101
|
Yasuno K, Ando S, Misumi S, Makino S, Kulski JK, Muratake T, Kaneko N, Amagane H, Someya T, Inoko H, Suga H, Kanemoto K, Tamiya G. Synergistic association of mitochondrial uncoupling protein (UCP) genes with schizophrenia. Am J Med Genet B Neuropsychiatr Genet 2007; 144B:250-3. [PMID: 17066476 DOI: 10.1002/ajmg.b.30443] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Many studies suggest that mitochondrial dysfunction is involved in the pathophysiology of schizophrenia. We performed a case-control study using tag SNPs in the mitochondrial uncoupling protein genes, UCP2, UCP4, and BMCP1/UCP5, to investigate their association with schizophrenia. These neuronal UCPs are expressed in various brain tissues and may exert a neuroprotective effect against increased oxidative stress. We found modest associations between schizophrenia and the four tag SNPs, rs660339 (odds ratio (OR) = 1.330; P = 0.0043) and rs649446 (OR = 0.739; P = 0.0069) in UCP2, and rs10807344 (OR = 0.622; P = 0.0029) and rs2270450 (OR = 0.704; P = 0.0043) in UCP4, all of which were statistically significant even after correcting for multiple comparisons. Moreover, we found a statistically significant synergistic interaction between UCP2 and UCP4 by using the multifactor dimensionality reduction (MDR) method. The synergistic interaction was also confirmed by the logistic regression analysis, where the maximal OR was obtained when the risk alleles at rs660339 and rs10807344 were simultaneously homozygous. Individuals possessing homozygous risk alleles at these two loci have a 7.6-fold risk of developing schizophrenia compared with those of minimal OR. Our findings suggest that UCP2 and UCP4 have a modest but important involvement in the genetic etiology of schizophrenia. This is the first report of the association between schizophrenia and neuronal UCPs.
Collapse
Affiliation(s)
- Katsuhito Yasuno
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
102
|
Makino S, Kaji R, Ando S, Tomizawa M, Yasuno K, Goto S, Matsumoto S, Tabuena MD, Maranon E, Dantes M, Lee LV, Ogasawara K, Tooyama I, Akatsu H, Nishimura M, Tamiya G. Reduced neuron-specific expression of the TAF1 gene is associated with X-linked dystonia-parkinsonism. Am J Hum Genet 2007; 80:393-406. [PMID: 17273961 PMCID: PMC1821114 DOI: 10.1086/512129] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 12/13/2006] [Indexed: 11/03/2022] Open
Abstract
X-linked dystonia-parkinsonism (XDP) is a movement disorder endemic to the Philippines. The disease locus, DYT3, has been mapped to Xq13.1. In a search for the causative gene, we performed genomic sequencing analysis, followed by expression analysis of XDP brain tissues. We found a disease-specific SVA (short interspersed nuclear element, variable number of tandem repeats, and Alu composite) retrotransposon insertion in an intron of the TATA-binding protein-associated factor 1 gene (TAF1), which encodes the largest component of the TFIID complex, and significantly decreased expression levels of TAF1 and the dopamine receptor D2 gene (DRD2) in the caudate nucleus. We also identified an abnormal pattern of DNA methylation in the retrotransposon in the genome from the patient's caudate, which could account for decreased expression of TAF1. Our findings suggest that the reduced neuron-specific expression of the TAF1 gene is associated with XDP.
Collapse
Affiliation(s)
- Satoshi Makino
- Department of Neurology and Neuroscience, University of Tokushima Graduate School of Medicine, Tokushima, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
103
|
Kaji R, Tamiya G, Makino S, Shimazu H, Murase N, Sakamoto T, Tooyama I, Urushihara R. [Dystonia update]. Rinsho Shinkeigaku 2006; 46:962. [PMID: 17432233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
|
104
|
Kawashima M, Tamiya G, Oka A, Hohjoh H, Juji T, Ebisawa T, Honda Y, Inoko H, Tokunaga K. Genomewide association analysis of human narcolepsy and a new resistance gene. Am J Hum Genet 2006; 79:252-63. [PMID: 16826516 PMCID: PMC1559501 DOI: 10.1086/505539] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 04/27/2006] [Indexed: 11/03/2022] Open
Abstract
Human narcolepsy is a hypersomnia that is affected by multiple genetic and environmental factors. One genetic factor strongly associated with narcolepsy is the HLA-DRB1*1501-DQB1*0602 haplotype in the human leukocyte antigen region on chromosome 6, whereas the other genetic factors are not clear. To discover additional candidate regions for susceptibility or resistance to human narcolepsy, we performed a genomewide association study, using 23,244 microsatellite markers. Two rounds of screening with the use of pooled DNAs yielded 96 microsatellite markers (including 16 markers on chromosome 6) with significantly different estimated frequencies in case and control pools. Markers not located on chromosome 6 were evaluated by the individual typing of 95 cases and 95 controls; 30 markers still showed significant associations. A strong association was displayed by a marker on chromosome 21 (21q22.3). The surrounding region was subjected to high-density association mapping with 14 additional microsatellite markers and 74 SNPs. One microsatellite marker (D21S0012m) and two SNPs (rs13048981 and rs13046884) showed strong associations (P < .0005; odds ratios 0.19-0.33). These polymorphisms were in a strong linkage disequilibrium, and no other polymorphism in the region showed a stronger association with narcolepsy. The region contains three predicted genes--NLC1-A, NLC1-B, and NLC1-C--tentatively named "narcolepsy candidate-region 1 genes," and NLC1-A and NLC1-C were expressed in human hypothalamus. Reporter-gene assays showed that the marker D21S0012m in the promoter region and the SNP rs13046884 in the intron of NLC1-A significantly affected expression levels. Therefore, NLC1-A is considered to be a new resistance gene for human narcolepsy.
Collapse
Affiliation(s)
- Minae Kawashima
- Department of Sleep Disorder Research (Alfresa), Graduate School of Medicine, University of Tokyo, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
105
|
Tomita K, Tamiya G, Ando S, Kitamura N, Koizumi H, Kato S, Horie Y, Kaneko T, Azuma T, Nagata H, Ishii H, Hibi T. AICAR, an AMPK activator, has protective effects on alcohol-induced fatty liver in rats. Alcohol Clin Exp Res 2006; 29:240S-5S. [PMID: 16385230 DOI: 10.1097/01.alc.0000191126.11479.69] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Previous work with metformin has shown that this antidiabetic agent improves nonalcoholic fatty liver in ob/ob mice. AMP-activated protein kinase (AMPK) is one of the major cellular regulators of lipid and glucose metabolism, and reportedly mediates the beneficial metabolic effects of metformin. In this study, we examined the effects of 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranoside (AICAR), an AMPK activator, on an experimental model of ethanol-induced hepatic steatosis. METHODS Rats were randomly divided into three groups: (A) rats fed ethanol-containing liquid diet for six weeks; (B) rats pair-fed ethanol-containing liquid diet for six weeks, during the last three weeks of which they were subcutaneously injected with 0.5 mg AICAR/g body weight per day; (C) rats pair-fed isocaloric liquid diet without ethanol for six weeks. At the end of the six-week period, the animals were sacrificed. Serum and liver specimens were analyzed using biochemical and histologic methods, as well as real-time PCR. RESULTS Chronic ethanol feeding resulted in fatty liver both histologically and biochemically, whereas AICAR administration attenuated the degree of change in the liver. AICAR also decreased the hepatic sterol regulatory factor binding protein-1c (SREBP-1c) and reduced fatty acid synthase (FAS) expression; these changes led to reduced triglyceride synthesis in rat livers. Furthermore, detection of 4-hydroxy-2-nonenal (4-HNE)-protein adducts showed that the AICAR treatment also decreased the products of lipid peroxidation. CONCLUSION In this preclinical rat model, AICAR, an AMPK activator, appears to protect the liver from fatty changes associated with chronic alcohol use. As such, AICAR may have a role in the treatment and prevention of alcohol-induced fatty liver.
Collapse
Affiliation(s)
- Kengo Tomita
- Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
106
|
Tomita K, Tamiya G, Ando S, Ohsumi K, Chiyo T, Mizutani A, Kitamura N, Toda K, Kaneko T, Horie Y, Han JY, Kato S, Shimoda M, Oike Y, Tomizawa M, Makino S, Ohkura T, Saito H, Kumagai N, Nagata H, Ishii H, Hibi T. Tumour necrosis factor alpha signalling through activation of Kupffer cells plays an essential role in liver fibrosis of non-alcoholic steatohepatitis in mice. Gut 2006; 55:415-24. [PMID: 16174657 PMCID: PMC1856073 DOI: 10.1136/gut.2005.071118] [Citation(s) in RCA: 323] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND While tumour necrosis factor alpha (TNF-alpha) appears to be associated with the development of non-alcoholic steatohepatitis (NASH), its precise role in the pathogenesis of NASH is not well understood. METHODS Male mice deficient in both TNF receptors 1 (TNFR1) and 2 (TNFR2) (TNFRDKO mice) and wild-type mice were fed a methionine and choline deficient (MCD) diet or a control diet for eight weeks, maintaining isoenergetic intake. RESULTS MCD dietary feeding of TNFRDKO mice for eight weeks resulted in attenuated liver steatosis and fibrosis compared with control wild-type mice. In the liver, the number of activated hepatic Kupffer cells recruited was significantly decreased in TNFRDKO mice after MCD dietary feeding. In addition, hepatic induction of TNF-alpha, vascular cell adhesion molecule 1, and intracellular adhesion molecule 1 was significantly suppressed in TNFRDKO mice. While in control animals MCD dietary feeding dramatically increased mRNA expression of tissue inhibitor of metalloproteinase 1 (TIMP-1) in both whole liver and hepatic stellate cells, concomitant with enhanced activation of hepatic stellate cells, both factors were significantly lower in TNFRDKO mice. In primary cultures, TNF-alpha administration enhanced TIMP-1 mRNA expression in activated hepatic stellate cells and suppressed apoptotic induction in activated hepatic stellate cells. Inhibition of TNF induced TIMP-1 upregulation by TIMP-1 specific siRNA reversed the apoptotic suppression seen in hepatic stellate cells. CONCLUSIONS Enhancement of the TNF-alpha/TNFR mediated signalling pathway via activation of Kupffer cells in an autocrine or paracrine manner may be critically involved in the pathogenesis of liver fibrosis in this NASH animal model.
Collapse
MESH Headings
- Animals
- Apoptosis
- Cell Adhesion Molecules/biosynthesis
- Choline Deficiency/complications
- Fatty Liver/complications
- Fatty Liver/metabolism
- Fatty Liver/pathology
- Gene Expression Regulation
- Kupffer Cells/metabolism
- Liver Cirrhosis, Experimental/etiology
- Liver Cirrhosis, Experimental/metabolism
- Liver Cirrhosis, Experimental/pathology
- Male
- Methionine/deficiency
- Mice
- Mice, Knockout
- Mitochondria, Liver/physiology
- Mutation
- RNA, Messenger/genetics
- Receptors, Tumor Necrosis Factor, Type I/deficiency
- Receptors, Tumor Necrosis Factor, Type I/genetics
- Receptors, Tumor Necrosis Factor, Type I/physiology
- Receptors, Tumor Necrosis Factor, Type II/deficiency
- Receptors, Tumor Necrosis Factor, Type II/genetics
- Receptors, Tumor Necrosis Factor, Type II/physiology
- Reverse Transcriptase Polymerase Chain Reaction/methods
- Signal Transduction
- Tissue Inhibitor of Metalloproteinase-1/biosynthesis
- Tissue Inhibitor of Metalloproteinase-1/genetics
- Tumor Necrosis Factor-alpha/biosynthesis
- Tumor Necrosis Factor-alpha/physiology
Collapse
Affiliation(s)
- K Tomita
- Department of Internal Medicine, School of Medicine, Keio University, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
107
|
Okano H, Bamba H, Hisa Y, Makino S, Ando S, Tamiya G, Goto S, Kaji R, Kimura H, Tooyama I. Immunohistochemical study of TAFII250 in the rat laryngeal nervous system. Histol Histopathol 2006; 20:1029-35. [PMID: 16136484 DOI: 10.14670/hh-20.1029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cause of spasmodic dysphonia, a dystonic disorder of the larynx, remains unclear. Recently, TAFII250, TATA-box binding protein associated factor, was suggested to be involved in dystonia parkinsonism. There is a possibility that TAFII250 is involved in spasmodic dysphonia, but little information is available about the expression of TAFII250 in the laryngeal nervous system. In this study, we investigated the localization of TAFII250 protein in the rat laryngeal nervous system by immunohistochemistry. TAFII250-immunoreactivity was detected in the nodose ganglion and superior cervical ganglion. In these nuclei, TAFII250 was localized in the nucleus of NeuroTrace-positive neurons but not in GFAP-positive glial cells. No positive cells were detected in the motor and parasympathetic nervous system. TAFII250-immunoreactivity was sustained between 3 and 7 days after vagotomy, but at 14 days expression was down-regulated in the distal part of the nodose ganglion. These findings suggest that TAFII250 plays an important role in the laryngeal innervation of the sensory and sympathetic nervous systems.
Collapse
Affiliation(s)
- H Okano
- Molecular Neuroscience Research Center, Shiga University of Medical Science, Setatukinowa-cho, Otsu, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
108
|
Kulski JK, Kenworthy W, Bellgard M, Taplin R, Okamoto K, Oka A, Mabuchi T, Ozawa A, Tamiya G, Inoko H. Gene expression profiling of Japanese psoriatic skin reveals an increased activity in molecular stress and immune response signals. J Mol Med (Berl) 2005; 83:964-75. [PMID: 16283139 DOI: 10.1007/s00109-005-0721-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Accepted: 08/08/2005] [Indexed: 01/06/2023]
Abstract
Gene expression profiling was performed on biopsies of affected and unaffected psoriatic skin and normal skin from seven Japanese patients to obtain insights into the pathways that control this disease. HUG95A Affymetrix DNA chips that contained oligonucleotide arrays of approximately 12,000 well-characterized human genes were used in the study. The statistical analysis of the Affymetrix data, based on the ranking of the Student t-test statistic, revealed a complex regulation of molecular stress and immune gene responses. The majority of the 266 induced genes in affected and unaffected psoriatic skin were involved with interferon mediation, immunity, cell adhesion, cytoskeleton restructuring, protein trafficking and degradation, RNA regulation and degradation, signalling transduction, apoptosis and atypical epidermal cellular proliferation and differentiation. The disturbances in the normal protein degradation equilibrium of skin were reflected by the significant increase in the gene expression of various protease inhibitors and proteinases, including the induced components of the ATP/ubiquitin-dependent non-lysosomal proteolytic pathway that is involved with peptide processing and presentation to T cells. Some of the up-regulated genes, such as TGM1, IVL, FABP5, CSTA and SPRR, are well-known psoriatic markers involved in atypical epidermal cellular organization and differentiation. In the comparison between the affected and unaffected psoriatic skin, the transcription factor JUNB was found at the top of the statistical rankings for the up-regulated genes in affected skin, suggesting that it has an important but as yet undefined role in psoriasis. Our gene expression data and analysis suggest that psoriasis is a chronic interferon- and T-cell-mediated immune disease of the skin where the imbalance in epidermal cellular structure, growth and differentiation arises from the molecular antiviral stress signals initiating inappropriate immune responses.
Collapse
Affiliation(s)
- Jerzy K Kulski
- Centre for Bioinformatics and Biological Computing, Murdoch University, South Street, Murdoch, Western Australia, 6150, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
109
|
Kaji R, Goto S, Tamiya G, Lee LV. [Molecular and anatomical bases of dystonia: X-linked recessive dystonia-parkinsonism (DYT3)]. Rinsho Shinkeigaku 2005; 45:811-4. [PMID: 16447732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Pathological findings in dystonia have been unclear. X-linked recessive dystonia-parkinsonism (XDP, DYT3), endemic in the Panay island, the Philippines, is characterized by the clinical onset with dystonia followed by parkinsonism. It provides a unique opportunity to explore the anatomical basis of dystonia, because it has discernible pathological changes even at its early phase of dystonia. After extensive searches for the anatomical basis in XDP, we found selective loss of striosomal neurons in the striatum in dystonic patients' brain. Because striosomal neurons inhibit nigrostriatal dopaminergic neurons via GABAergic innervation, the striosomal lesion could account for dopamine excess in the striatum, which in turn causes a hyperkinetic state or dystonia. We also identified the causative gene as one of the general transcription factor genes, TAF1. This abnormality markedly reduced the expression of dopamine D2 receptor gene (DRD2) in neurons. XDP has certain similarities to Huntington disease not only in pathological and clinical findings, but also the molecular mechanism, which disturbs expression of genes essential for striatal neurons, such as DRD2. Therapeutic intervention may become possible through pharmacological measures that affect gene expression.
Collapse
Affiliation(s)
- Ryuji Kaji
- Department of Clinical Neuroscience, Tokushima University
| | | | | | | |
Collapse
|
110
|
Tamiya G. [Genetic dissection of dystonia]. No To Shinkei 2005; 57:935-44. [PMID: 16363633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Affiliation(s)
- Gen Tamiya
- Human Neurogenetics, Department of Neurology, Tokushima University Graduate School of Medicine, 2-50-1 Kuramoto-cho, Tokushima 770-8503, Japan
| |
Collapse
|
111
|
Kimura T, Yoshida K, Shimada A, Jindo T, Sakaizumi M, Mitani H, Naruse K, Takeda H, Inoko H, Tamiya G, Shinya M. Genetic linkage map of medaka with polymerase chain reaction length polymorphisms. Gene 2005; 363:24-31. [PMID: 16226856 DOI: 10.1016/j.gene.2005.07.043] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Revised: 06/15/2005] [Accepted: 07/22/2005] [Indexed: 11/28/2022]
Abstract
With recent improvements in genetic and genomic infrastructures, great interest has been taken in genetic dissection of multi-factorial traits. A genetic map consisting of markers that are highly polymorphic and rapidly genotyped is essential for the genetic mapping of such a complex trait. Medaka, Oryzias latipes, is an excellent model system for genetic studies. To promote genetic mapping of complex traits in medaka we developed the first high-throughput and genome-wide marker set in the organism by using its genomic information and the bioinformatic techniques. We tested 545 primer pairs and obtained 265 co-dominant markers between two inbred strains, HNI and Hd-rR. Our map, consisting of 231 uniquely mapped markers, covers 1257.3 centimorgan (cM) of the medaka genome with an average interval distance of 5.4 cM. Furthermore, the newly designed markers were examined for polymorphisms among six medaka inbred strains: HNI, Hd-rR and four additional strains. Most of our markers are simple sequence length polymorphisms (SSLPs) and can be rapidly genotyped by an automated system under a single polymerase chain reaction (PCR) condition. Together with the genotyping data of six medaka inbred strains, our new marker set provides a powerful tool for genome-wide analysis of complex biological phenomena found widely in medaka populations.
Collapse
Affiliation(s)
- Tetsuaki Kimura
- Department of Molecular Life Science, Course of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
112
|
Goto S, Lee LV, Munoz EL, Tooyama I, Tamiya G, Makino S, Ando S, Dantes MB, Yamada K, Matsumoto S, Shimazu H, Kuratsu JI, Hirano A, Kaji R. Functional anatomy of the basal ganglia in X-linked recessive dystonia-parkinsonism. Ann Neurol 2005; 58:7-17. [PMID: 15912496 DOI: 10.1002/ana.20513] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Dystonia is a neurological syndrome characterized by sustained muscle contractions that produce repetitive twisting movements or abnormal postures. X-linked recessive dystonia parkinsonism (XDP; DYT3; Lubag) is an adult-onset disorder that manifests severe and progressive dystonia with a high frequency of generalization. In search for the anatomical basis for dystonia, we performed postmortem analyses of the functional anatomy of the basal ganglia based on the striatal compartments (ie, the striosomes and the matrix compartment) in XDP. Here, we provide anatomopathological evidence that, in the XDP neostriatum, the matrix compartment is relatively spared in a unique fashion, whereas the striosomes are severely depleted. We also document that there is a differential loss of striatal neuron subclasses in XDP. In view of the three-pathway basal ganglia model, we postulate that the disproportionate involvement of neostriatal compartments and their efferent projections may underlie the manifestation of dystonia in patients with XDP. This study is the first to our knowledge to show specific basal ganglia pathology that could explain the genesis of dystonia in human heredodegenerative movement disorders, suggesting that dystonia may result from an imbalance in the activity between the striosomal and matrix-based pathways.
Collapse
Affiliation(s)
- Satoshi Goto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
113
|
Katoh T, Mano S, Munkhbat B, Tounai K, Oyungerel G, Chae GT, Han H, Jia GJ, Tokunaga K, Munkhtuvshin N, Tamiya G, Inoko H. Genetic features of Khoton Mongolians revealed by SNP analysis of the X chromosome. Gene 2005; 357:95-102. [PMID: 16125340 DOI: 10.1016/j.gene.2005.06.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Revised: 05/30/2005] [Accepted: 06/16/2005] [Indexed: 11/23/2022]
Abstract
The Khoton Mongolian population is a small and relatively isolated ethnic group residing predominantly in the northwestern part of Mongolia. A recent genetic study of the Y chromosome revealed that the major Mongolian ethnic groups have a relatively close genetic affinity to populations in the northern part of East Asia, while the Khoton population reflected an apparent genetic differentiation from the other Mongolian populations. To further investigate the genetic features of the Khoton and the other Mongolian populations, we analyzed the single nucleotide polymorphisms (SNPs) in the Xq13.3 region, which is thought to have an extremely low level of recombination in the human X chromosome. We found that the frequency distribution of Xq13.3 haplotypes in the Khoton population was substantially different from those in three other Mongolian populations (Khalkh, Uriankhai, and Zakhchin). The same relationship was also revealed by the results from the population tree and principal-component (PC) analysis based on the allele frequencies. These results are largely consistent with the hypothesis that the Khoton population descended from a nomadic tribe of Turkish origin, which has been supported by previous anthropological, historical, and Y-chromosome studies. However, the population structure analysis produced an additional finding, namely, that the Khoton population is likely to be an admixed population.
Collapse
Affiliation(s)
- Toru Katoh
- Molecular Life Science, School of Medicine, Tokai University, Bohseidai, Isehara, Kanagawa, 259-1193, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
114
|
Tamiya G, Shinya M, Imanishi T, Ikuta T, Makino S, Okamoto K, Furugaki K, Matsumoto T, Mano S, Ando S, Nozaki Y, Yukawa W, Nakashige R, Yamaguchi D, Ishibashi H, Yonekura M, Nakami Y, Takayama S, Endo T, Saruwatari T, Yagura M, Yoshikawa Y, Fujimoto K, Oka A, Chiku S, Linsen SEV, Giphart MJ, Kulski JK, Fukazawa T, Hashimoto H, Kimura M, Hoshina Y, Suzuki Y, Hotta T, Mochida J, Minezaki T, Komai K, Shiozawa S, Taniguchi A, Yamanaka H, Kamatani N, Gojobori T, Bahram S, Inoko H. Whole genome association study of rheumatoid arthritis using 27 039 microsatellites. Hum Mol Genet 2005; 14:2305-21. [PMID: 16000323 DOI: 10.1093/hmg/ddi234] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A major goal of current human genome-wide studies is to identify the genetic basis of complex disorders. However, the availability of an unbiased, reliable, cost efficient and comprehensive methodology to analyze the entire genome for complex disease association is still largely lacking or problematic. Therefore, we have developed a practical and efficient strategy for whole genome association studies of complex diseases by charting the human genome at 100 kb intervals using a collection of 27,039 microsatellites and the DNA pooling method in three successive genomic screens of independent case-control populations. The final step in our methodology consists of fine mapping of the candidate susceptible DNA regions by single nucleotide polymorphisms (SNPs) analysis. This approach was validated upon application to rheumatoid arthritis, a destructive joint disease affecting up to 1% of the population. A total of 47 candidate regions were identified. The top seven loci, withstanding the most stringent statistical tests, were dissected down to individual genes and/or SNPs on four chromosomes, including the previously known 6p21.3-encoded Major Histocompatibility Complex gene, HLA-DRB1. Hence, microsatellite-based genome-wide association analysis complemented by end stage SNP typing provides a new tool for genetic dissection of multifactorial pathologies including common diseases.
Collapse
Affiliation(s)
- Gen Tamiya
- Department of Molecular Life Science, Course of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Bohseidai, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
115
|
Matsuzaka Y, Okamoto K, Mabuchi T, Iizuka M, Ozawa A, Oka A, Tamiya G, Kulski JK, Inoko H. Identification and characterization of novel variants of the thioredoxin reductase 3 new transcript 1 TXNRD3NT1. Mamm Genome 2005; 16:41-9. [PMID: 15674732 DOI: 10.1007/s00335-004-2416-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2004] [Accepted: 08/24/2004] [Indexed: 11/29/2022]
Abstract
We have identified and characterized a new gene sequence, TXNRD3NT1, whose transcripts, corresponding to the EST AA430236, were found by Affymetrix DNA chip analysis to be significantly down regulated in affected psoriatic tissue. The full-length cDNA of TXNRD3NT1 was isolated and characterized by combining 5'- and 3'-RACE (rapid amplication of cDNA ends) with screening a keratinocyte cDNA library, designing appropriate PCR primers, cloning amplified products, sequencing, and sequence analysis. Because part of this gene overlaps the previously described thioredoxin reductase 3 (TXNRD3) gene, we have named it TXNRD3NT1 (TXNRD3 new transcript 1). The full-length TXNRD3NT1 cDNA has 1133 nucleotides with a 251-bp 3-UTRand 2 poly(A)signal variants and 2 poly (A) sites. The TXNRD3NT1 cDNA ORF encodes for 133 amino acids, with the first four residues coding for a tubulin-beta mRNA autoregulation signal. Mapping the cDNA nucleotide sequence to the human genome sequence revealed that the TXNRD3NT1 gene has 4 exons located on Chromosome 3, at position 3q21. Exons 1 and 2 of the TXNRD3NT1 gene overlap with exons 15 and 16 of the thioredoxin reductase 2 gene which has different ORFs to that of TXNRD3NT1. The translation initiation codon ATG was found in exon 3 of the TXNRD3NT1 gene. RT-PCR showed that the full-length variant of the TXNRD3NT1 gene was expressed in only four issues (pancreas, esophagus, bone marrow, and keratinocytes) of the 30 different tissues tested. In most other tissues, an aberrant and truncated form of the transcript (i.e., missing exon 3 and part of exon 4) was detected. The result of a preliminary association study between psoriasis and single microsatellite marker of the TXNRD3NT1 gene suggests that it may not be a significant genetic determinant of psoriasis. However, we cannot exclude the possibility that other sequence variants may still exist within the TXNRD3NT1 gene. Sequence analysis of the TXNRD3NT1 gene from 8 psoriasis patients and 8 healthy controls revealed a number of synonymous SNPs that may be useful markers for future disease association studies.
Collapse
Affiliation(s)
- Yasunari Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
116
|
Katoh T, Munkhbat B, Tounai K, Mano S, Ando H, Oyungerel G, Chae GT, Han H, Jia GJ, Tokunaga K, Munkhtuvshin N, Tamiya G, Inoko H. Genetic features of Mongolian ethnic groups revealed by Y-chromosomal analysis. Gene 2005; 346:63-70. [PMID: 15716011 DOI: 10.1016/j.gene.2004.10.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2004] [Revised: 10/12/2004] [Accepted: 10/21/2004] [Indexed: 11/27/2022]
Abstract
About 20 ethnic groups reside in Mongolia. On the basis of genetic and anthropological studies, it is believed that Mongolians have played a pivotal role in the peopling of Central and East Asia. However, the genetic relationships among these ethnic groups have remained obscure, as have their detailed relationships with adjacent populations. We analyzed 16 binary and 17 STR polymorphisms of human Y chromosome in 669 individuals from nine populations, including four indigenous ethnic groups in Mongolia (Khalkh, Uriankhai, Zakhchin, and Khoton). Among these four Mongolian populations, the Khalkh, Uriankhai, and Zakhchin populations showed relatively close genetic affinities to each other and to Siberian populations, while the Khoton population showed a closer relationship to Central Asian populations than to even the other Mongolian populations. These findings suggest that the major Mongolian ethnic groups have a close genetic affinity to populations in northern East Asia, although the genetic link between Mongolia and Central Asia is not negligible.
Collapse
Affiliation(s)
- Toru Katoh
- Molecular Life Science, School of Medicine, Tokai University, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
117
|
Matsuzaka Y, Okamoto K, Mabuchi T, Iizuka M, Ozawa A, Oka A, Tamiya G, Kulski JK, Inoko H. Identification, expression analysis and polymorphism of a novel RLTPR gene encoding a RGD motif, tropomodulin domain and proline/leucine-rich regions. Gene 2005; 343:291-304. [PMID: 15588584 DOI: 10.1016/j.gene.2004.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Revised: 09/01/2004] [Accepted: 09/10/2004] [Indexed: 11/20/2022]
Abstract
We describe the isolation and characterization of a full-length cDNA encoded by a gene that was significantly down-regulated in the affected skin of patients with psoriasis vulgaris. The cDNA was isolated from a keratinocyte cDNA library and its sequence was found to correspond to a hypothetical locus recorded in GenBank with the accession number . The nucleotide sequence of the full-length cDNA was found to have an open reading frame of 1365 amino acids and to span approximately 12 kb of genomic DNA with 39 exons on chromosome 16q22. The deduced amino acid sequence contains four distinct structural regions, an RGD motif, a leucine-rich repeat (LRR) region, a tropomodulin domain, and a proline-rich domain. The gene was consequently designated as RLTPR (RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein). The RLTPR hypothetical protein has a functional domain organization similar to Acan125, a myosin-binding protein expressed by Acanthamoeba castellanni. RT-PCR with RLTPR PCR primers amplified products from cDNAs prepared from all of the 30 different tissues that we examined including thymus, spleen, colon, skin, skin keratinocytes, skin fibroblasts and fetal skin. During the course of screening the human keratinocyte cDNA library, some alternative splicing was also detected in three regions of the RLTPR gene. In addition, sequence analysis of the RLTPR genes from eight psoriasis patients and eight healthy controls revealed a number of synonymous and nonsynonymous SNPs that may be useful markers for future disease association studies.
Collapse
Affiliation(s)
- Yasunari Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
118
|
Matsuzaka Y, Okamoto K, Yoshikawa Y, Takaki A, Oka A, Mabuchi T, Iizuka M, Ozawa A, Tamiya G, Kulski JK, Inoko H. hRDH-E2 gene polymorphisms, variable transcriptional start sites, and psoriasis. Mamm Genome 2005; 15:668-75. [PMID: 15457346 DOI: 10.1007/s00335-004-2349-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2003] [Accepted: 03/25/2004] [Indexed: 10/26/2022]
Abstract
hRDH-E2 is a member of the short-chain alcohol dehydrogenase/reductase (SDR) family that converts retinol to retinaldehyde as the first and rate-limiting step in the retinoic acid synthetic pathway. This pathway is critical for the maintenance of epidermal homeostasis in vivo. Previously, we reported that the mRNA levels of hRDH-E2 in psoriatic skin were elevated significantly compared with that in healthy individual skin and psoriatic unaffected skin. The gene encoding hRDH-E2 is located on Chromosome 8 close to a candidate region for psoriasis and therefore is a functional and positional candidate for this disorder. In the present study, the transcription start sites for hRDH-E2 gene transcription in the lung were found to be more upstream of those that were identified previously in keratinocytes. Consequently, differences in the nucleotide sequence were determined for all of the coding exons, untranslated regions, and at least 2850 bp of 5'-noncoding sequence of hRDH-E2 by direct sequencing of polymerase chain reaction (PCR)-amplified DNA samples obtained from 8 psoriatic patients and 8 healthy controls. One polymorphic microsatellite marker at the noncoding 3' end of the gene and six single nucleotide polymorphisms (SNPs) (three in the 5' flanking sequence, two in the coding sequence, and one in the intronic sequence) were identified. One of the SNPs was nonsynonymous in the second exon with an allelic variation between the amino acid sequences Arg and Trp. The microsatellite marker and the six SNPs were all genotyped in 100 Japanese psoriatic patients and 120 controls. However, there were no statistically significant differences in the genotype or allele frequency distributions between the cases and controls. On this basis, we conclude that the polymorphisms that we detected for the hRDH-E2 gene do not contribute to the etiology of psoriasis but may be important in diseases of other tissues.
Collapse
Affiliation(s)
- Yasunari Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
119
|
Kaji R, Goto S, Tamiya G, Ando S, Makino S, Lee LV. Molecular dissection and anatomical basis of dystonia: X-linked recessive dystonia-parkinsonism (DYT3). J Med Invest 2005; 52 Suppl:280-3. [PMID: 16366515 DOI: 10.2152/jmi.52.280] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Pathological findings in dystonia have been unclear. X-linked recessive dystonia-parkinsonism (XDP, DYT3), endemic in the Panay island, the Philippines, is characterized by the clinical onset with dystonia followed by parkinsonism. It provides a unique opportunity to explore the anatomical basis of dystonia, because it has discernible pathological changes even at its early phase of dystonia. After extensive searches for the anatomical basis in XDP, we found selective loss of striosomal neurons in the striatum in dystonic patients' brain. Because striosomal neurons inhibit nigrostriatal dopaminergic neurons via GABAergic innervation, the striosomal lesion could account for dopamine excess in the striatum, which in turn causes a hyperkinetic state or dystonia. We also identified the causative gene as one of the general transcription factor genes, TAF1. XDP has certain similarities to Huntington disease not only in pathological and clinical findings, but also the molecular mechanism, which disturbs expression of genes essential for striatal neurons, such as DRD2. Therapeutic intervention may become possible through pharmacological measures that affect gene expression.
Collapse
Affiliation(s)
- Ryuji Kaji
- Department of Clinical Neuroscience, Institute of Health Biosciences, The University of Tokushima,Graduate School, Japan
| | | | | | | | | | | |
Collapse
|
120
|
Matsumoto T, Yukawa W, Nozaki Y, Nakashige R, Shinya M, Makino S, Yagura M, Ikuta T, Imanishi T, Inoko H, Tamiya G, Gojobori T. Novel algorithm for automated genotyping of microsatellites. Nucleic Acids Res 2004; 32:6069-77. [PMID: 15557284 PMCID: PMC534627 DOI: 10.1093/nar/gkh946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits. Microsatellite genotyping requires detection of the products of polymerase chain reaction (PCR) amplification by electrophoresis, and analysis of the peak data for discrimination of the true allele. A high-throughput genotyping approach requires computer-based automation at both the detection and analysis phases. In order to achieve this, complicated peak patterns from individual alleles must be interpreted in order to assign alleles. Previous methods consider limited types of noise peaks and cannot provide enough accuracy. By pattern recognition of various types of noise peaks, such as stutter peaks and additional peaks, we have achieved an overall average accuracy of 94% for allele calling in our actual data. Our algorithm is crucial for a high-throughput genotyping system for microsatellite markers by reducing manual editing and human errors.
Collapse
Affiliation(s)
- Toshiko Matsumoto
- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Tokyo, Japan.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
121
|
Tomita K, Azuma T, Kitamura N, Tamiya G, Ando S, Nagata H, Kato S, Inokuchi S, Nishimura T, Ishii H, Hibi T. Leptin deficiency enhances sensitivity of rats to alcoholic steatohepatitis through suppression of metallothionein. Am J Physiol Gastrointest Liver Physiol 2004; 287:G1078-85. [PMID: 15475485 DOI: 10.1152/ajpgi.00107.2004] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oxidative stress is stated to be a central mechanism of hepatocellular injury in alcohol-induced liver injury. Recent reports have shown that Kupffer cell dysfunction in the leptin-deficient state contributes partly to the increased sensitivity to endotoxin liver injury. Here we report that leptin also plays a key role in the development of alcoholic liver injury and that leptin signaling in hepatocytes is involved in cellular mechanisms that mediate ethanol-induced oxidative stress. We found that chronic ethanol feeding in leptin receptor-deficient Zucker (fa/fa) rats for 6 wk resulted in a much more severe liver injury and augmented accumulation of hepatic lipid peroxidation compared with control littermates. The hepatic induction of stress-response and antioxidant proteins, such as metallothionein (MT)-1 and -2, was significantly suppressed in fa/fa rats after chronic ethanol feeding. Zinc concentration in liver was also decreased in fa/fa rats, compared with control littermates. In primary cultured hepatocytes from fa/fa rats, incubation with ethanol significantly suppressed MT-1 and -2 expressions. Addition of leptin to leptin-deficient ob/ob mouse primary hepatocytes led to an increase in MT-1 and -2 mRNA levels and a decrease in oxidative stress after incubation with ethanol. In conclusion, leptin deficiency enhances sensitivity of rats to alcohol-induced steatohepatitis through hepatocyte-specific interaction of MT-1 and -2 and resultant exaggeration of oxidative stress in hepatocytes. These findings suggest that leptin resistance in hepatocytes is an important mechanism of alcohol-induced liver injury.
Collapse
Affiliation(s)
- Kengo Tomita
- Department of Internal Medicine, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
122
|
Abstract
The maximum likelihood estimation (MLE) is one of the most popular ways to estimate haplotype frequencies of a population with genotype data whose linkage phases are unknown. The MLE is commonly implemented in the use of the Expectation-Maximization (EM) algorithm. It is known that the EM algorithm carries the risk that an estimator may converge erroneously to one of the local maxima or saddle points of the likelihood surface, resulting in serious errors in the MLE of haplotype frequencies. In this note, by theoretical treatments we present the necessary and sufficient conditions that the local maxima or saddle points on the likelihood surface appear. As a rule of thumb, that the difference between the coupling and repulsive haplotype frequencies in phase known individuals is 3/2 times larger than the frequency of phase ambiguous individuals is the sufficient condition that the likelihood surface is unimodal. Moreover, we present the analytic solution to the biallelic two-locus problem, and construct a general algorithm to obtain the global maximum.
Collapse
Affiliation(s)
- S Mano
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
123
|
Nakajima T, Wooding S, Sakagami T, Emi M, Tokunaga K, Tamiya G, Ishigami T, Umemura S, Munkhbat B, Jin F, Guan-Jun J, Hayasaka I, Ishida T, Saitou N, Pavelka K, Lalouel JM, Jorde LB, Inoue I. Natural selection and population history in the human angiotensinogen gene (AGT): 736 complete AGT sequences in chromosomes from around the world. Am J Hum Genet 2004; 74:898-916. [PMID: 15077204 PMCID: PMC1181984 DOI: 10.1086/420793] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2003] [Accepted: 02/25/2004] [Indexed: 11/03/2022] Open
Abstract
Several lines of evidence suggest that patterns of genetic variability in the human angiotensinogen gene (AGT) contribute to phenotypic variability in human hypertension. The A(-6) promoter variant of AGT is associated with higher plasma angiotensinogen levels and increased risk of essential hypertension. The geographic distribution of the A(-6) variant leads to the intriguing hypothesis that the G(-6) promoter variant has been selectively advantageous outside Africa. To test these hypotheses, we investigated the roles of population history and natural selection in shaping patterns of genetic diversity in AGT, by sequencing the entire AGT gene (14400 bp) in 736 chromosomes from Africa, Asia, and Europe. We found that the A(-6) variant is present at higher frequency in African populations than in non-African populations. Neutrality tests found no evidence of a departure from selective neutrality, when whole AGT sequences were compared. However, tests restricted to sites in the vicinity of the A(-6)G polymorphism found evidence of a selective sweep. Sliding-window analyses showed that evidence of the sweep is restricted to sites in tight linkage disequilibrium (LD) with the A(-6)G polymorphism. Further, haplotypes carrying the G(-6) variant showed elevated levels of LD, suggesting that they have risen recently to high frequency. Departures from neutral expectation in some but not all regions of AGT indicate that patterns of diversity in the gene cannot be accounted for solely by population history, which would affect all regions equally. Taken together, patterns of genetic diversity in AGT suggest that natural selection has generally favored the G(-6) variant over the A(-6) variant in non-African populations. However, important localized effects may also be present.
Collapse
Affiliation(s)
- Toshiaki Nakajima
- Division of Genetic Diagnosis, The University of Tokyo, Tokyo 108-8639, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
124
|
Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda JI, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo MDF, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, R. Gopinath G, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S. Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol 2004; 2:e162. [PMID: 15103394 PMCID: PMC393292 DOI: 10.1371/journal.pbio.0020162] [Citation(s) in RCA: 267] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Accepted: 04/01/2004] [Indexed: 01/08/2023] Open
Abstract
The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
Collapse
Affiliation(s)
- Tadashi Imanishi
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Takeshi Itoh
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 2Bioinformatics Laboratory, Genome Research Department, National Institute of Agrobiological SciencesIbarakiJapan
| | - Yutaka Suzuki
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 68Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of TokyoTokyoJapan
| | - Claire O'Donovan
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Satoshi Fukuchi
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | | | - Roberto A Barrero
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Takuro Tamura
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 8BITS CompanyShizuokaJapan
| | - Yumi Yamaguchi-Kabata
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Motohiko Tanino
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Kei Yura
- 9Quantum Bioinformatics Group, Center for Promotion of Computational Science and Engineering, Japan Atomic Energy Research InstituteKyotoJapan
| | - Satoru Miyazaki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Kazuho Ikeo
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Keiichi Homma
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Arek Kasprzyk
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Tetsuo Nishikawa
- 10Reverse Proteomics Research InstituteChibaJapan
- 11Central Research Laboratory, HitachiTokyoJapan
| | - Mika Hirakawa
- 12Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyotoJapan
| | - Jean Thierry-Mieg
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
- 14Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique MathematiqueMontpellierFrance
| | - Danielle Thierry-Mieg
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
- 14Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physique MathematiqueMontpellierFrance
| | - Jennifer Ashurst
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Libin Jia
- 16National Cancer Institute, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Mitsuteru Nakao
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Michael A Thomas
- 17Department of Biological Sciences, Idaho State UniversityPocatello, IdahoUnited States of America
| | - Nicola Mulder
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Youla Karavidopoulou
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Lihua Jin
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Sangsoo Kim
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | | | - Boris Lenhard
- 19Center for Genomics and Bioinformatics, Karolinska InstitutetStockholmSweden
| | - Eric Eveno
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Yoshiyuki Suzuki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Chisato Yamasaki
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Jun-ichi Takeda
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Craig Gough
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Phillip Hilton
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Yasuyuki Fujii
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Hiroaki Sakai
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 22Tokyo Research Laboratories, Kyowa Hakko Kogyo CompanyTokyoJapan
| | - Susumu Tanaka
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Clara Amid
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Matthew Bellgard
- 24Centre for Bioinformatics and Biological Computing, School of Information Technology, Murdoch UniversityMurdoch, Western AustraliaAustralia
| | - Maria de Fatima Bonaldo
- 25Medical Education and Biomedical Research Facility, University of IowaIowa City, IowaUnited States of America
| | - Hidemasa Bono
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Susan K Bromberg
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | - Anthony J Brookes
- 19Center for Genomics and Bioinformatics, Karolinska InstitutetStockholmSweden
| | - Elspeth Bruford
- 28HUGO Gene Nomenclature Committee, University College LondonLondonUnited Kingdom
| | | | - Claude Chelala
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | - Christine Couillault
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | | | - Marie-Anne Debily
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | | | - Inna Dubchak
- 32Lawrence Berkeley National Laboratory, BerkeleyCaliforniaUnited States of America
| | - Toshinori Endo
- 33Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | | | - Eduardo Eyras
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Kaoru Fukami-Kobayashi
- 35Bioresource Information Division, RIKEN BioResource Center, RIKEN Tsukuba InstituteIbarakiJapan
| | - Gopal R. Gopinath
- 36Genome Knowledgebase, Cold Spring Harbor LaboratoryCold Spring Harbor, New YorkUnited States of America
| | - Esther Graudens
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Yoonsoo Hahn
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | - Michael Han
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Ze-Guang Han
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
| | - Kousuke Hanada
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideki Hanaoka
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Erimi Harada
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Katsuyuki Hashimoto
- 38Division of Genetic Resources, National Institute of Infectious DiseasesTokyoJapan
| | - Ursula Hinz
- 34Swiss Institute of BioinformaticsGenevaSwitzerland
| | - Momoki Hirai
- 39Graduate School of Frontier Sciences, Department of Integrated Biosciences, University of TokyoChibaJapan
| | - Teruyoshi Hishiki
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Ian Hopkinson
- 41Department of Primary Care and Population Sciences, Royal Free University College Medical School, University College LondonLondonUnited Kingdom
- 42Clinical and Molecular Genetics Unit, The Institute of Child HealthLondonUnited Kingdom
| | - Sandrine Imbeaud
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Hidetoshi Inoko
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Alexander Kanapin
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Yayoi Kaneko
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Takeya Kasukawa
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Janet Kelso
- 44South African National Bioinformatics Institute, University of the Western CapeBellvilleSouth Africa
| | - Paul Kersey
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | | | | | - Bernhard Korn
- 46RZPD Resource Center for Genome ResearchHeidelbergGermany
| | - Vladimir Kuryshev
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Izabela Makalowska
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Takashi Makino
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Shuhei Mano
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Regine Mariage-Samson
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
| | - Jun Mashima
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideo Matsuda
- 49Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka UniversityOsakaJapan
| | - Hans-Werner Mewes
- 23MIPS—Institute for Bioinformatics, GSF—National Research Center for Environment and HealthNeuherbergGermany
| | - Shinsei Minoshima
- 50Medical Photobiology Department, Photon Medical Research Center, Hamamatsu University School of MedicineShizuokaJapan
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | | | - Hideki Nagasaki
- 51Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Naoki Nagata
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Rajni Nigam
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | - Osamu Ogasawara
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | | | - Masafumi Ohtsubo
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Norihiro Okada
- 53Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of TechnologyKanagawaJapan
| | - Toshihisa Okido
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Satoshi Oota
- 35Bioresource Information Division, RIKEN BioResource Center, RIKEN Tsukuba InstituteIbarakiJapan
| | - Motonori Ota
- 54Global Scientific Information and Computing Center, Tokyo Institute of TechnologyTokyoJapan
| | - Toshio Ota
- 22Tokyo Research Laboratories, Kyowa Hakko Kogyo CompanyTokyoJapan
| | - Tetsuji Otsuki
- 55Molecular Biology Laboratory, Medicinal Research Laboratories, Taisho Pharmaceutical CompanySaitamaJapan
| | | | - Annemarie Poustka
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Shuang-Xi Ren
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
| | - Naruya Saitou
- 56Department of Population Genetics, National Institute of GeneticsShizuokaJapan
| | - Katsunaga Sakai
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Shigetaka Sakamoto
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Ryuichi Sakate
- 39Graduate School of Frontier Sciences, Department of Integrated Biosciences, University of TokyoChibaJapan
| | - Ingo Schupp
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Florence Servant
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Stephen Sherry
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Rie Shiba
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Nobuyoshi Shimizu
- 52Department of Molecular Biology, Keio University School of MedicineTokyoJapan
| | - Mary Shimoyama
- 27Medical College of Wisconsin, MilwaukeeWisconsinUnited States of America
| | | | - Bento Soares
- 25Medical Education and Biomedical Research Facility, University of IowaIowa City, IowaUnited States of America
| | - Charles Steward
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Makiko Suwa
- 51Computational Biology Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Mami Suzuki
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Aiko Takahashi
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Gen Tamiya
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
- 43Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai UniversityKanagawaJapan
| | - Hiroshi Tanaka
- 33Department of Bioinformatics, Medical Research Institute, Tokyo Medical and Dental UniversityTokyoJapan
| | - Todd Taylor
- 57Human Genome Research Group, Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Joseph D Terwilliger
- 58Columbia University and Columbia Genome CenterNew York, New YorkUnited States of America
| | - Per Unneberg
- 59Department of Biotechnology, Royal Institute of TechnologyStockholmSweden
| | - Vamsi Veeramachaneni
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Shinya Watanabe
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Laurens Wilming
- 15The Wellcome Trust Sanger Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Norikazu Yasuda
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 7Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics ConsortiumTokyoJapan
| | - Hyang-Sook Yoo
- 18Korea Research Institute of Bioscience and BiotechnologyTaejeonKorea
| | - Marvin Stodolsky
- 60Biology Division and Genome Task Group, Office of Biological and Environmental Research, United States Department of EnergyWashington, D.CUnited States of America
| | - Wojciech Makalowski
- 48Pennsylvania State UniversityUniversity Park, PennsylvaniaUnited States of America
| | - Mitiko Go
- 61Faculty of Bio-Science, Nagahama Institute of Bio-Science and TechnologyShigaJapan
| | - Kenta Nakai
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Toshihisa Takagi
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
| | - Minoru Kanehisa
- 12Bioinformatics Center, Institute for Chemical Research, Kyoto UniversityKyotoJapan
| | - Yoshiyuki Sakaki
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 57Human Genome Research Group, Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - John Quackenbush
- 62Institute for Genomic ResearchRockville, MarylandUnited States of America
| | - Yasushi Okazaki
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Yoshihide Hayashizaki
- 26Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokohama InstituteKanagawaJapan
| | - Winston Hide
- 44South African National Bioinformatics Institute, University of the Western CapeBellvilleSouth Africa
| | - Ranajit Chakraborty
- 63Center for Genome Information, Department of Environmental Health, University of CincinnatiCincinnati, OhioUnited States of America
| | - Ken Nishikawa
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Hideaki Sugawara
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Yoshio Tateno
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
| | - Zhu Chen
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
- 37Chinese National Human Genome Center at ShanghaiShanghaiChina
- 64State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai Second Medical UniversityShanghaiChina
| | | | - Peter Tonellato
- 65PointOne SystemsWauwatosa, WisconsinUnited States of America
| | - Rolf Apweiler
- 4EMBL Outstation—European Bioinformatics Institute, Wellcome Trust Genome CampusCambridgeUnited Kingdom
| | - Kousaku Okubo
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Lukas Wagner
- 13National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Stefan Wiemann
- 47Molecular Genome Analysis, German Cancer Research Center-DKFZHeidelbergGermany
| | - Robert L Strausberg
- 16National Cancer Institute, National Institutes of HealthBethesda, MarylandUnited States of America
| | - Takao Isogai
- 10Reverse Proteomics Research InstituteChibaJapan
- 66Graduate School of Life and Environmental Sciences, University of TsukubaIbarakiJapan
| | - Charles Auffray
- 20Genexpress—CNRS—Functional Genomics and Systemic Biology for HealthVillejuif CedexFrance
- 21Sino-French Laboratory in Life Sciences and GenomicsShanghaiChina
| | - Nobuo Nomura
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
| | - Takashi Gojobori
- 1Integrated Database Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 5Center for Information Biology and DNA Data Bank of Japan, National Institute of GeneticsShizuokaJapan
- 67Department of Genetics, Graduate University for Advanced StudiesShizuokaJapan
| | - Sumio Sugano
- 3Human Genome Center, The Institute of Medical Science, The University of TokyoTokyoJapan
- 40Functional Genomics Group, Biological Information Research Center, National Institute of Advanced Industrial Science and TechnologyTokyoJapan
- 68Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of TokyoTokyoJapan
| |
Collapse
|
125
|
Tomita K, Azuma T, Kitamura N, Nishida J, Tamiya G, Oka A, Inokuchi S, Nishimura T, Suematsu M, Ishii H. Pioglitazone prevents alcohol-induced fatty liver in rats through up-regulation of c-Met. Gastroenterology 2004; 126:873-85. [PMID: 14988841 DOI: 10.1053/j.gastro.2003.12.008] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Treatment of steatosis is important in preventing development of fibrosis in alcoholic liver diseases. This study aimed to examine if pioglitazone, an antidiabetic reagent serving as a ligand of peroxisome proliferator-activated receptor gamma (PPAR gamma), could prevent alcoholic fatty liver. METHODS Rats fed with an ethanol-containing liquid diet were given the reagent at 10 mg/kg per day intragastrically for 6 weeks. Hepatic genes involved in actions of the reagent were mined by transcriptome analyses, and their changes were confirmed by real-time polymerase chain reaction and Western blotting analyses. The direct effects of pioglitazone on primary-cultured hepatocytes were also assessed in vitro. RESULTS Pioglitazone significantly attenuated steatosis and lipid peroxidation elicited by chronic ethanol exposure without altering insulin resistance. Mechanisms for improving effects of the reagent appeared to involve restoration of the ethanol-induced down-regulation of c-Met and up-regulation of stearoyl-CoA desaturase (SCD). Such effects of pioglitazone on the c-Met signaling pathway resulted from its tyrosine phosphorylation and resultant up-regulation of the apolipoprotein B (apoB)-mediated lipid mobilization from hepatocytes through very low-density lipoprotein (VLDL) as well as down-regulation of sterol regulatory element binding protein (SREBP) -1c and SCD levels and a decrease in triglyceride synthesis in the liver. CONCLUSIONS Pioglitazone activates c-Met and VLDL-dependent lipid retrieval and suppresses triglyceride synthesis and thereby serves as a potentially useful stratagem to attenuate ethanol-induced hepatic steatosis.
Collapse
Affiliation(s)
- Kengo Tomita
- Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
126
|
Hui J, Oka A, Tomizawa M, Tay GK, Kulski JK, Penhale WJ, Iaschi SPA, Makino S, Tamiya G, Inoko H. Identification of two new C4 alleles by DNA sequencing and evidence for a historical recombination of serologically defined C4A and C4B alleles. ACTA ACUST UNITED AC 2004; 63:263-9. [PMID: 14989717 DOI: 10.1111/j.1399-0039.2004.0175.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Nucleotide polymorphisms of the C4 genes were investigated by direct sequencing of seven different homozygous typing cells from the 10IHW panels. Two novel sequences were identified within the C4d region of the C4 genes. Our sequencing analyses extend previous findings suggesting that a recombination hot spot is likely to have occurred between codon positions 1157 and 1186 within the C4d region. The classification of electrophoretically defined C4A and C4B alleles can be further subtyped by sequencing. Because the central major histocompatibility complex region that carries various copies of the C4 gene has been associated with a range of disorders; further analysis at the sequence level within the C4 locus may provide informative genetic markers for the investigation of disease-associated polymorphisms.
Collapse
Affiliation(s)
- J Hui
- School of Surgery and Pathology, Division of Pathology, The University of Western Australia, Nedlands, Western Australia, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
127
|
Okamoto K, Matsuzaka Y, Yoshikawa Y, Takaki A, Kulski JK, Tamiya G, Inoko H. Identification of NAD+-dependent isocitrate dehydrogenase 3 gamma-like (IDH3GL) gene and its genetic polymorphisms. Gene 2004; 323:141-8. [PMID: 14659887 DOI: 10.1016/j.gene.2003.09.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We have identified a novel human gene designated as IDH3GL (isocitrate dehydrogenase 3 gamma-like) that is expressed specifically in human testis. The gene corresponds in sequence to an EST (expressed sequence tag) A1476435 that was first detected by differential expression analysis using a microarray assay. The full-length cDNA sequence (1037 bp) was isolated from the human testis 5'-3'-RACE cDNA libraries and found to have 83% nucleotide sequence identity with part of the IDH3G (isocitrate dehydrogenase 3 gamma). The IDH3GL gene consists of 3 exons spanning approximately 220 kb within the region of the NELL1 gene on chromosome 11p15.1. Sequence analysis of the IDH3GL cDNA revealed the presence of a premature stop codon at nucleotide positions 337-339 that results in a truncated peptide with 112 amino acids. This stop codon is conserved in various human ethnic populations and in the chimpanzee (Pan troglodytes). In order to assess the functional status of IDH3GL, especially in relation to the presence of the putative premature stop codon, single nucleotide polymorphisms (SNPs) were screened in the upstream, coding and non-coding regions of the IDH3GL gene in a Japanese population. As a result, a total of 10 SNPs were identified, seven were novel and one of them was a non-synonymous amino acid substitution from Leu to Val. We conclude that the IDH3GL gene sequence is a splice variant of the NELL1 gene and that it probably evolved from a transposed pseudogene of the IDH3 gene.
Collapse
Affiliation(s)
- Koichi Okamoto
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Kanagawa 259-1193, Isehara, Japan
| | | | | | | | | | | | | |
Collapse
|
128
|
Toda T, Momose Y, Murata M, Tamiya G, Yamamoto M, Hattori N, Inoko H. Toward identification of susceptibility genes for sporadic Parkinson's disease. J Neurol 2004; 250 Suppl 3:III40-3. [PMID: 14579123 DOI: 10.1007/s00415-003-1307-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
To identify susceptibility genes for Parkinson's disease (PD) and to establish tailor-made medicine for PD, we studied 20 single nucleotide polymorphisms (SNPs) in 18 candidate genes for association with PD. We found that homozygosity for the V66M polymorphism of the BDNF gene occurs more frequently in PD patients than in unaffected controls and confirmed an association with the S18Y polymorphism of the UCHL1 gene. We further started microsatellite marker-based genome-wide association studies by using the pooled DNA method. We have finished checking approximately 6800 markers and found some significant associations (p=3.9 x 10(-6)) on chromosome 1 where other studies showed a linkage. Genes in linkage disequilibrium with these markers may be associated with pathogenesis of PD.
Collapse
Affiliation(s)
- Tatsushi Toda
- Division of Functional Genomics, Department of Post-Genomics and Diseases, Osaka University Graduate School of Medicine, 2-2-B9 Yamadaoka, Suita, 565-0871, Osaka, Japan.
| | | | | | | | | | | | | |
Collapse
|
129
|
Romphruk AV, Oka A, Romphruk A, Tomizawa M, Choonhakarn C, Naruse TK, Puapairoj C, Tamiya G, Leelayuwat C, Inoko H. Corneodesmosin gene: no evidence for PSORS 1 gene in North-eastern Thai psoriasis patients. Tissue Antigens 2003; 62:217-24. [PMID: 12956875 DOI: 10.1034/j.1399-0039.2003.00056.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Psoriasis vulgaris, a common inflammatory skin disorder, is known to be associated with the HLA-Cw*06 allele. It has been recently suggested by microsatellite mapping that a real susceptible gene for psoriasis resides in the approximately 100-kb genomic region telomeric of the HLA-C gene. In this respect, the corneodesmosin (CDSN) gene 160-kb telomeric of HLA-C is a strong candidate because of its location and its functional role in corneocyte cohesion and desquamation. In fact, a significant association between CDSN polymorphism and psoriasis was recently recognized in Caucasian populations. However, this association has not been replicated in other studies, being still controversial. In this study, we investigated the genetic polymorphism of the CDSN gene in 139 psoriasis patients and 144 healthy controls in the North-eastern Thai population. By direct sequencing technique, a total of 28 polymorphic sites were found, consisting of 26 single nucleotide polymorphisms (SNPs) and two indels (insertion/deletion). Among them, six SNPs have not been previously reported. Through this analysis, as many as 28 different SNP/indel haplotypes within the CDSN gene were identified. Seven SNPs and one indel, namely 9C, 614 A, 722T, 971T, 1215G, 1243C, 1331G and 1606AAG (deletion), revealed significant deviation in the allelic frequencies of the patients from those of the healthy controls. However, none of them are likely to be responsible for controlling the susceptibility of psoriasis, but these associations can be explained by a linkage disequilibrium to a real pathogenic allele of a nearby gene. Further, the large variations between the CDSN SNP/indel haplotypes and the psoriatic major histocompatibility complex (MHC) haplotypes also make it unlikely that CDSN is a major psoriasis-susceptible gene.
Collapse
Affiliation(s)
- A V Romphruk
- Blood Transfusion Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | | | | | | | | | | | | | | | | | | |
Collapse
|
130
|
Oka A, Hayashi H, Tomizawa M, Okamoto K, Suyun L, Hui J, Kulski JK, Beilby J, Tamiya G, Inoko H. Localization of a non-melanoma skin cancer susceptibility region within the major histocompatibility complex by association analysis using microsatellite markers. Tissue Antigens 2003; 61:203-10. [PMID: 12694569 DOI: 10.1034/j.1399-0039.2003.00007.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The major histocompatibility complex (MHC) is known to have a role in the development of non-melanoma skin cancer (NMSC), although the genes and mechanisms involved have yet to be determined. To identify the susceptibility locus for NMSC within the MHC, we used a collection of well-defined polymorphic microsatellite markers from the Human leucocyte antigen (HLA) region for an association analysis of 150 cases with NMSC and 200 healthy controls selected from the Busselton population in Western Australia. High-resolution mapping was undertaken using a total of 40 highly polymorphic markers located at regular intervals across the HLA region (3.6Mb). Polymerase chain reaction (PCR) analysis was initially performed on pooled DNA markers to detect those markers that showed different allele profiles. Statistically significant differences in allelic frequencies (differentiating alleles) were found between cases and controls at three polymorphic microsatellite loci within a 470-kb genomic susceptibility region ranging between 6 kb centromeric of the HLA-B gene and intron 5 of the DDR gene. Interestingly, this genome region corresponded completely with the psoriasis-susceptibility locus. The three differentiating alleles and another four markers outside the susceptibility region were then PCR tested by individual genotyping of cases and controls. The newly identified susceptibility locus for NMSC within the MHC was found to be significantly different between the cases and controls by comparisons of allele frequencies at the three differentiating loci estimated from DNA pools and then confirmed by individual genotyping. This is the first study using high density microsatellite markers to localize a NMSC susceptibility region within the human genome.
Collapse
Affiliation(s)
- A Oka
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
131
|
Okamoto K, Makino S, Yoshikawa Y, Takaki A, Nagatsuka Y, Ota M, Tamiya G, Kimura A, Bahram S, Inoko H. Identification of I kappa BL as the second major histocompatibility complex-linked susceptibility locus for rheumatoid arthritis. Am J Hum Genet 2003; 72:303-12. [PMID: 12509789 PMCID: PMC379224 DOI: 10.1086/346067] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2002] [Accepted: 10/29/2002] [Indexed: 02/05/2023] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory joint disease with a complex etiology in which environmental factors within a genetically susceptible host maneuver the innate and adaptive arms of the immune system toward recognition of autoantigens. This ultimately leads to joint destruction and clinical symptomatology. Despite the identification of a number of disease-susceptibility regions across the genome, RA's major genetic linkage remains with the major histocompatibility complex (MHC), which contains not only the key immune-response class I and class II genes but also a host of other loci, some with potential immunological relevance. Inside the MHC itself, the sole consistent RA association is that with HLA-DRB1, although this does not encode all MHC-related susceptibility. Indeed, in a set of Japanese patients with RA and a control group, we previously reported the presence of a second RA-susceptibility gene within the telomeric human leukocyte antigen (HLA) class III region. Using microsatellites, we narrowed the susceptibility region to 70 kb telomeric of the TNF cluster, known to harbor four expressed genes (I kappa BL, ATP6G, BAT1, and MICB). Here, using numerous single-nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms, we identify the second RA-susceptibility locus within the HLA region, as the T allele of SNP 96452 (T/A), in the promoter region (position -62) of the I kappa BL gene (P=.0062). This -62T/A SNP disrupts the putative binding motif for the transcriptional repressor, delta EF1, and hence may influence the transcription of I kappa BL, homologous to I kappa B alpha, the latter being a known inhibitor of NF kappa B, which is central to innate immunity. Therefore, the MHC may harbor RA genetic determinants affecting the innate and adaptive arms of the immune system.
Collapse
Affiliation(s)
- Koichi Okamoto
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Satoshi Makino
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Yoko Yoshikawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Asumi Takaki
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Yumie Nagatsuka
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Masao Ota
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Gen Tamiya
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Akinori Kimura
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Seiamak Bahram
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan; Fuji-Gotemba Research Laboratories, Chugai Pharmaceuticals, Shizuoka, Japan; Research and Development Center, Nisshinbo Industries, Chiba, Japan; Institute of Organ Transplants, Reconstructive Medicine and Tissue Engineering, and Department of Legal Medicine, Shinshu University School of Medicine, Nagano, Japan; Department of Molecular Pathogenesis, Division of Adult Disease, Medical Research Institute, Tokyo Medical and Dental University, Tokyo; and INSERM-CReS Centre de Recherche d’Immunologie et d’Hematologie, Strasbourg, France
| |
Collapse
|
132
|
Tsuji H, Okamoto K, Matsuzaka Y, Iizuka H, Tamiya G, Inoko H. SLURP-2, a novel member of the human Ly-6 superfamily that is up-regulated in psoriasis vulgaris. Genomics 2003; 81:26-33. [PMID: 12573258 DOI: 10.1016/s0888-7543(02)00025-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
By microarray assay we identified ESTs (expressed sequence tags) whose expression was predominantly increased in the affected skin of patients with psoriasis vulgaris. Among them, a full-length cDNA sequence corresponding to one of those ESTs (AI829641) was isolated by screening of cultured human keratinocyte cDNA libraries. This cDNA encodes a novel member of the Ly-6/uPAR superfamily, designated SLURP-2 (secreted Ly-6/uPAR related protein 2). SLURP-2 has an open reading frame of 97 amino acids containing 10 conserved cysteine residues. SLURP-2 has a single functional copy within the LY6 superfamily gene cluster at chromosome 8q24.3. RT-PCR (reverse transcriptase-polymerase chain reaction) expression analysis revealed that SLURP-2 was expressed in multiple tissues, mainly in the epithelial cells including the skin and keratinocytes, but not in spleen or bone marrow. Comparison of the expression of this gene among the psoriatic lesional and nonlesional skin of patients and the normal skin of healthy individuals detected by quantitative real-time RT-PCR analysis disclosed that SLURP-2 was up-regulated threefold in psoriatic lesional skin. These findings suggest that SLURP-2 may be involved in the pathophysiology of psoriasis through its role in keratinocyte hyperproliferation and/or T cell differentiation/activation.
Collapse
Affiliation(s)
- Hitomi Tsuji
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | | | | | | | | | | |
Collapse
|
133
|
Matsuzaka Y, Okamoto K, Tsuji H, Mabuchi T, Ozawa A, Tamiya G, Inoko H. Identification of the hRDH-E2 gene, a novel member of the SDR family, and its increased expression in psoriatic lesion. Biochem Biophys Res Commun 2002; 297:1171-80. [PMID: 12372410 DOI: 10.1016/s0006-291x(02)02344-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To identify novel psoriasis-associated genes, we focused on several ESTs (expressed sequence tags) whose expression was predominantly increased in the affected skin in patients with psoriasis vulgaris, as assessed by microarray assay. In this paper, a full-length cDNA corresponding to one of those ESTs (AI440266) was isolated by screening of cultured human keratinocyte cDNA libraries. This cDNA has an open reading frame of a 309-amino-acid protein, sharing significant homology to one of the short-chain alcohol dehydrogenase/reductase (SDR) families that can catalyze the first and rate-limiting step that generates retinaldehyde from retinol. So, this gene was designated as hRDH-E2 (human epidermal retinal dehydrogenase 2). The hRDH-E2 gene has a single functional copy on chromosome 8q12.1, spanning approximately 20kb with seven exons. The deduced amino acid sequence contains three motifs that are conserved in the SDR family. Qualitative RT-PCR demonstrated that the mRNA levels of hRDH-E2 were significantly elevated in the affected skin in psoriasis patients as compared to the unaffected skin in patients and the normal skin in healthy individual. These results suggest that hRDH-E2 may be involved in the pathogenesis of psoriasis through its critical role in retinol metabolism in keratinocyte proliferation.
Collapse
MESH Headings
- Alcohol Dehydrogenase/chemistry
- Aldehyde Oxidoreductases/biosynthesis
- Aldehyde Oxidoreductases/chemistry
- Aldehyde Oxidoreductases/genetics
- Amino Acid Motifs
- Amino Acid Sequence
- Base Sequence
- Blotting, Northern
- Blotting, Southern
- Cell Division
- Chromosomes, Human, Pair 2
- DNA, Complementary/metabolism
- Exons
- Expressed Sequence Tags
- Gene Library
- Genome, Human
- Humans
- Keratinocytes/enzymology
- Keratinocytes/metabolism
- Models, Genetic
- Molecular Sequence Data
- Poly A/metabolism
- Protein Structure, Tertiary
- Psoriasis/enzymology
- RNA, Messenger/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Amino Acid
- Tissue Distribution
Collapse
Affiliation(s)
- Yasunari Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | |
Collapse
|
134
|
Carter K, Oka A, Tamiya G, Bellgard MI. Bioinformatics issues for automating the annotation of genomic sequences. Genome Inform 2002; 12:204-11. [PMID: 11791239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
The rapid explosion in the amount of biological data being generated worldwide is surpassing efforts to manage analysis of the data. As part of an ongoing project to automate and manage bioinformatics analysis, the authors have designed and implemented a simple automated annotation system, which is described in this paper. The system is applied to existing GenBank/DDBJ/EMBL entries and compared with existing annotations to illustrate not only potential errors but also that they are generally not up-to-date, as a result of new versions of analysis tools and updates of genomic repositories. We highlight the important Bioinformatics issues of storage and management of information to ensure data and results are kept up-to-date in light of new information becoming available. Surprisingly, from just four database entries, a significant number of new features were found. We describe the results as well as identify important issues that need to be addressed in order to automate the re-analysis/re-annotation of genomic sequences within a reasonable timeframe.
Collapse
Affiliation(s)
- K Carter
- Centre for Bioinformatics and Biological Computing, Murdoch University, Murdoch WA 6150, Australia.
| | | | | | | |
Collapse
|
135
|
Matsuzaka Y, Tounai K, Denda A, Tomizawa M, Makino S, Okamoto K, Keicho N, Oka A, Kulski JK, Tamiya G, Inoko H. Identification of novel candidate genes in the diffuse panbronchiolitis critical region of the class I human MHC. Immunogenetics 2002; 54:301-9. [PMID: 12185533 DOI: 10.1007/s00251-002-0470-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2002] [Revised: 05/01/2002] [Indexed: 11/24/2022]
Abstract
Diffuse panbronchiolitis (DPB) is an unusual form of bronchiolar disease affecting exclusively East Asians. Strong associations of DPB with the class I human leukocyte antigens HLA-B54 in Japan and China and HLA-A11 in Korea suggest that the susceptible locus for DPB is located between the HLA-B and HLA-A genes. We have previously reported that the susceptibility gene for DPB could be localized within a 200-kb segment between the S and TFIIH loci in the HLA class I region, using refined microsatellite-based association mapping. However, no genes have been recognized in this candidate region to date. In order to identify a novel candidate gene for DPB from this segment, the expressed sequence tag databases were searched using the genomic sequence. As a result, a cDNA clone was isolated from a human lung cDNA library. This gene, designated C6orf37 (Chromosome 6 open reading frame 37), spans approximately 2.5 kb and consists of two exons encoding a 235-amino acid protein, sharing homology with the mucin-like domain of human zonadhesin, which is a sperm multiple-domain transmembrane protein with the sperm zona pellucida binding activity. Unexpectedly, RT-PCR analysis detected transcripts from the anti-sense DNA strand of this C6orf37 locus. The gene designated as C6orf37OS (C6orf37 Opposite Strand) and represented by these anti-sense transcripts contained no open reading frame. The transcripts from C6orf37 and C6orf37OS were observed in numerous tissues, with most-abundant expression in lung, kidney, and testis. Taken together, these results, especially the abundant expression in lung, indicate that C6orf37 and C6orf37OS are excellent candidate genes for DPB.
Collapse
MESH Headings
- Amino Acid Sequence
- Asian People/genetics
- Base Sequence
- Chromosome Mapping
- Chromosomes, Human, Pair 6/genetics
- Cloning, Molecular
- DNA, Complementary/genetics
- Gene Expression Profiling
- Genes, MHC Class I
- Genes, Overlapping
- Genetic Predisposition to Disease
- HLA-B Antigens/genetics
- Humans
- Membrane Proteins/chemistry
- Molecular Sequence Data
- Mucins
- Open Reading Frames
- Organ Specificity
- Polynucleotide Adenylyltransferase
- Protein Structure, Tertiary
- Proteins/genetics
- Pulmonary Disease, Chronic Obstructive/ethnology
- Pulmonary Disease, Chronic Obstructive/genetics
- RNA, Antisense/biosynthesis
- RNA, Antisense/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Alignment
- Sequence Homology, Amino Acid
- Transcription, Genetic
Collapse
Affiliation(s)
- Yasunari Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
136
|
Katoh T, Mano S, Ikuta T, Munkhbat B, Tounai K, Ando H, Munkhtuvshin N, Imanishi T, Inoko H, Tamiya G. Genetic isolates in East Asia: a study of linkage disequilibrium in the X chromosome. Am J Hum Genet 2002; 71:395-400. [PMID: 12082643 PMCID: PMC379171 DOI: 10.1086/341608] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2002] [Accepted: 05/02/2002] [Indexed: 11/03/2022] Open
Abstract
The background linkage disequilibrium (LD) in genetic isolates is of great interest in human genetics. Although many empirical studies have evaluated the background LD in European isolates, such as the Finnish and Sardinians, few data from other regions, such as Asia, have been reported. To evaluate the extent of background LD in East Asian genetic isolates, we analyzed the X chromosome in the Japanese population and in four Mongolian populations (Khalkh, Khoton, Uriankhai, and Zakhchin), the demographic histories of which are quite different from one another. Fisher's exact test revealed that the Japanese and Khalkh, which are the expanded populations, had the same or a relatively higher level of LD than did the Finnish, European American, and Sardinian populations. In contrast, the Khoton, Uriankhai, and Zakhchin populations, which have kept their population size constant, had a higher background LD. These results were consistent with previous genetic anthropological studies in European isolates and indicate that the Japanese and Khalkh populations could be utilized in the fine mapping of both complex and monogenic diseases, whereas the Khoton, Uriankhai, and Zakhchin populations could play an important role in the initial mapping of complex disease genes.
Collapse
Affiliation(s)
- T Katoh
- Department of Genetic Information, Division of Molecular Life Science, School of Medicine, Tokai University, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
137
|
Hui J, Oka A, Tamiya G, Tomizawa M, Kulski JK, Penhale WJ, Tay GK, Iizuka M, Ozawa A, Inoko H. Corneodesmosin DNA polymorphisms in MHC haplotypes and Japanese patients with psoriasis. Tissue Antigens 2002; 60:77-83. [PMID: 12366786 DOI: 10.1034/j.1399-0039.2002.600110.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In order to examine the relationship between corneodesmosin (CDSN) and psoriasis we have determined the presence of CDSN polymorphisms by DNA sequencing in (a) nine B-LCL cell lines of major histocompatibility complex ancestral haplotypes known to be associated with psoriasis vulgaris including 13.1AH, 46.1AH, 46.2 and 57.1AH, and in (b) a group of 267 unrelated individuals comprising Japanese psoriasis patients (n = 101) and Japanese subjects without the disease (n = 166). Three novel CDSN gene sequences were identified. In addition, we have classified the 18 alleles into seven main groups based on phylogeny of non-synonymous substitutions. However, we have found no statistically significant differences between the patients and the unaffected individuals in any of these groups. These findings indicate that CDSN is not a major psoriasis susceptibility gene.
Collapse
Affiliation(s)
- J Hui
- Department of Pathology, The University of Western Australia, Nedlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
138
|
Matsuzaka Y, Makino S, Okamoto K, Oka A, Tsujimura A, Matsumiya K, Takahara S, Okuyama A, Sada M, Gotoh R, Nakatani T, Ota M, Katsuyama Y, Tamiya G, Inoko H. Susceptibility locus for non-obstructive azoospermia is localized within the HLA-DR/DQ subregion: primary role of DQB1*0604. Tissue Antigens 2002; 60:53-63. [PMID: 12366783 DOI: 10.1034/j.1399-0039.2002.600107.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Non-obstructive azoospermia is a male infertility characterized by no or little sperm in semen as a result of a congenital dysfunction in spermatogenesis. Previous studies have reported a higher prevalence of particular human leukocyte antigen (HLA) antigens in non-obstructive azoospermia. As the expression of the RING3 gene located in the HLA class II region was predominant in the testis, mainly around spermatids and pachytene spermatocytes, it is tempting to speculate that RING3 is one of the strong candidate genes responsible for the pathogenesis of the disease. In this study, the genetic polymorphism in the RING3 gene was investigated by the direct sequencing technique. As a result, a total of 14 single nucleotide polymorphisms were identified. Among them, six were localized in the coding region but none of them was accompanied by an amino-acid substitution. No significant difference in the allelic distribution at these 14 polymorphic sites was observed between the patients and healthy controls, suggesting that the susceptible gene for non-obstructive azoospermia is not the RING3 gene. Then, in order to map the susceptibility locus for non-obstructive azoospermia precisely within the HLA region, 11 polymorphic microsatellite markers distributed from the SACM2L gene just outside the HLA class II region (187 kb telomeric of the DPB1 gene) to the OTF3 gene in the HLA class I region were subjected to association analysis in the patients. Statistical analysis of distribution in the allelic frequency at each microsatellite locus demonstrated that the pathogenic gene for non-obstructive azoospermia is located within the HLA-DR/DQ subregion. In fact, DRB1*1302 and DQB1*0604 were found to be strongly associated with non-obstructive azoospermia by polymerase chain reaction-based DNA typing. Further, haplotype analysis suggested that the DQB1*0604 allele may play a decisive role in the pathogenesis of non-obstructive azoospermia.
Collapse
Affiliation(s)
- Y Matsuzaka
- Department of Molecular life Science, Tokai University School of Medicine, Ishehara, Kanagwa, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
139
|
Nagayasu E, Nagakura K, Akaki M, Tamiya G, Makino S, Nakano Y, Kimura M, Aikawa M. Association of a determinant on mouse chromosome 18 with experimental severe Plasmodium berghei malaria. Infect Immun 2002; 70:512-6. [PMID: 11796577 PMCID: PMC127666 DOI: 10.1128/iai.70.2.512-516.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Experimental severe malaria (ESM; also known as experimental cerebral malaria) is an acute lethal syndrome caused by infection with Plasmodium berghei ANKA and associated with coma and other neurological manifestations in mice. Various inbred strains of mice exhibit differences in susceptibility to the development of ESM. For example, C57BL/6 mice are highly susceptible and DBA/2 mice are relatively resistant. We report here the results of a genomewide scan for host genomic regions that control resistance to ESM in DBA/2 mice using an F(2) intercross population of susceptible and resistant strains. A region of mid-chromosome 18 was found to be a major determinant of resistance to ESM.
Collapse
Affiliation(s)
- Eiji Nagayasu
- Institute of Science and Technology. Division of Molecular Life Science, School of Medicine. Division of Infectious Diseases, Tokai University, Isehara 259-1193, Japan
| | | | | | | | | | | | | | | |
Collapse
|
140
|
Shiina T, Ando A, Suto Y, Kasai F, Shigenari A, Takishima N, Kikkawa E, Iwata K, Kuwano Y, Kitamura Y, Matsuzawa Y, Sano K, Nogami M, Kawata H, Li S, Fukuzumi Y, Yamazaki M, Tashiro H, Tamiya G, Kohda A, Okumura K, Ikemura T, Soeda E, Mizuki N, Kimura M, Bahram S, Inoko H. Genomic anatomy of a premier major histocompatibility complex paralogous region on chromosome 1q21-q22. Genome Res 2001; 11:789-802. [PMID: 11337475 PMCID: PMC311078 DOI: 10.1101/gr.175801] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Human chromosomes 1q21-q25, 6p21.3-22.2, 9q33-q34, and 19p13.1-p13.4 carry clusters of paralogous loci, to date best defined by the flagship 6p MHC region. They have presumably been created by two rounds of large-scale genomic duplications around the time of vertebrate emergence. Phylogenetically, the 1q21-25 region seems most closely related to the 6p21.3 MHC region, as it is only the MHC paralogous region that includes bona fide MHC class I genes, the CD1 and MR1 loci. Here, to clarify the genomic structure of this model MHC paralogous region as well as to gain insight into the evolutionary dynamics of the entire quadriplication process, a detailed analysis of a critical 1.7 megabase (Mb) region was performed. To this end, a composite, deep, YAC, BAC, and PAC contig encompassing all five CD1 genes and linking the centromeric +P5 locus to the telomeric KRTC7 locus was constructed. Within this contig a 1.1-Mb BAC and PAC core segment joining CD1D to FCER1A was fully sequenced and thoroughly analyzed. This led to the mapping of a total of 41 genes (12 expressed genes, 12 possibly expressed genes, and 17 pseudogenes), among which 31 were novel. The latter include 20 olfactory receptor (OR) genes, 9 of which are potentially expressed. Importantly, CD1, SPTA1, OR, and FCERIA belong to multigene families, which have paralogues in the other three regions. Furthermore, it is noteworthy that 12 of the 13 expressed genes in the 1q21-q22 region around the CD1 loci are immunologically relevant. In addition to CD1A-E, these include SPTA1, MNDA, IFI-16, AIM2, BL1A, FY and FCERIA. This functional convergence of structurally unrelated genes is reminiscent of the 6p MHC region, and perhaps represents the emergence of yet another antigen presentation gene cluster, in this case dedicated to lipid/glycolipid antigens rather than antigen-derived peptides.
Collapse
Affiliation(s)
- Takashi Shiina
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Asako Ando
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yumiko Suto
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Fumio Kasai
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Atsuko Shigenari
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Nobusada Takishima
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Eri Kikkawa
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Kyoko Iwata
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yuko Kuwano
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yuka Kitamura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yumiko Matsuzawa
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Kazumi Sano
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Masahiro Nogami
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Hisako Kawata
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Suyun Li
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Yasuhito Fukuzumi
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Masaaki Yamazaki
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Hiroyuki Tashiro
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Gen Tamiya
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Atsushi Kohda
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Katsuzumi Okumura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Toshimichi Ikemura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Eiichi Soeda
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Nobuhisa Mizuki
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Minoru Kimura
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Seiamak Bahram
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| | - Hidetoshi Inoko
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan; Department of Biological Science, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; Bioscience Research Laboratory, Fujiya Co., Ltd., Soya, Hadano, Kanagawa 257-0031, Japan; Faculty of Bioresources, Mie University, Tsu, Mie 514-0008, Japan; Department of Evolutionary Genetics, National Institute of Genetics, Mishima, Shizuoka 411-0801, Japan; Tsu Kuba, Life Science Center, The Institute of Physical and Chemical Research (RIKEN), Yatabe-choh, Tsukuba, Ibaraki 305-0861, Japan; Department of Ophthalmology, Yokohama City University School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0004, Japan; INSERM-CReS, Centre de Recherche d'Immunologie et d'Hématologie, 67085 Strasbourg, France
| |
Collapse
|
141
|
Matsuzaka Y, Makino S, Nakajima K, Tomizawa M, Oka A, Bahram S, Kulski JK, Tamiya G, Inoko H. New polymorphic microsatellite markers in the human MHC class III region. Tissue Antigens 2001; 57:397-404. [PMID: 11556964 DOI: 10.1034/j.1399-0039.2001.057005397.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The human major histocompatibility complex (MHC) class III region spanning approximately 760 kb is characterized by a remarkably high gene density with 59 expressed genes (one gene every 12.9 kb). Recently, susceptibility loci to numerous diseases, such as Graves disease, Crohn disease, and SLE have been suggested to be localized to this region, as assessed by associations mainly with genetic polymorphisms of TNF and TNF-linked microsatellite loci. However, it has been difficult to precisely localize these susceptibility loci to a single gene due to a paucity to date of polymorphic markers in the HLA class III region. To facilitate disease mapping within this region, we have analyzed 2 approximately 5 bases short tandem repeats (microsatellites) in this region. A total of 297 microsatellites were identified from the genomic sequence, consisting of 69 di-, 62 tri-, 107 tetra-, and 59 penta-nucleotide repeats. It was noted that among them as many as 17 microsatellites were located within the coding sequence of expressed genes (NOTCH4, PBX2, RAGE, G16, LPAAT, PPT2, TNXB, P450-CYP21B, G9a, HSP70-2, HSP70-1, HSP-hom, MuTSH5 and BAT2). Eight microsatellite repeats were collected as polymorphic markers due to their high number of alleles (11.9 on average) as well as their high polymorphic content value (PIC) (0.63). By combining the 38 and the 22 polymorphic microsatellites we have previously collected in the HLA class I and class II regions, respectively, we have now established a total of 68 novel genetic markers which are uniformly interspersed with a high density of one every 63.3 kb throughout the HLA region. This collection of polymorphic microsatellites will enable us to search for the location of any disease susceptible loci within the HLA region by association analysis.
Collapse
Affiliation(s)
- Y Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
142
|
Matsuzaka Y, Makino S, Nakajima K, Tomizawa M, Oka A, Kimura M, Bahram S, Tamiya G, Inoko H. New polymorphic microsatellite markers in the human MHC class II region. Tissue Antigens 2000; 56:492-500. [PMID: 11169238 DOI: 10.1034/j.1399-0039.2000.560602.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The human major histocompatibility complex (MHC) class II region spans approximately 1.1 Mb and presently contains over 30 functional genes Susceptibility loci to numerous diseases, mainly of autoimmune nature are known to map to the this region, as assessed by associations with particular HLA class II alleles. However, it has been difficult to precisely localize these susceptibility loci to a single gene, for example DQB1 or DRB1, due to the tight linkage disequilibrium observed in the HLA class II region. To facilitate disease mapping within this region, we have analyzed 2 to approximately 5 bases short tandem repeats (microsatellites) in this same region. A total of 494 microsatellites were identified from the genomic sequence of the HLA class II region. These consist of 158 di-, 65 tri-, 163 tetra-, and 108 pent-nucleotide repeats, out of which four were located within the coding sequence of expressed genes (Daxx, BING1, RXRB and COL11A2). Twenty-two repeats were selected as polymorphic markers due to their high (average) number of alleles (8.9) as well as their high polymorphic content value (PIC) (0.58). These novel polymorphic microsatellites will provide useful genetic markers in HLA-related research, such as genetic mapping of HLA class II-associated diseases, transplantation matching, population genetics, identification of recombination hot spots as well as linkage disequilibrium studies.
Collapse
Affiliation(s)
- Y Matsuzaka
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
143
|
Okamoto K, Tamiya G, Inoko H. [Susceptibility genes in rheumatoid arthritis]. Ryumachi 2000; 40:917-26. [PMID: 11210777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
|
144
|
Yamada K, Ogawa H, Tamiya G, Ikeno M, Morita M, Asakawa S, Shimizu N, Okazaki T. Genomic organization, chromosomal localization, and the complete 22 kb DNA sequence of the human GCMa/GCM1, a placenta-specific transcription factor gene. Biochem Biophys Res Commun 2000; 278:134-9. [PMID: 11071865 DOI: 10.1006/bbrc.2000.3775] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genomic sequence of the human GCMa/GCM1 gene, a mammalian homologue of Drosophila melanogaster GCM, was determined. Drosophila GCM is a neural transcription factor that regulates glial cell fate. The mammalian homolog however, is a placenta-specific transcription factor that is necessary for placental development. The 22 kb DNA sequence spanning the GCMa gene contains six exons and five introns, encoding a 2.8 kb cDNA. Overall genomic organization is similar for the human and mouse. Several potential binding sites for transcription factors like GATA, Oct-1, and bHLH proteins were found in the 5'-flanking region of the human gene. A DNA motif for GCM protein binding exists in the 5'-flanking region that is highly homologous with that of the mouse gene. The location of this gene was mapped to chromosome 6 using fluorescence in situ hybridization.
Collapse
Affiliation(s)
- K Yamada
- Institute for Comprehensive Medical Science, Fujita Health University, School of Medicine, Toyoake, Aichi, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
145
|
Tomita K, Sato M, Kajiwara K, Tanaka M, Tamiya G, Makino S, Tomizawa M, Mizutani A, Kuwano Y, Shiina T, Ishii H, Kimura M. Gene structure and promoter for Crad2 encoding mouse cis-retinol/3alpha-hydroxysterol short-chain dehydrogenase isozyme. Gene 2000; 251:175-86. [PMID: 10876094 DOI: 10.1016/s0378-1119(00)00194-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Cis-retinol/androgen dehydrogenase type 2 (CRAD2) has been shown to catalyze the dehydrogenation of retinols, including 9-cis retinol, and also to exhibit 3alpha- and 17beta- hydroxysteroid dehydrogenase activities. To examine the function of this enzyme and regulation of its gene, the Crad2 gene was cloned from a mouse genomic DNA library and characterized. The complete mouse CRAD2-coding region was found in four exons spanning an approximately 5kb region. The nucleotide sequences of the exons encoding 316 amino acids were identical to those of the previously reported mouse Crad2 cDNA. Primer extension analysis and RNase protection assay were used to map the major transcription initiation sites to the positions lying 87 and 89 base pairs upstream of the ATG translation start codon. The region proximal to the initiation sites exhibited the absence of both TATAA and CAAT boxes. This region had hepatocyte nuclear factor binding sites, consistent with its predominant expression in the liver. Computer analysis of an approximately 7.5kb 5'-flanking region also suggested the presence of binding sites for AP-1, SREBP1, HSF2, c-Rel, c-Myc, CREBP, GATA, Ets, E2F, and Oct-1, suggesting that various factors including retinoic acid, cholesterol, various kinds of stress, the cell cycle, and cyclic AMP may regulate the expression of this gene. Fluorescence in-situ hybridization analysis showed that Crad2 is located at the terminus of mouse chromosome 10, an area that corresponds to band 10D3, suggesting that RDH-related SDRs may be located together in the cluster locus. Northern blot hybridization and RT-PCR analysis demonstrated that CRAD2 was expressed not in early embryonic stages, and not in embryonic stem cells, but instead in the gastrointestinal tract during later embryonic development and adult stage. In conclusion, we have presented the first complete structural analysis, including that of the promoter and chromosomal location, of a member of the retinol/androgen dehydrogenase subfamily of the group of the short-chain dehydrogenase/reductase (SDR) isozymes. Our findings will provide the basis for in-vitro or in-vivo studies concerning the regulation of retinol and androgen metabolism and enable determination of the mechanism of diseases related to retinol, retinal, retinoic acid, and androgen.
Collapse
MESH Headings
- Alcohol Oxidoreductases/genetics
- Amino Acid Sequence
- Animals
- Base Sequence
- Cells, Cultured
- Chromosome Mapping
- DNA/chemistry
- DNA/genetics
- Embryo, Mammalian/cytology
- Embryo, Mammalian/enzymology
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Enzymologic
- Genes/genetics
- In Situ Hybridization, Fluorescence
- Isoenzymes/genetics
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Sequence Analysis, DNA
- Tissue Distribution
- Transcription, Genetic
Collapse
Affiliation(s)
- K Tomita
- Department of Molecular Life Science, School of Medicine, Tokai University, Bohseidai, Isehara, 259-1193, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
146
|
Keicho N, Ohashi J, Tamiya G, Nakata K, Taguchi Y, Azuma A, Ohishi N, Emi M, Park MH, Inoko H, Tokunaga K, Kudoh S. Fine localization of a major disease-susceptibility locus for diffuse panbronchiolitis. Am J Hum Genet 2000; 66:501-7. [PMID: 10677310 PMCID: PMC1288103 DOI: 10.1086/302786] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Diffuse panbronchiolitis affecting East Asians is strongly associated with the class I human leukocyte antigen (HLA) alleles. Recent observations suggest that a major disease-susceptibility gene may be located between the HLA-B and HLA-A loci in the class I region of the major histocompatibility complex on chromosome 6. To test this possibility, we analyzed 14 polymorphic markers in 92 Japanese patients and 93 healthy controls. Of these, seven marker alleles, including HLA-B54 and HLA-A11, were significantly associated with the disease. Maximum-likelihood haplotype analysis and subsequent direct determination of individual haplotypes identified a group of disease-associated haplotypes, one of which contained all seven disease-associated marker alleles. Another haplotype, containing HLA-B*5504, was also associated with the disease. All these haplotypes seem to have diverged from a common ancestral haplotype in East Asians and share a specific segment containing three consecutive markers between the S and TFIIH loci in the class I region. Furthermore, one of the markers within the candidate region showed the highest delta value, indicating the strongest association. Of 20 Korean patients with diffuse panbronchiolitis, 17 also shared the combination of the disease-associated marker alleles within the candidate region. These results indicate that an HLA-associated major susceptibility gene for diffuse panbronchiolitis is probably located within the 200 kb in the class I region 300 kb telomeric of the HLA-B locus on the chromosome 6p21.3.
Collapse
Affiliation(s)
- N Keicho
- Department of Respiratory Medicine, Graduate School of Medicine, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
147
|
Shiina T, Tamiya G, Oka A, Takishima N, Yamagata T, Kikkawa E, Iwata K, Tomizawa M, Okuaki N, Kuwano Y, Watanabe K, Fukuzumi Y, Itakura S, Sugawara C, Ono A, Yamazaki M, Tashiro H, Ando A, Ikemura T, Soeda E, Kimura M, Bahram S, Inoko H. Molecular dynamics of MHC genesis unraveled by sequence analysis of the 1,796,938-bp HLA class I region. Proc Natl Acad Sci U S A 1999; 96:13282-7. [PMID: 10557312 PMCID: PMC23939 DOI: 10.1073/pnas.96.23.13282] [Citation(s) in RCA: 141] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The intensely studied MHC has become the paradigm for understanding the architectural evolution of vertebrate multigene families. The 4-Mb human MHC (also known as the HLA complex) encodes genes critically involved in the immune response, graft rejection, and disease susceptibility. Here we report the continuous 1,796,938-bp genomic sequence of the HLA class I region, linking genes between MICB and HLA-F. A total of 127 genes or potentially coding sequences were recognized within the analyzed sequence, establishing a high gene density of one per every 14.1 kb. The identification of 758 microsatellite provides tools for high-resolution mapping of HLA class I-associated disease genes. Most importantly, we establish that the repeated duplication and subsequent diversification of a minimal building block, MIC-HCGIX-3.8-1-P5-HCGIV-HLA class I-HCGII, engendered the present-day MHC. That the currently nonessential HLA-F and MICE genes have acted as progenitors to today's immune-competent HLA-ABC and MICA/B genes provides experimental evidence for evolution by "birth and death," which has general relevance to our understanding of the evolutionary forces driving vertebrate multigene families.
Collapse
Affiliation(s)
- T Shiina
- Department of Genetic Information, Division of Molecular Life Science, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa 259-1193, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
148
|
Oka A, Tamiya G, Tomizawa M, Ota M, Katsuyama Y, Makino S, Shiina T, Yoshitome M, Iizuka M, Sasao Y, Iwashita K, Kawakubo Y, Sugai J, Ozawa A, Ohkido M, Kimura M, Bahram S, Inoko H. Association analysis using refined microsatellite markers localizes a susceptibility locus for psoriasis vulgaris within a 111 kb segment telomeric to the HLA-C gene. Hum Mol Genet 1999; 8:2165-70. [PMID: 10545595 DOI: 10.1093/hmg/8.12.2165] [Citation(s) in RCA: 127] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The HLA-Cw6 antigen has been associated with psoriasis vulgaris despite racial and ethnic differences. However, it remains unclear whether it is the HLA-Cw6 antigen itself or a closely linked, hitherto unidentified, locus that predisposes to the disease. Here, in order to map the susceptibility locus for psoriasis vulgaris precisely within the HLA class I region, 11 polymorphic microsatellite markers distributed throughout a 1060 kb segment surrounding the HLA-C locus were subjected to association analysis in Japanese psoriasis vulgaris patients. Statistical analyses of the distribution and deviation from Hardy-Weinberg equilibrium of the allelic frequency at each micro-satellite locus revealed that the pathogenic gene for psoriasis vulgaris is located within a reduced interval of 111 kb spanning 89-200 kb telomeric of the HLA-C gene. In addition to three known genes, POU5F1, TCF19 and S, this 111 kb fragment contains four new, expressed genes identified in the course of our genomic sequencing of the entire HLA class I region. Therefore, these seven genes are the potential candidates for susceptibility to psoriasis vulgaris.
Collapse
Affiliation(s)
- A Oka
- Department of Genetic Information, Tokai University School of Medicine,Bohseidai, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
149
|
Tamiya G, Shiina T, Oka A, Tomizawa M, Ota M, Katsuyama Y, Yoshitome M, Makino S, Kimura M, Inoko H. New polymorphic microsatellite markers in the human MHC class I region. Tissue Antigens 1999; 54:221-8. [PMID: 10519358 DOI: 10.1034/j.1399-0039.1999.540302.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The human major histocompatibility complex (MHC) class I region is believed to contain a large number of genes encoding susceptible factors for diseases such as Behcet's disease, Graves disease and psoriasis vulgaris. To identify the causative genes of those diseases, we have conducted large-scale genomic sequencing and determined the 1.8 Mb entire HLA class I region from the MICB gene to the HLA-F gene. During the course of genomic sequencing, a total of 731 microsatellite sequences with dinucleotide to pentanucleotide repeats were found in this region. Previously, we reported that 26 microsatellites between MICB and S on the most centromeric side of the class I region, and between HSR1 and HLA-92/L in the midst of the class I region were highly polymorphic, and served as excellent genetic markers. In this paper, in order to fill the gaps with no known polymorphic microsatellites available in the HLA class I region, 12 new polymorphic microsatellite markers were recruited from the 1.8 Mb region including the remaining class I segments, namely between S and HSR1, and between HLA-92/L and HLA-F The average number of alleles at these new microsatellite loci was 8.2 with a polymorphism content value (PIC) of 0.63. These 38 markers in total almost uniformly interspersed in the HLA class I region will enable us to search precisely for the location of disease susceptible loci within the HLA class I region by association and for linkage analyses.
Collapse
Affiliation(s)
- G Tamiya
- Department of Genetic Information, Tokai University of Medicine, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
150
|
Ota M, Mizuki N, Katsuyama Y, Tamiya G, Shiina T, Oka A, Ando H, Kimura M, Goto K, Ohno S, Inoko H. The critical region for Behçet disease in the human major histocompatibility complex is reduced to a 46-kb segment centromeric of HLA-B, by association analysis using refined microsatellite mapping. Am J Hum Genet 1999; 64:1406-10. [PMID: 10205273 PMCID: PMC1377878 DOI: 10.1086/302364] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
The HLA-B51 allele is known to be associated with Behçet disease. Recently, we found a higher risk for Behçet disease in the MICA gene, 46 kb centromeric of HLA-B, by investigation of GCT repetitive polymorphism within exon 5 of MICA. The pathogenic gene causing Behçet disease, however, has remained uncertain. Here, eight polymorphic microsatellite markers, distributed over a 900-kb region surrounding the HLA-B locus, were subjected to association analysis for Behçet disease. Statistical studies of associated alleles detected on each microsatellite locus showed that the pathogenic gene for Behçet disease is most likely found within a 46-kb segment between the MICA and HLA-B genes. The results of this mapping study, and the results of an earlier study of ours, suggest that MICA is a strong candidate gene for the development of Behçet disease.
Collapse
Affiliation(s)
- M Ota
- Departments of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|