Yuichiro Nishida

Housekeeping and tissue-specific genes in mouse tissues

BackgroundThis study aims to characterize the housekeeping and tissue-specific genes in 15 mouse tissues by using the serial analysis of gene expression (SAGE) strategy which indicates the relative level of expression for each transcript matched to the tag.ResultsHere, we identified constantly expressed housekeeping genes, such as eukaryotic translation elongation factor 2, which is expressed in all tissues without significant difference in expression levels. Moreover, most of these genes were not regulated by experimental conditions such as steroid hormones, adrenalectomy and gonadectomy. In addition, we report previously postulated housekeeping genes such as peptidyl-prolyl cis-trans isomerase A, glyceraldehyde-3-phosphate dehydrogenase and beta-actin, which are expressed in all the tissues, but with significant difference in their expression levels. We have also identified genes uniquely detected in each of the 15 tissues and other tissues from public databases.ConclusionThese identified housekeeping genes could represent appropriate controls for RT-PCR and northern blot when comparing the expression levels of genes in several tissues. The results reveal several tissue-specific genes highly expressed in testis and pituitary gland. Furthermore, the main function of tissue-specific genes expressed in liver, lung and bone is the cell defence, whereas several keratins involved in cell structure function are exclusively detected in skin and vagina. The results from this study can be used for example to target a tissue for agent delivering by using the promoter of tissue-specific genes. Moreover, this study could be used as basis for further researches on physiology and pathology of these tissues.

Expression of conjoined genes: another mechanism for gene regulation in eukaryotes.

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation.

Effect of Low-Intensity Aerobic Exercise on Insulin-Like Growth Factor-I and Insulin-Like Growth Factor-Binding Proteins in Healthy Men

Increased concentrations of circulating insulin-like growth factor-I (IGF-I) or IGF-I relative to IGF-binding proteins (IGFBPs) are associated with increased risk of developing several forms of cancer. Conversely, exercise is linked with reduced risk. This study aims to investigate the effect of a low-intensity exercise program on circulating levels of IGF-I, IGFBP-1, and IGFBP-3, in previously sedentary males. Fourteen healthy men participated in cycle ergometer training at lactate threshold intensity for 60 min/day, 5 days/week for 6 weeks. After aerobic training, insulin sensitivity improved by 20%, while fasting insulin levels decreased by 13%. Simultaneously, low-intensity aerobic training decreased the circulating levels of IGF-I by 9%, while IGFBP-1 levels increased by 16%. An interesting finding was that higher pretraining level of IGF-I was associated with greater decline in IGF-I with training. Insulin-sensitizing low-intensity aerobic exercise is thus considered to be an effective method for downregulating IGF-I and upregulating IGFBP-1 levels.

Regulation of skeletal muscle transcriptome in elderly men after 6 weeks of endurance training at lactate threshold intensity.

A compromised muscle function due to aging, sarcopenia and reduced level of physical activity can lead to metabolic complications and chronic diseases. Endurance exercise counters these diseases by inducing beneficial adaptations whose molecular mechanisms remain unclear. We have investigated the transcriptomic changes following mild-intensity endurance training in skeletal muscle of elderly men. Seven healthy subjects followed an exercise program of cycle ergometer training at lactate threshold (LT) level for 60 min/day, five times/week during six weeks. Physiological and transcriptomic changes were analyzed before and after training. LT training decreased percentage body fat and fasting levels of plasma glucose, while increasing high-density lipoprotein cholesterol and lecithin-cholesterol acyltransferase levels. Transcriptomic analysis revealed fast-to-slow fiber type transition, increased amount of mtDNA encoded transcripts and modulation of 12 transcripts notably related to extracellular matrix (ECM), oxidative phosphorylation (OXPHOS), as well as partially characterized and novel transcripts. The training simultaneously induced the expression of genes related to slow fiber type transition, OXPHOS and ECM, which might contribute to the improvement of glucose and lipid metabolisms and whole body aerobic capacity.

Identification and classification of genes regulated by phosphatidylinositol 3-kinase- and TRKB-mediated signalling pathways during neuronal differentiation in two subtypes of the human neuroblastoma cell line SH-SY5Y

BackgroundSH-SY5Y cells exhibit a neuronal phenotype when treated with all-trans retinoic acid (RA), but the molecular mechanism of activation in the signalling pathway mediated by phosphatidylinositol 3-kinase (PI3K) is unclear. To investigate this mechanism, we compared the gene expression profiles in SK-N-SH cells and two subtypes of SH-SY5Y cells (SH-SY5Y-A and SH-SY5Y-E), each of which show a different phenotype during RA-mediated differentiation.FindingsSH-SY5Y-A cells differentiated in the presence of RA, whereas RA-treated SH-SY5Y-E cells required additional treatment with brain-derived neurotrophic factor (BDNF) for full differentiation. After exposing cells to a PI3K inhibitor, LY294002, we identified 386 genes and categorised these genes into two clusters dependent on the PI3K signalling pathway during RA-mediated differentiation in SH-SY5Y-A cells. Transcriptional regulation of the gene cluster, including 158 neural genes, was greatly reduced in SK-N-SH cells and partially impaired in SH-SY5Y-E cells, which is consistent with a defect in the neuronal phenotype of these cells. Additional stimulation with BDNF induced a set of neural genes that were down-regulated in RA-treated SH-SY5Y-E cells but were abundant in differentiated SH-SY5Y-A cells.ConclusionWe identified gene clusters controlled by PI3K- and TRKB-mediated signalling pathways during the differentiation of two subtypes of SH-SY5Y cells. The TRKB-mediated bypass pathway compensates for impaired neural function generated by defects in several signalling pathways, including PI3K in SH-SY5Y-E cells. Our expression profiling data will be useful for further elucidation of the signal transduction-transcriptional network involving PI3K or TRKB.

Regulation of Muscle Genes by Moderate Exercise

Moderate-intensity exercise at the lactate threshold (LT) is considered to be a safe and effective training regimen for improving metabolic syndrome. The aim of the current study was to investigate the effects of moderate exercise performed at the LT on skeletal muscle gene expression. 6 healthy men participated in cycle ergometer training at LT, 60 min/d, 5 d/wk for 12 wks. Muscle samples were collected after 5 d of training, and then 2 d after training at wks 6 and 12. Quantitative real-time PCR analysis revealed that the expression of peroxisome proliferator activated receptor co-activated 1alpha was significantly increased at 1 h after the training session on day 5. Moreover, using serial analysis gene expression, we found that moderate training for 6 and 12 wks simultaneously induced the expression of a number of metabolic genes involved in the TCA cycle, beta-oxidation, and electron transport. Furthermore, several genes encoding antioxidant enzymes and contractile apparatus were induced. The expression levels of 233 novel transcripts were also altered in response to moderate exercise. Thus, moderate training at the LT is a sufficient stimulus to induce the expression of numerous genes implicated in the development of metabolic syndrome, transcripts involved in the contractile apparatus, and novel transcripts.

The Utilization of a Biopsy Needle to Obtain Small Muscle Tissue Specimens to Analyze the Gene and Protein Expression

Recent analytical methods such as real-time polymerase chain reaction (PCR) and Western blotting have now enabled us to analyze the gene and protein expression from small amounts of tissue. A fine needle muscle biopsy is thus expected to obtain a minimally sufficient amount of skeletal muscle to make a successful analysis. As a result, we used this fine needle muscle biopsy technique to obtain muscle tissue specimens from the vastus lateral muscle in 40 participants. The amount of tissue obtained by the fine needle was 5.2 +/- 3.2 mg (mean +/- standard deviation). The total RNA extracted was 3.0 +/- 1.4 microg and the total protein extracted was 2203 +/- 1541 microg. Furthermore, the skeletal muscle tissue specimens obtained by the regular needle technique and blood sample were used as the control. Those specimens were used to measure the gene expression of beta-myosin heavy chain slow (beta-MHC slow) by real-time PCR and the protein expression of monocalboxylate transporter 1 (MCT-1) by Western blotting. Beta-MHC slow gene expression was detected in both samples obtained by a fine and a regular needle biopsy, but not in a blood sample. Furthermore, the MCT-1 protein was detected in samples obtained by a fine needle muscle biopsy. These results indicated that the fine needle muscle biopsy is therefore a useful technique to obtain skeletal muscle specimens at least to analyze the gene and protein expression.

Effects of home-based exercise and branched-chain amino acid supplementation on aerobic capacity and glycemic control in patients with cirrhosis.

The aim of the current study is to examine whether home‐based step exercise at anaerobic threshold (AT) and branched‐chain amino acid (BCAA) supplementation improve aerobic capacity, ectopic fat in liver and muscle, and glycemic control in patients with liver cirrhosis.

Estimating rotavirus vaccine effectiveness in Japan using a screening method

abstract Rotavirus gastroenteritis is a highly contagious, acute viral disease that imposes a significant health burden worldwide. In Japan, rotavirus vaccines have been commercially available since 2011 for voluntary vaccination, but vaccine coverage and effectiveness have not been evaluated. In the absence of a vaccination registry in Japan, vaccination coverage in the general population was estimated according to the number of vaccines supplied by the manufacturer, the number of children who received financial support for vaccination, and the size of the target population. Patients with rotavirus gastroenteritis were identified by reviewing the medical records of all children who consulted 6 major hospitals in Saga Prefecture with gastroenteritis symptoms. Vaccination status among these patients was investigated by reviewing their medical records or interviewing their guardians by telephone. Vaccine effectiveness was determined using a screening method. Vaccination coverage increased with time, and it was 2-times higher in municipalities where the vaccination fee was supported. In the 2012/13 season, vaccination coverage in Saga Prefecture was 14.9% whereas the proportion of patients vaccinated was 5.1% among those with clinically diagnosed rotavirus gastroenteritis and 1.9% among those hospitalized for rotavirus gastroenteritis. Thus, vaccine effectiveness was estimated as 69.5% and 88.8%, respectively. This is the first study to evaluate rotavirus vaccination coverage and effectiveness in Japan since vaccination began.

Immunogenicity and Safety after Booster Vaccination of Diphtheria, Tetanus, and Acellular Pertussis in Young Adults: an Open Randomized Controlled Trial in Japan

ABSTRACT The recent increase of pertussis in young adults in Japan is hypothesized to be due in part to waning protection from the acellular pertussis vaccine. While a booster immunization may prevent an epidemic of pertussis among these young adults, little is known about the safety and immunogenicity of such a booster with the diphtheria, tetanus, and acellular pertussis vaccine (DTaP), which is currently available in Japan. One hundred and eleven medical students with a mean age of 19.4 years were randomly divided into 2 groups of 55 and 56 subjects and received, respectively, 0.2 or 0.5 ml of DTaP. Immunogenicity was assessed by performing the immunoassay using serum, and the geometric mean concentration (GMC), GMC ratio (GMCR), seropositive rate, and booster response rate were calculated. Adverse reactions and adverse events were monitored for 7 days after vaccination. After booster vaccination in the two groups, significant increases were found in the antibodies against pertussis toxin, filamentous hemagglutinin, diphtheria toxoid, and tetanus toxoid, and the booster response rates for all subjects reached 100%. The GMCs and GMCRs against all antigens were significantly higher in the 0.5-ml group than in the 0.2-ml group. No serious adverse events were observed. Frequencies of local reactions were similar in the 2 groups, although the frequency of severe local swelling was significantly higher in the 0.5-ml group. These data support the acceptability of booster immunization using both 0.2 and 0.5 ml of DTaP for young adults for controlling pertussis. (This study was registered at UMIN-CTR under registration number UMIN000010672.)