg/kg, ip) for 2 weeks. The gene expression and protein expression of Per2 in the hippocampus were increased by MAP treatment. In the hippocampus, Per2 gene expression was under the regulation of circadian rhythm and increases in Per2 expression were due to the phase shift induced by chronic MAP treatment. These findings suggest that unique expression changes of period protein-related proteins in the hippocampus occur in MAP abuse.

Amphetamine-Related Disorders↗

PubMed2005

Influence of the 3'-UTR-length of mKIAA cDNAs and their sequence features to the mRNA expression level in the brain.

We have previously described the sequence features of approximately 1500 mouse KIAA (mKIAA) genes in comparison with those of human KIAA genes (Okazaki, N., Kikuno, R., Inamoto, S., Hara, Y., Nagase, T., Ohara, O., and Koga, H. 2002, DNA Res., 9, 179-188; Okazaki, N., Kikuno, R., Ohara, R., Inamoto, S., Aizawa, H., Yuasa, S., Nakajima, D., Nagase, T., Ohara, O., and Koga, H. 2003, DNA Res., 10, 35-48; Okazaki, N., Kikuno, R., Ohara, R., Inamoto, S., Koseki, H., Hiraoka, S., Saga, Y., Nagase, T., Ohara, O., and Koga, H. 2003, DNA Res., 10, 167-180; and Okazaki, N., F-Kikuno, R., Ohara, R., Inamoto, S., Koseki, H., Hiraoka, S., Saga, Y., Seino, S., Nishimura, M., Kaisho, T., Hoshino, K., Kitamura, H., Nagase, T., Ohara, O., and Koga, H. 2004, DNA Res., 11, 205-218). To validate the orthologous relationship between mKIAA and KIAA genes in detail, we examined their chromosomal positions and evolutionary rate of synonymous substitutions and confirmed that >93% of the mKIAA/KIAA gene pairs are orthologous. During the sequence analysis of mKIAA genes, we found that 3'-untranslated region (3'-UTR) lengths of mKIAA and KIAA genes are extremely long. In the meanwhile, we have also examined the tissue-specific expression of approximately 1700 mKIAA genes using cDNA microarray and verified predominantly their expression in adult brain (Koga, H., Yuasa, S., Nagase, T., Shimada, K., Nagano, M., Imai, K., Ohara, R., Nakajima, D., Murakami, M., Kawai, M., Miki, F., Magae, J., Inamoto, S., Okazaki, N., Ohara, O. 2004, DNA Res., 11, 293-304). To connect these two evidences, we statistically analysed the relationship between them by using the mKIAA genes. Consequently, a positive correlation was observed between the 3'-UTR lengths and the relative expression intensities in adult brain. Furthermore, we searched sequence elements in the 3'-UTR possibly related with their expression and found some candidates regarding the brain-specific expression.

3' Untranslated Regions↗

PubMed2005

Microarray analysis of host gene-expression during intracellular nests formation of Trypanosoma cruzi amastigotes.

The intracellular pathogens utilize numerous cellular components of host cells to advance the infection as well as to enter the host cell. Analyzing the host cellular response enables us to get a better understanding of the pathogenesis, and subsequently indicate possible therapeutic targets. We therefore analyzed gene-expression profile of NIH3T3 fibroblast cells infected by Trypanosoma, a representative intracellular pathogen similar to Leishmania, using custom-designed cDNA microarray consisting of 1,701 mKIAA cDNAs. Focusing on intracellular nest formation of Trypanosoma cruzi amastigotes, we profiled the host gene-expression at 8 days post-infection and found several degrees of change in 16 mKIAA genes. Among these genes, 10 were up-regulated and 6 were down-regulated. Assuming that these genes had important roles in the infection's progression, we performed semi-quantitative RT-PCR analysis and con-firmed the gene expression change of 4 genes. Furthermore, 5 genes were mapped on cadherin signaling pathway using pathway analysis software. These results indicate significance of the host cellular pathway in the proliferative stage of Trypanosoma cruzi amastigotes.

Animals↗

PubMed2004

A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins II: public release of inaugural version of InGaP database containing gene/protein expression profiles for 127 mouse KIAA genes/proteins.

The inaugural version of the InGaP database (Integrative Gene and Protein expression database; http://www.kazusa.or.jp/ingap/index.html) is a comprehensive database of gene/protein expression profiles of 127 mKIAA genes/proteins related to hypothetical ones obtained in our ongoing cDNA project. Information about each gene/protein consists of cDNA microarray analysis, subcellular localization of the ectopically expressed gene, and experimental data using anti-mKIAA antibody such as Western blotting and immunohistochemical analyses. KIAA cDNAs and their mouse counterparts, mKIAA cDNAs, were mainly isolated from cDNA libraries derived from brain tissues, thus we expect our database to contribute to the field of neuroscience. In fact, cDNA microarray analysis revealed that nearly half of our gene collection is predominantly expressed in brain tissues. Immunohistochemical analysis of the mouse brain provides functional insight into the specific area and/or cell type of the brain. This database will be a resource for the neuroscience community by seamlessly integrating the genomic and proteomic information about the mouse KIAA genes/proteins.

Animals↗

PubMed2002

Limited dorsal myeloschisis associated with multiple vertebral segmentation disorder.

A 3-year-old girl was admitted to our department with spina bifida occulta. At birth, thoracic dysplasia with severe respiratory dysfunction and a soft pedunculated mass connecting with an intradural mass were noted. The patient did not start to walk and partial removal of the intradural mass was performed via a laminectomy of the fused vertebrae. There was no boundary between the spinal cord and the mass and the histological diagnosis of this mass was connective tissue. The anomalies in this case were considered to be multiple vertebral segmentation disorder (MVSD) and limited dorsal myeloschisis. The coincidence of these anomalies might suggest the causal genesis of MVSD.

Child, Preschool↗