Search PubMed⌕ Search

Biomedical subjects

Kikuya Kato

Publications and source records attributed to Kikuya Kato.

26 records · Page 2Linked to original sources
PubMed2003

Adapter-tagged competitive PCR (ATAC-PCR)--a high-throughput quantitative PCR method for microarray validation.

Adapter-tagged competitive PCR (ATAC-PCR) is an advanced version of competitive quantitative PCR that is characterized by the addition of unique adapters to cDNA derived from each sample RNA. Using multiple adapters, we can accurately measure the relative expression ratios of many samples, with a calibration curve obtained from internal standards included in the same reaction. ATAC-PCR can identify differences in gene expression as small as twofold, even from very small amounts of sample RNA. This technique is suitable for confirming results obtained with cDNA microarrays or differential display, and it can process more than a thousand of genes per day when used in conjunction with a capillary DNA sequencer.

Animals↗
PubMed2002

Differentially expressed genes in sporadic amyotrophic lateral sclerosis spinal cords--screening by molecular indexing and subsequent cDNA microarray analysis.

To analyze the genes related to the pathophysiology of sporadic amyotrophic lateral sclerosis (SALS) we performed gene profiling of SALS spinal cords using molecular indexing combined with cDNA microarray. Eighty-four fragments were cloned in the first screening procedure with molecular indexing. Subsequent quantitative microarray screening revealed 11 genes which were differentially expressed in SALS. Real-time RT-PCR verified that the expression level of the following six genes was altered in SALS: dorfin, metallothionein-3, 30 kDa TATA-binding protein-associated factor, neugrin, ubiquitin-like protein 5 and macrophage-inhibiting factor-related protein-8. These results indicated that genes associated with the ubiquitin-proteasome system, oxidative toxicity, transcription, neuronal differentiation and inflammation might be involved in the pathogenesis of SALS.

Adult↗
PubMed2002

Modulation of polyglutamine-induced cell death by genes identified by expression profiling.

The majority of triplet-repeat diseases are caused by mutated genes with an extended polyglutamine tract, exemplified by Huntington's disease (HD). In order to model HD pathogenesis in a controlled system, we developed stable PC12 cell lines that express exon 1 fragments of the huntingtin gene with 23 or 74 polyglutamines driven by an inducible doxycycline (dox)-sensitive promoter (HD-23Q or HD-74Q). We aimed to identify early perturbations induced by the mutation by studying expression levels of 1824 genes at 0, 5, 10 and 18 hours after induction, using adaptor-tagged competitive PCR (ATAC-PCR). At these time points, the cells show no appreciable death or mitochondrial impairment and very low inclusion levels. A total of 126 genes, including 69 known genes, exhibited statistically significant alterations in the HD-74Q cell lines but no changes in the HD-23Q lines. We tested 11 of these genes for their abilities to modulate polyglutamine-induced cell death in transiently transfected cell models. Five genes [glucose transporter 1 (Glut1), phosphofructokinase muscle isozyme (Pfkm), prostate glutathione-S -transferase 2 (Gstm2), RNA-binding motif protein 3 (Rbm3) and KRAB-A interacting protein 1 (Krip-1)] significantly suppressed cell death in both neuronal precursor and non-neuronal cell lines, suggesting that these transcriptional changes were relevant to polyglutamine pathology. The efficient recovery of functionally relevant genes supports the utility of gene expression profiling for discovering pathways related to pathogenesis, and the importance of analyzing molecular events in the early stages of disease.

Animals↗
PubMed2002

Comparison of gene expression profiling during postnatal development of mouse dentate gyrus and cerebellum.

Both the dentate gyrus of the hippocampus and the cerebellar cortex consist mainly of granule cells and develop postnatally. The granule cells in both tissues are presumed to be similar. Changes in gene expression were analyzed during the postnatal development of the dentate gyrus. Altogether, expression patterns of 1,937 genes were determined by adaptor-tagged competitive PCR. More than 90% of the genes belong to groups characterized by elevated expression either at earlier or later stages of development. A majority of the genes expressed showed marked changes during the developmental process, but there was little correlation between gene function and expression, unlike that observed during mouse postnatal cerebellar development. Despite anatomical and physiological similarities between these two processes, the gene expression profiles are completely different.

Animals↗
PubMed2002

Molecular classification of primary breast tumors possessing distinct prognostic properties.

The natural progression of breast cancer differs greatly between patients; the precise prediction of this disease course will improve the efficacy of therapeutics. Gene expression profiling may elucidate the undiscovered biological variations between seemingly similar cancers, leading to a new cancer classification system valuable in accurate diagnosis. The expression levels of 2412 genes, derived from 98 cancer samples, were precisely recorded by a high throughput RT-PCR technique, adapter-tagged competitive PCR. Subsequent cluster analysis revealed a molecular profile, correlating with estrogen receptor levels and the presence of lymph node metastases. We analyzed 301 cancer samples for the expression patterns of 21 genes critical in this categorization. The classification of the samples into three major groups was verified utilizing principal component analysis. This molecular classification system correlated significantly with early recurrence, independent of lymph node status. This malignant potential is associated with the expression levels of a group of genes, which comprise a set of candidates potentially useful in diagnostic prediction. These genes and the associated control mechanisms may also be effective therapeutic targets.

Breast Neoplasms↗
PubMed1990

A Collection of cDNA Clones with Specific Expression Patterns in Mouse Brain.

A total of 950 cDNA clones were randomly selected from mouse cerebellar cDNA libraries, and of these, about 130 clones were found to correspond to mRNAs which were expressed unequally between the cerebellum and other parts of mouse brain. Their distribution patterns in adult mouse brain were analysed by in situ hybridization, and eight clones were found restricted to specific regions of the brain, including four clones specific to cerebellar granule cells and one clone specific to Purkinje cells. Another 27 clones were preferentially expressed in a diverse, but distinctive subpopulation of brain cells. Among them seven clones were especially abundant in specific nuclei, and three in specific fibre bundles. These clones will be useful in defining new subpopulations of brain cells characterized by different gene expression.

Journal Article↗
PubMedDate not supplied

Adaptor-tagged competitive PCR: study of the mammalian nervous system.

Adaptor-tagged competitive PCR (ATAC-PCR) is an advanced form of quantitative competitive PCR, and enables high-throughput analysis of gene expression. We applied this technique to the postnatal cerebellar development. Data analysis with terms representing reported functions revealed a correlation between gene expression and functions. We also analyzed the cell death induced by extended polyglutamine, a model of a neurodegenerative disorder. We identified genes with expression patterns specific to the cell death, and evaluated their functions by in vitro transfection experiments.

Animals↗