九州大学 研究者情報
論文一覧
柴田 弘紀(しばた ひろき) データ更新日:2023.06.27

准教授 /  生体防御医学研究所 附属高深度オミクスサイエンスセンター システム生命科学府 生命医科学講座


原著論文
1. Matsuno Y, Torisu T, Umeno J, Shibata H, Hirano A, Fuyuno Y, Okamoto Y, Fujioka S, Kawasaki K, Moriyama T, Nagasue T, Zeze K, Hirakawa Y, Kawatoko S, Yutaka Koga Y, Oda Y, Esaki M, Kitazono T., One-year clinical efficacy and safety of indigo naturalis for active ulcerative colitis: a real-world prospective study, Intest Res., 20, 2, 260-268, 2022.04, Background/Aims: Recent studies suggested a favorable effect of indigo naturalis (IN) in inducing remission for refractory ul- cerative colitis (UC), however, the maintenance effect of IN for patients with UC remains unknown. Therefore, we conducted a prospective uncontrolled open-label study to analyze the efficacy and safety of IN for patients with UC. Methods: Patients with moderate to severe active UC (clinical activity index [CAI] ≥ 8) took 2 g/day of IN for 52 weeks. CAI at weeks 0, 4, 8, and 52 and Mayo endoscopic subscore (MES) and Geboes score (GS) at weeks 0, 4, and 52 were assessed. Clinical remission (CAI ≤ 4), mucosal healing (MES ≤ 1), and histological healing (GS ≤ 1) rates at each assessment were evaluated. Overall adverse events (AEs) during study period were also evaluated. The impact of IN on mucosal microbial composition was assessed using 16S ribosomal RNA gene sequences. Results: Thirty-three patients were enrolled. The rates of clinical remission at weeks 4, 8, and 52 were 67%, 76%, and 73%, respectively. The rates of mucosal healing at weeks 4 and 52 were 48% and 70%, respectively. AEs occurred in 17 patients (51.5%) during follow-up. Four patients (12.1%) showed severe AEs, among whom 3 manifested acute colitis. No significant alteration in the mucosal microbial composition was observed with IN treatment. Conclusions: One-year treatment of moderate to severe UC with IN was effective. IN might be a promising therapeutic option for maintaining remis- sion in UC, although the relatively high rate of AEs should be considered. (Intest Res 2022;20:260-268).
2. Isomoto A, Shoguchi E, Hisata K, Inoue J, Sun Y, Inaba K, Satoh N, Ogawa T, Shibata H., Active expression of genes for protein modification enzymes in the venom gland of habu snakes, Toxins (Basel), 14, 300, 2022.04, Genes encoding snake venom toxins have been studied extensively. However, genes involved in the modification and functioning of venom proteins are little known. Protobothrops is a genus of pit vipers, which are venomous and inhabit the Nansei (Southwest) islands of Japan, Taiwan China, Vietnam, Thailand, Myanmar, Nepal, Bhutan, and India. Our previous study decoded the genome of Protobothrops flavoviridis, a species endemic to the Nansei Islands, Japan, and revealed unique evolutionary processes of some venom genes. In this study, we analyzed genes that are highly expressed in venom glands to survey genes for candidate enzymes or chaperone proteins involved in toxin folding and modification. We found that, in addition to genes that encode venom proteins and ribosomal proteins, genes that encode protein disulfide isomerase (PDI) family members (orthologs of human P4HB and PDIA3), Selenoprotein M (SELENOM), and Calreticulin (CALR) are highly expressed in venom glands. Since these enzymes or chaperones are involved in protein modification and potentially possess protein folding functions, we propose that P4HB, SELENOM, CALR, and PDIA3 encode candidate enzymes or chaperones to confer toxic functions upon the venom transcriptome..
3. Nagasue T, Hirano A, Torisu T, Umeno J, Shibata H, Moriyama T, Kawasaki K, Fujioka S, Fuyuno Y, Matsuno Y, Esaki M, Kitazono T., The compositional structure of the small intestinal microbial community via balloon-assisted enteroscopy, Digestion, 8, 1, 1-11, 2022.04, Introduction: An association has been found between human-gut microbiota and various diseases (e.g., metabolic disease) by analyzing fecal or colonic microbiota. Despite the importance of the small intestinal microbiota, sampling difficulties prevent its full analysis. We investigated the composition and metagenomic functions of microbiota along the small intestine and compared them with the microbiota from feces and from other gastrointestinal (GI) sites. Methods: Mucosal samples from the six GI sites (stomach, duodenum, distal jejunum, proximal ileum, terminal ileum, and rectum) were collected under balloon-assisted enteroscopy. Fecal samples were collected from all participants. The microbial structures and metagenomic functions of the small intestinal mucosal microbiota were compared with those from feces and other GI sites using 16S ribosomal RNA gene sequencing. Results: We analyzed 133 samples from 29 participants. Microbial beta diversity analysis showed that the jejunum and ileum differed significantly from the lower GI tract and the feces (p
4. Fan L, Miura S, Shimojo T, Sugino H, Fujioka R, Shibata H., A novel 1-bp deletion variant in DAG1 in Japanese familial asymptomatic hyper-CK-emia, Hum Genome Var., 9, 1, 4, 2022.01, Asymptomatic hyper-CK-emia (ASCK) is characterized by persistent elevation of creatine kinase (CK) in serum without any neurological symptoms. We ascertained a two-generation family of ASCK patients without clear neurological abnormalities except for the high levels of serum CK (810.5 ± 522.4 U/L). We identified a novel 1-bp deletion variant in the DAG1 gene shared by the patients in the family (NM_001177639: exon 3: c.930delC:p.R311Gfs*70). The variant causes premature termination of translation at codon 477, resulting in a protein product completely devoid of the essential DAG1 domain. Since ASCK has been associated with DAG1 in only one case carrying compound heterozygous missense variants, our new finding of a novel 1-bp deletion revealed the previously unknown dominant effect of DAG1 on ASCK..
5. Shibata E, Morita K, Kayamori K, Tange S, Shibata H, Harazono Y, Michi Y, Ikeda T, Harada H, Imoto I, Yoda T., Detection of novel fusion genes by next generation sequencing-based targeted RNA-sequencing analysis in adenoid cystic carcinoma of head and neck., Oral Surg Oral Med Oral Pathol Oral Radiol., 132, 4, 426-433, 2021.10, Objective. Adenoid cystic carcinoma (AdCC) is a rare, indolent salivary gland tumor that is reported to be driven by fusion genes. However, MYB/MYBL1-NFIB fusions have been detected in only Study Design. We investigated 20 AdCC cases using a targeted RNA-sequencing panel to identify gene fusions and performed qRT-PCR to assess MYB, MYBL1, and NFIB expression levels.
Results. A total of 36 fusion transcripts in 15 cases were detected and validated by Sanger sequencing. The MYB-NFIB and MYBL1-NFIB fusion genes were detected in nine and three cases, respectively, in a mutually exclusive manner. Furthermore, novel gene fusions, namely NFIB-EPB41L2, MAP7-NFIB, NFIB-MCMDC2, MYBL1-C8orf34, C8orf34-NFIB, and NFIB-CASC20, were identified. Among them, NFIB-EPB41L2 and NFIB-MCMDC2 are thought to activate MYB and MYBL1 expression, respectively, through the insertion of a genomic segment in proximity to MYB and MYBL1 genes, respectively..
6. Tanaka T, Matsuno Y, Torisu T, Shibata H, Hirano A, Umeno J, Kawasaki K, Fujioka S, Fuyuno Y, Moriyama T, Esaki M, Kitazono T., Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma., Medicine (Baltimore) 100 (38): e27287 (2021)., 100, 38, e27287, 2021.09, To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.
Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.
Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants’ microbiota.
H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways “replication and repair,” “translation,” and “nucleotide metabolism” were downregulated in MALT lymphoma patients.
H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma..
7. Morikawa T, Miura S, Tateishi T, Noda K, Shibata H., A Japanese hereditary spastic paraplegia family with a rare nonsynonymous variant in the SPAST gene., Hum Genome Var., 8, 21, 2021.05, Spastic paraplegia (SPG) type 4 is an autosomal dominant SPG caused by functional variants in the SPAST gene. We examined a Japanese family with three autosomal dominant SPG patients. These patients presented with typical symptoms of SPG, such as spasticity of the lower limbs. We identified a rare nonsynonymous variant, NM_014946.4: c.1252G>A [p.Glu418Lys], in all three family members. This variant has previously been reported in a Russian SPG family as a “likely pathogenic” variant. Ascertainment of additional patients carrying this variant in an unrelated Japanese SPG family further supports its pathogenicity. Molecular diagnosis of SPG4 in this family with hereditary spastic paraplegia is confirmed. .
8. Miura S, Shimojo T, Morikawa T, Kamada T, Uchiyama Y, Kurata S, Fujioka R, Shibata H., Familial paroxysmal kinesigenic dyskinesia with a novel missense variant (Arg2866Trp) in NBEA., J Hum Genet., 66, 8, 805-811, 2021.03, Paroxysmal kinesigenic dyskinesia (PKD) is a movement disorder characterized by episodic involuntary movement attacks triggered by sudden movements, acceleration, or intention to move. We ascertained two Japanese familial cases with PKD. The proband is a 22-year-old woman who had noted sudden brief ( C [p.Gln2992His] in FAT2 and NM_015678: c.8596C > T [p.Arg2866Trp] in NBEA). Real time quantitative PCR analysis of Nbea mRNA levels in the developing rat brain revealed peak at postnatal day 28 and decline at postnatal day 56. This result might match the most common clinical course of PKD from the point of view of the most common age at remission. NBEA has been reported to be responsible for neurodevelopmental disease accompanied by epilepsy. We concluded the variant in NBEA most likely to be responsible for our familial cases of PKD..
9. Morikawa T, Ohishi H, Kosaka K, Shimojo T, Nagano A, Taniguchi I, Fujioka R, Moriyama K, Unoki M, Takahashi M, Nakao M, Izumi Y, Bamba T, Sasaki H, Miura S, Shibata H. , Ddhd1 knockout mouse as a model for familial spastic paraplegia, Biosci Rep., 41, 2, BSR20204171, 2021.02, We have previously reported a novel homozygous 4-bp deletion in DDHD1 as the respon- sible variant for spastic paraplegia type 28 (SPG28; OMIM#609340). The variant causes a frameshift, resulting in a functionally null allele in the patient. DDHD1 encodes phospholi- pase A1 (PLA1) catalyzing phosphatidylinositol to lysophosphatidylinositol (LPI). To clarify the pathogenic mechanism of SPG28, we established Ddhd1 knockout mice (Ddhd1[−/−]) carrying a 5-bp deletion in Ddhd1, resulting in a premature termination of translation at a position similar to that of the patient. We observed a significant decrease in foot–base angle (FBA) in aged Ddhd1(−/−) (24 months of age) and a significant decrease in LPI 20:4 (sn-2) in Ddhd1(−/−) cerebra (26 months of age). These changes in FBA were not observed in 14 months of age. We also observed significant changes of expression levels of 22 genes in the Ddhd1(−/−) cerebra (26 months of age). Gene Ontology (GO) terms relating to the nervous system and cell–cell communications were significantly enriched. We conclude that the re- duced signaling of LPI 20:4 (sn-2) by PLA1 dysfunction is responsible for the locomotive abnormality in SPG28, further suggesting that the reduction of downstream signaling such as GPR55 which is agonized by LPI is involved in the pathogenesis of SPG28..
10. Miura S, Kosaka K, Shimojo T, Matsuura E, Noda K, Fujioka R, Mori S, Umehara F, Iwaki T, Yamamoto K, Saitsu H, Shibata H., Intronic variant in IQGAP3 associated with hereditary neuropathy with proximal lower dominancy, urinary disturbance, and paroxysmal dry cough., J Hum Genet., 65, 9, 717-725, 2020.09, In 2008, we reported a clinically and genetically new type of autosomal dominant disorder of motor and sensory neuropathy with proximal dominancy in the lower extremities, urinary disturbance, and paroxysmal dry cough. To identify the nucleotide variant causative of this disease, we reanalyzed the linkage of the original Japanese pedigree including seven newly ascertained subjects with updated information. We assigned the locus of the disease to 1p13.3-q23 (maximum logarithm-of-odds score = 2.71). Exome sequencing for five patients and one healthy relative from the pedigree revealed 2526 patient-specific single- nucleotide variants (SNVs). By rigorous filtering processes using public databases, our linkage results, and functional prediction, followed by Sanger sequencing of the pedigree and 520 healthy Japanese individuals, we identified an intronic SNV in IQGAP3, a gene known to be associated with neurite outgrowth. Upon pathological examination of the sural nerve, moderate, chronic, mainly axonal neuropathy was observed. By histochemical analyses, we observed a patient-specific increase of IQGAP3 expression in the sural nerve. We concluded that the variant of IQGAP3 is associated with the disease in our pedigree..
11. Gakuhari T, Nakagome S, Rasmussen S, Allentoft M, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H., Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations., Commun Biol., 3, 1, 437-437, 2020.08, Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia..
12. Zeze K, Hirano A, Torisu T, Esaki M, Shibata H, Moriyama T, Umeno J, Fujioka S, Okamoto Y, Fuyuno Y, Matsuno Y, Kitazono T., Mucosal dysbiosis in patients with gastrointestinal follicular lymphoma., Hematol Oncol., 38, 2, 181-188, 2020.04, Because the pathogenesis of gastrointestinal follicular lymphoma (GI-FL) remains unclear, no standardized treatment strategy has been established. Of the gastrointes- tinal lymphomas, gastric mucosa-associated lymphoid tissue lymphomas are strongly associated with Helicobacter pylori; hence, the microbiota may be involved in GI-FL pathogenesis. However, the association between GI-FL and the microbiota remains uninvestigated. Therefore, we compared the mucosal microbiotas of GI-FL patients with those of controls to identify microbiota changes in GI-FL patients. Mucosal biopsy sam- ples were obtained from the second portion of the duodenum from 20 GI-FL patients with duodenal lesions and 20 controls. Subsequent 16S rRNA gene sequencing was per- formed on these samples. QIIME pipeline and LEfSe software were used to analyze the microbiota. The GI-FL patients had significantly lower alpha diversity (P = .049) than did the controls, with significant differences in the microbial composition (P = .023) evalu- ated by the beta diversity metrics between the two groups. Comparing the taxonomic compositions indicated that the genera Sporomusa, Rothia, and Prevotella and the family Gemellaceae were significantly less abundant in the GI-FL patients than in the controls. GI-FL patients presented altered duodenal mucosal microbial compositions, suggesting that the microbiota might be involved in the GI-FL pathogenesis..
13. Inamaru K, Takeuchi A, Maeda M, Shibata H, Fukumaki Y, Oda-Ueda N, Hattori S, Ohno M, Chijiwa T., Discovery of the gene encoding novel Small Serum Protein (SSP), SSP-6, of Protobothrops flavoviridis snake and evolutionary pathway of SSPs., Toxins (Basel), 12, 3, 177-177, 2020.03, Small serum proteins (SSPs) are low-molecular-weight proteins in snake serum with affinities for various venom proteins. Five SSPs, PfSSP-1 through PfSSP-5, have been reported in Protobothrops flavoviridis (“habu”, Pf) serum so far. Recently, we reported that the five genes encoding these PfSSPs are arranged in tandem on a single chromosome. However, the physiological functions and evolutionary origins of the five SSPs remain poorly understood. In a detailed analysis of the habu draft genome, we found a gene encoding a novel SSP, SSP-6. Structural analysis of the genes encoding SSPs and their genomic arrangement revealed the following: (1) SSP-6 forms a third SSP subgroup; (2) SSP-5 and SSP-6 were present in all snake genomes before the divergence of non- venomous and venomous snakes, while SSP-4 was acquired only by venomous snakes; (3) the composition of paralogous SSP genes in snake genomes seems to reflect snake habitat differences; and (4) the evolutionary emergence of SSP genes is probably related to the physiological functions of SSPs, with an initial snake repertoire of SSP-6 and SSP-5. SSP-4 and its derivative, SSP-3, as well as SSP-1 and SSP-2, appear to be venom-related and were acquired later..
14. Suryamohan K, Krishnankutty SP, Guillory J, Jevit M, Schroeder M, Wu M, Kuriakose B, Perumal RC, Koludarov I, Mathew OK, Goldstein LD, Senger K, Vargas D, Chaudhuri S, Muraleedharan M, Goel R, Chen YJJ, Ratan A, Liu P, Faherty B, Shibata H, Baca M, Sagolla M, Ziai J, Wright GA, Stinson J, Kirkpatrick DS, Hannoush RN, Durinck S, Modrusan Z, Stawiski EW, Wiley K, Raudsepp T, Kini RM, Zachariah A, Seshagiri S., The Indian cobra genome and transcriptome enables comprehensive identification of venom toxins., Nat Genet., 52, 106-117, 2020.01, Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome- enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant anti- venom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake. Our assembly has a scaffold N50 of 223.35 Mb, with 19 scaffolds containing 95% of the genome. Of the 23,248 predicted protein-coding genes, 12,346 venom-gland-expressed genes constitute the ‘venom-ome’ and this included 139 genes from 33 toxin families. Among the 139 toxin genes were 19 ‘venom-ome-specific toxins’ (VSTs) that showed venom- gland-specific expression, and these probably encode the minimal core venom effector proteins. Synthetic venom reconstituted through recombinant VST expression will aid in the rapid development of safe and effective synthetic antivenom. Additionally, our genome could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery..
15. Ogawa T, Oda-Ueda N, Hisata K, Nakamura H, Chijiwa T, Hattori S, Isomoto A, Yugeta H, Yamasaki S, Fukumaki Y, Ohno M, Satoh N, Shibata H., Alternative mRNA splicing in three venom families underlying a possible production of divergent venom proteins of the Habu snake, Protobothrops flavoviridis., Toxins, 11, 10, 581-581, 2019.10, Snake venoms are complex mixtures of toxic proteins encoded by various gene families that function synergistically to incapacitate prey. A huge repertoire of snake venom genes and proteins have been reported, and alternative splicing is suggested to be involved in the production of divergent gene transcripts. However, a genome-wide survey of the transcript repertoire and the extent of alternative splicing still remains to be determined. In this study, the comprehensive analysis of transcriptomes in the venom gland was achieved by using PacBio sequencing. Extensive alternative splicing was observed in three venom protein gene families, metalloproteinase (MP), serine protease (SP), and vascular endothelial growth factors (VEGF). Eleven MP and SP genes and a VEGF gene are expressed as a total of 81, 61, and 8 transcript variants, respectively. In the MP gene family, individual genes are transcribed into different classes of MPs by alternative splicing. We also observed trans-splicing among the clustered SP genes. No other venom genes as well as non-venom counterpart genes exhibited alternative splicing. Our results thus indicate a potential contribution of mRNA alternative and trans-splicing in the production of highly variable transcripts of venom genes in the habu snake..
16. Chijiwa T, Inamaru K, Takeuchi A, Maeda M, Yamaguchi K, Shibata H, Hattori S, Oda-Ueda N, Ohno M., Unique structure (construction and configuration) and evolution of the array of small serum protein genes of Protobothrops flavoviridis snake., Biosci Rep., 39, 7, BSR20190560-BSR20190560, The nucleotide sequence of Protobothrops flavoviridis (Pf) 30534 bp genome segment which contains genes encoding small serum proteins (SSPs) was deciphered. The genome segment contained five SSP genes (PfSSPs), PfSSP-4, PfSSP-5, PfSSP-1, PfSSP-2, and PfSSP-3 in this order and had characteristic configuration and constructions of the particu- lar nucleotide sequences inserted. Comparison between the configurations of the inserted chicken repeat-1 (CR1) fragments of P. flavoviridis and Ophiophagus hannah (Oh) showed that the nucleotide segment encompassing from PfSSP-1 to PfSSP-2 was inverted. The in- active form of PfSSP-1, named PfSSP-1δ(ψ), found in the intergenic region (I-Reg) between PfSSP-5 and PfSSP-1 had also been destroyed by insertions of the plural long interspersed nuclear elements (LINEs) and DNA transposons. The L2 LINE inserted into the third intron or the particular repetitive sequences inserted into the second intron structurally divided five PfSSPs into two subgroups, the Long SSP subgroup of PfSSP-1, PfSSP-2 and PfSSP-5 or the Short SSP subgroup of PfSSP-3 and PfSSP-4. The mathematical analysis also showed that PfSSPs of the Long SSP subgroup evolved alternately in an accelerated and neutral manner, whereas those of the Short SSP subgroup evolved in an accelerated manner. More- over, the ortholog analysis of SSPs of various snakes showed that the evolutionary emerging order of SSPs was as follows: SSP-5, SSP-4, SSP-2, SSP-1, and SSP-3. The unique inter- pretation about accelerated evolution and the novel idea that the transposable elements such as LINEs and DNA transposons are involved in maintaining the host genome besides its own transposition natures were proposed., 2019.07.
17. Ryuta Fujioka, Junko Nagai, Yoshihiro Yamanishi, Hiroki Shibata, Correlation analysis between thyroid-related hormones and the plasma concentration of amino acids., Bulletin of Bepppu University Junior College, 38, 17-23, 2019.02, Thyroid-related hormones (TRHs) are involved the regulation of endocrine function and metabolic processes of the thyroid gland, and hyperthyroidism is known to cause tremors, weight loss, and excessive sweating. As a part of examining the relationship between TRHs and the metabolism of amino acid in the plasma, we analyzed the correlation between TRHs and plasma levels of amino acids using samples from seven healthy volunteers. We measured three types of TRHs: thyroid-stimulating hormone (TSH), free triiodothyronine (FT3), and free thyroxine (FT4) in addition to 39 different amino acids including the 20 proteinogenic amino acids in the plasma collected from the healthy volunteers. We observed significant correlations between levels of taurine and FT4 (p = 0.018), valine and FT4 (p = 0.043), hydroxyproline and TSH (p = 0.049), and citrulline and TSH (p = 0.011). We also observed a correlation between the levels of hydroxyproline and citruline (p = 0.0079). These results suggest that the interaction between hydroxyproline and citrulline may be involved in plasma amino acid metabolism of TRHs..
18. Shiroh Miura, Kengo Kosaka, Ryuta Fujioka, Yusuke Uchiyama, Tomofumi Shimojo, Takuya Morikawa, Azusa Irie, Takayuki Taniwaki, Hiroki Shibata, TDRKH is a candidate gene responsible for an autosomal dominant distal hereditary motor neuropathy., European Journal of Medical Genetics, In press., 2018.11, Spinocerebellar ataxia 27 (SCA27) is an autosomal dominant SCA caused by variants in the fibroblast growth factor 14 (FGF14) gene. We examined a Japanese SCA patient whose deceased father also suffered from SCA. The patient was a 63-year-old male. He graduated from junior high school but received no further education. The predominant complaint was slowly progressive dysarthria and gait disturbance, which appeared at age 47. He showed pathological saccadic dysmetria, saccadic intrusions into smooth pursuit eye movements, dysarthria, and limb and truncal ataxia. His gait was wide-based but he did not require a walking stick. Limb muscle strength was intact. Deep tendon reflexes were normal or slightly reduced. Pathological reflexes were absent. He demonstrated mildly impaired vibration sense in the lower limbs. There was no urinary dysfunction. Brain MRI showed cerebellar atrophy without brainstem involvement. We first confirmed the absence of repeat expansion in genes known to be responsible for SCAs 1–3, 6–8, 10, 12, 17, 36 and dentatorubral-pallidoluysian atrophy. By exome analysis, we identified a novel heterozygous variant (NM_004115, c.529A>T; Lys177X) in exon 4 of the FGF14 gene. This variant is expected to generate a truncated FGF14 protein lacking the heparin binding sites, those are likely to modify the activity of FGF14. We confirmed the absence of the variant in 502 healthy Japanese individuals by Sanger sequencing. There is no record of the variant in public databases. We conclude that the novel variation in FGF14 is causative for SCA27 in this patient..
19. Shiroh Miura, Kengo Kosaka, Ryuta Fujioka, Yusuke Uchiyama, Tomofumi Shimojo, Takuya Morikawa, Azusa Irie, Takayuki Taniwaki, Hiroki Shibata, Spinocerebellar ataxia 27 with a novel nonsense variant (Lys177X) in FGF14., European Journal of Medical Genetics, 62: 172-176., 2018.07, Spinocerebellar ataxia 27 (SCA27) is an autosomal dominant SCA caused by variants in the fibroblast growth factor 14 (FGF14) gene. We examined a Japanese SCA patient whose deceased father also suffered from SCA. The patient was a 63-year-old male. He graduated from junior high school but received no further education. The predominant complaint was slowly progressive dysarthria and gait disturbance, which appeared at age 47. He showed pathological saccadic dysmetria, saccadic intrusions into smooth pursuit eye movements, dysarthria, and limb and truncal ataxia. His gait was wide-based but he did not require a walking stick. Limb muscle strength was intact. Deep tendon reflexes were normal or slightly reduced. Pathological reflexes were absent. He demonstrated mildly impaired vibration sense in the lower limbs. There was no urinary dysfunction. Brain MRI showed cerebellar atrophy without brainstem involvement. We first confirmed the absence of repeat expansion in genes known to be responsible for SCAs 1–3, 6–8, 10, 12, 17, 36 and dentatorubral-pallidoluysian atrophy. By exome analysis, we identified a novel heterozygous variant (NM_004115, c.529A>T; Lys177X) in exon 4 of the FGF14 gene. This variant is expected to generate a truncated FGF14 protein lacking the heparin binding sites, those are likely to modify the activity of FGF14. We confirmed the absence of the variant in 502 healthy Japanese individuals by Sanger sequencing. There is no record of the variant in public databases. We conclude that the novel variation in FGF14 is causative for SCA27 in this patient..
20. Shuzo Iwanishi, Shohei Zaitsu, Hiroki Shibata, Eiji Nitasaka, An albino mutant of the Japanese rat snake (Elaphe climacophora) carries a nonsense mutation in the tyrosinase gene. , Genes & Genetic Systems, 93: 163-167., 2018.07, The Japanese rat snake (Elaphe climacophora) is a common species in Japan and is widely distributed across the Japanese islands. An albino mutant of the Japanese rat snake (“pet trade” albino) has been bred and traded by hobbyists for around two decades because of its remarkable light-yellowish coloration with red eyes, attributable to a lack of melanin. Another albino Japanese rat snake mutant found in a natural population of the Japanese rat snake at high frequency in Iwakuni City, Yamaguchi Prefecture is known as “Iwakuni no Shirohebi”. It has been conserved by the government as a natural monument. The Iwakuni albino also lacks melanin, having light-yellowish body coloration and red eyes. Albino mutants of several organisms have been studied, and mutation of the tyrosinase gene (TYR) is responsible for this phenotype. By determining the sequence of the TYR coding region of the pet trade albino, we identified a nonsense mutation in the second exon. Furthermore, RT-PCR revealed that TYR transcripts were not detected in this snake. These findings suggest that mutation of TYR is responsible for the albino phenotype of the pet trade line of the Japanese rat snake. However, the Iwakuni albino did not share this TYR mutation; thus, these two albino lines differ in their origins..
21. Hiroki Shibata, Takahito Chijiwa, Naoko Oda-Ueda, Hitomi Nakamura, Kazuaki Yamaguchi, Shousaku Hattori, Kazumi Matsubara, Yoichi Matsuda, Akifumi Yamashita, Akiko Isomoto, Kazuki Mori, Kosuke Tashiro, Satoru Kuhara, Shinichi Yamasaki, Manabu Fujie, Hiroki Goto, Ryo Koyanagi, Takeshi Takeuchi, Yasuyuki Fukumaki, Motonori Ohno, Eiichi Shoguchi, Kanako Hisata, Noriyuki Satoh, Tomohisa Ogawa, The habu genome reveals an evolutionary background of venom protein genes., Sceintific Reports, 8: 11300., 2018.07, Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 nonvenom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition..
22. Kae Koganebuchi, Takashi Gakuhari, Hirohiko Takeshima, Kimitoshi Sato, Kiyotaka Fujii, Toshihiro Kumabe, Satoshi Kasagi, Takehiro Sato, Atsushi Tajima, Hiroki Shibata, Motoyuki Ogawa, Hiroki Oota, A new targeted capture method using bacterial artificial chromosome (BAC) libraries as baits for sequencing relatively large genes, PLoS One, 13(7): e0200170., 2018.07, To analyze a specific genome region using next-generation sequencing technologies, the enrichment of DNA libraries with targeted capture methods has been standardized. For enrichment of mitochondrial genome, a previous study developed an original targeted capture method that use baits constructed from long-range polymerase chain reaction (PCR) amplicons, common laboratory reagents, and equipment. In this study, a new targeted capture method is presented, that of bacterial artificial chromosome (BAC) double capture (BDC), modifying the previous method, but using BAC libraries as baits for sequencing a relatively large gene. We applied the BDC approach for the 214 kb autosomal region, ring finger protein 213, which is the susceptibility gene of moyamoya disease (MMD). To evaluate the reliability of BDC, cost and data quality were compared with those of a commercial kit. While the ratio of duplicate reads was higher, the cost was less than that of the commercial kit. The data quality was sufficiently the same as that of the kit. Thus, BDC can be an easy, low-cost, and useful method for analyzing individual genome regions with substantial length..
23. Hugh McColl1, Fernando Racimo, Lasse Vinner, Fabrice Demeter, Takashi Gakuhari, J. Víctor Moreno-Mayar, George van Driem, Uffe Gram Wilken, Andaine Seguin-Orlando, Constanza de la Fuente Castro, Sally Wasef, Rasmi Shoocongdej, Viengkeo Souksavatdy, Thongsa Sayavongkhamdy, Mohd Mokhtar Saidin, Morten E. Allentoft, Takehiro Sato, Anna-Sapfo Malaspinas, Farhang A. Aghakhanian, Thorfinn Korneliussen, Ana Prohaska, Ashot Margaryan, Peter de Barros Damgaard, Supannee Kaewsutthi, Patcharee Lertrit, Thi Mai Huong Nguyen, Hsiao-chun Hung, Thi Minh Tran, Huu Nghia Truong, Giang Hai Nguyen, Shaiful Shahidan, Ketut Wiradnyana, Hiromi Matsumae, Nobuo Shigehara, Minoru Yoneda, Hajime Ishida, Tadayuki Masuyama, Yasuhiro Yamada, Atsushi Tajima, Hiroki Shibata, Atsushi Toyoda, Tsunehiko Hanihara, Shigeki Nakagome, Thibaut Deviese, Anne-Marie Bacon, Philippe Duringer, Jean-Luc Ponche, Laura Shackelford, Elise Patole-Edoumba, Anh Tuan Nguyen, Bérénice Bellina-Pryce, Jean-Christophe Galipaud, Rebecca Kinaston, Hallie Buckley, Christophe Pottier, Simon Rasmussen, Tom Higham, Robert A. Foley, Marta Mirazón Lahr, Ludovic Orlando, Martin Sikora, Maude E. Phipps, Hiroki Oota, Charles Higham, David M. Lambert, Eske Willerslev, Ancient genomics reveals four prehistoric migration waves into Southeast Asia. , Science, 361: 88-92., 2018.07, The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA,1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory..
24. Atushi Hirano, Junji Umeno, Yasuharu Okamoto, Hiroki Shibata, Yoshitoshi Ogura, Tomohiko Moriyama, Takehiro Torisu, Shin Fujioka, Yuta Fuyuno, Yutaka Kawarabayashi, Takayuki Matsumoto, Takanari Kitazono, Motohiro Esaki , A comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis., J Gastroenterol Hepatol., In press., 2018.02, Background and Aim: The gut microbiota is suggested to play an important role in the pathogenesis of ulcerative colitis (UC). However, interindividual and spatial variations hamper the identification of UC-related changes. We thus investigated paired mucosa-associated microbiota obtained from both inflamed and non-inflamed sites of UC patients and corresponding sites of non-inflammatory bowel disease (IBD) controls.
Methods: Mucosal biopsies of both inflamed and non-inflamed sites were obtained from 14 patients with active UC of the left-sided or proctitis type. Paired mucosal biopsies of the corresponding sites were obtained from 14 non-IBD controls. The microbial community structure was investigated using 16S ribosomal RNA gene sequences, followed by data analysis using QIIME and LEfSe softwares.
Results: Microbial alpha diversity in both inflamed and non-inflamed sites was significantly lower in UC patients compared with non-IBD controls. There were more microbes of the genus Cloacibacterium and the Tissierellaceae family, and there were less microbes of the genus Neisseria at the inflamed site when compared with the non-inflamed site in UC patients. Decreased abundance of the genera Prevotella, Eubacterium, Neisseria, Leptotrichia, Bilophila, Desulfovibrio, and Butyricimonas was evident at the inflamed site of UC patients compared with the corresponding site of non-IBD controls. Among these taxa, the genera Prevotella and Butyricimonas were also less abundant at the noninflamed site of UC patients compared with the corresponding site in non-IBD controls.
Conclusions: Mucosal microbial dysbiosis occurs at both inflamed and non-inflamed sites in UC patients. The taxa showing altered abundance in UC patients might mediate colonic inflammation..
25. Chihiro Iwaya, Hidetoshi Kitajima, Ken Yamamoto, Yasutaka Maeda, Noriyuki Sonoda, Hiroki Shibata, Toyoshi Inoguchi. , DNA methylation of the Klf14 gene region on whole blood provide prediction for the chronic inflammation at the adipose tissue. , Biochem Biophys Res Commun., 497, 908-915, 2018.02, Krüppel-Like Factor 14 (KLF14) gene, which appears to be a master regulator of gene expression in the adipose tissue and have previously been associated with BMI and Type 2 diabetes (T2D) by large genome-wide association studies. In order to find predictive biomarkers for the development of T2D, it is necessary to take epigenomic changes affected by environmental factors into account. This study focuses on ageing and obesity, which are T2D risk factors, and examines epigenetic changes and inflammatory changes. We investigated DNA methylation changes in the Klf14 promoter region in different organs of mice for comparing aging and weight. We found that methylation levels of these sites were increased with aging and weight in the spleen, the adipose tissue, the kidney, the lung, the colon and the whole blood cells. In addition, in the spleen, the adipose tissue and the whole blood, these epigenetic changes were also significantly associated with inflammatory levels. Moreover, not only Klf14, but also expression levels of some downstream genes were decreased with methylation in the spleen, the adipose tissue and the whole blood cells. Taken together, our results suggest that methylation changes of Klf14 in those tissues may be associated with changes in gene expression and inflammation on the adipose tissue of obesity and T2D. In addition, the methylation changes in the whole blood cells may serve as a predictive epigenetic biomarker for the development of T2D..
26. Fuminori Yamaji, Akio Soeda, Hiroki Shibata, Takuya Morikawa, Kodai Suzuki, Shozo Yoshida, Shinji Ogura., A new mutation of congenital methemoglobinemia exacerbated after methylene blue treatment., Acute Med Surg., 5, 199-201, 2018.02, Case: Methylene blue is useful for the treatment of methemoglobinemia. However, even after the patient’s methemoglobin (metHb)
rate has improved, careful observation is important because they could have undiagnosed congenital methemoglobinemia. In this
case, a 67-year-old man underwent gastrointestinal endoscopy with the use of lidocaine for local anesthesia. During the examination,
he complained of dyspnea and had low SpO2 despite normal PaO2 and SaO2. He was transferred to our department as a suspected
case of acquired methemoglobinemia.
Outcome: The patient’s metHb level was 26.2%. We administered methylene blue i.v. and his metHb level subsequently decreased
to 1.6%. However, his metHb level gradually increased to 18.2%, and we suspected that he had congenital methemoglobinemia. We
administered riboflavin and ascorbic acid orally, and his metHb level decreased to 6.4%. We also obtained genomic DNA from the
patient and identified a novel variant of CYB5R3.
Conclusion: We report a novel variant of congenital methemoglobinemia that deteriorated after methylene blue treatment..
27. Hiroki Shibata, Shuichi Sakata, Yuzo Hirano, Eiji Nitasaka, Ai Sakabe. , Facultative parthenogenesis validated by DNA analyses in the green anaconda (Eunectes murinus)., Plos ONE, 12, 12, e0189654, 2017.12, In reptiles, the mode of reproduction is typically sexual. However, facultative parthenogenesis occurs in some Squamata, such as Komodo dragon (Varanus komodoensis) and Burmese python (Python bivittatus). Here, we report facultative parthenogenesis in the green anaconda (Eunectes murinus). We found two fully developed female neonates and 17 undeveloped eggs in the oviduct of a female anaconda isolated from other individuals for eight years and two months at Ueno Zoo, Japan. To clarify the zygosity of the neonates, we analyzed 18 microsatellite markers of which 16 were informative. We observed only maternal alleles and no paternal alleles for all 16 markers. To examine the possibility of the long-term sperm storage, we estimated allele frequencies in a putative parental stock by genotyping five unrelated founders. If all founders, including the mother, are originated from a single Mendelian population, then the probability that the neonates were produced by sexual reproduction with an unrelated male via long-term sperm storage was infinitesimally small (2.31E-32 per clutch). We also examined samples from two additional offspring that the mother delivered eight years before her death. We consistently observed paternal alleles in these elder offspring, indicating that the mother had switched from sexual reproduction to asexual reproduction during the eight years of isolation. This is the first case of parthenogenesis in Eunectes to be validated by DNA analysis, and suggests that facultative parthenogenesis is widespread in the Boidae..
28. 藤岡竜太, 三浦史郎, 山田浩平, 柴田弘紀, 家族歴のない脊髄小脳失調症6型の遺伝学的解析, 別府大学短期大学紀要, 37, 87-91, 2018.02, 電位依存性カルシウムチャネルα1Aサブユニット遺伝子であるCACNA1A遺伝子上にあるDNAの三塩基配列CAGリピートの異常伸長が脊髄小脳失調症6型(Spinocerebellar ataxia type 6: SCA6)の発症に関わることが知られている。SCA6の原因遺伝子であるCACNA1A遺伝子上ではCAGリピート数が健常者では4から19, 罹患者では21から33となる。また、SCA6は家族歴のある常染色体優性遺伝性の罹患者が多く、日本では優性遺伝性の脊髄小脳失調症の約30%を占めている。本研究では孤発性(非遺伝性)のSCA6の罹患者および両親の末梢血検体を使用し、遺伝学的解析によるCAGリピート異常から家族歴の遺伝性を検証した。結果としてSCA6の罹患者はCAGリピートの異常伸長(変異アレルでリピート数23)が認められた。さらに遺伝学的解析により両親とも健常であるが、おそらく父親由来の正常アレルから罹患者の変異アレルに表現促進現象が起こったのではないかと示唆された。これらのことから孤発性の症例でも遺伝学的解析により原因の究明ができる可能性が考えられる。.
29. Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kazuhito Noda, Kengo Kosaka, Takayuki Taniwaki, Hiroki Shibata, A novel missense variation (Q220R) of GNB4 encoding a guanine nucleotide-binding protein, beta-4 in a Japanese autosomal dominant motor and sensory neuropathy family., European Journal of Medical Genetics, 60, 9, 474-478, 2016.06, Dominant intermediate CharcoteMarieeTooth disease F (CMTDIF) is an autosomal dominant hereditary form of CharcoteMarieeTooth disease (CMT) caused by variations in the guanine nucleotide-binding protein, subunit beta-4 gene (GNB4). We examined two Japanese familial cases with CMT. Case 1 was a 49-year-old male whose chief complaint was slowly progressive gait disturbance and limb dysesthesia that appeared at the age of 47. On neurological examination, he showed hyporeflexia or areflexia, distal limb muscle weakness, and distal sensory impairment with lower dominancy. Nerve conduction studies demonstrated demyelinating sensorimotor neuropathy with reduced action potentials in the lower limbs. Case 2 was an 80-year-old man, Case 1's father, who reported difficulty in riding a bicycle at the age of 76. On neurological examination, he showed areflexia in the upper and lower limbs. Distal sensory
impairment in the lower limbs was also observed. Nerve conduction studies revealed mainly axonal involvement. Exome sequencing identified a novel heterozygous nonsynonymous variant (NM_021629.3:c.659T > C [p.Gln220Arg]) in GNB4 exon 8, which is known to be responsible for CMT. Sanger sequencing confirmed that both patients are heterozygous for the variation, which causes an amino acid substitution, Gln220Arg, in the highly conserved region of the WD40 domain of GNB4. The frequency of this variant in the Exome Aggregation Consortium Database was 0.000008247, and we confirmed its absence in 502 Japanese control subjects. We conclude that this novel GNB4 variant is causative for CMTDIF in these patients, who represent the first record of the disease in the Japanese
population..
30. Itsuki Taniguchi, Chihiro Iwaya, Keizo Ohnaka, Hiroki Shibata, Ken Yamamoto, Genome-wide DNA methylation analysis reveals hypomethylation in the low-CpG promoter regions in lymphoblastoid cell lines., Human Genomics, 10.1186/s40246-017-0106-6, 11, 8-8, 2017.05, Background: Epidemiological studies of DNA methylation profiles may uncover the molecular mechanisms through
which genetic and environmental factors contribute to the risk of multifactorial diseases. There are two types of
commonly used DNA bioresources, peripheral blood cells (PBCs) and EBV-transformed lymphoblastoid cell lines (LCLs),
which are available for genetic epidemiological studies. Therefore, to extend our knowledge of the difference in DNA
methylation status between LCLs and PBCs is important in human population studies that use these DNA sources to
elucidate the epigenetic risks for multifactorial diseases. We analyzed the methylation status of the autosomes for 192
and 92 DNA samples that were obtained from PBCs and LCLs, respectively, using a human methylation 450 K array.
After excluding SNP-associated methylation sites and low-call sites, 400,240 sites were subjected to analysis using a
generalized linear model with cell type, sex, and age as the independent variables.
Results: We found that the large proportion of sites showed lower methylation levels in LCLs compared with PBCs,
which is consistent with previous reports. We also found that significantly different methylation sites tend to be located
on the outside of the CpG island and in a region relatively far from the transcription start site. Additionally, we
observed that the methylation change of the sites in the low-CpG promoter region was remarkable. Finally, it was
shown that the correlation between the chronological age and ageing-associated methylation sites in ELOVL2 and
FHL2 in the LCLs was weaker than that in the PBCs.
Conclusions: The methylation levels of highly methylated sites of the low-CpG-density promoters in PBCs decreased
in the LCLs, suggesting that the methylation sites located in low-CpG-density promoters could be sensitive to
demethylation in LCLs. Despite being generated from a single cell type, LCLs may not always be a proxy for DNA from
PBCs in studies of epigenome-wide analysis attempting to elucidate the role of epigenetic change in disease risks.
Keywords: DNA methylation, Lymphoblastoid cell lines, Epigenome-wide analysis, Epigenetic epidemiology, Human
methylation array.
31. 藤岡竜太, 三浦史郎, 青木浩介, 本岡大道, 柴田弘紀, Unverricht-Lundborg病検体を使用したPCRによるCSTB(Cystatin B)遺伝子の異常リピートの検討, 別府大学短期大学紀要, 36, 71-75, 2017.02, CSTB(Cystatin B)遺伝子の異常リピートにより引き起こされる進行性ミオクローヌスてんかんの一病型であるウンフェルリヒト・ルントボルク病(Unverricht-Lundborg disease:ULD)の可能性のある検体の遺伝子解析研究である。進行性ミオクローヌスてんかんの中でCSTB(Cystatin B)遺伝子のリピート異常が原因の疾患はULDとして知られている。ULDを調べるために放射性同位体(Radioisotope:RI)を使用したサザンブロッティングによる解析が行われる。そこで本研究では、簡便なポリメラーゼ連鎖反応(Polymerase chain reaction: PCR)を使用してCSTBの異常リピートの検出を試み、診断手法の確立およびULDの診断に寄与できないか検討した。PCRの結果、健常者と比較して患者では異常リピートと考えられるDNA増幅を確認したがサンガーシークエンスによる配列確認により異常リピートではなく、別の配列の挿入が示唆される結論に至った。.
32. Vanessa Romero, Kazuyoshi Hosomichi, Hiroki Shibata, Hirofumi Nakaoka, Ituro Inoue, Structural comparison and evolution of filaggrin gene within primates., BMC Evolutionary Biology, 10.1186/s12862-016-0851-5., 17, 1, 10-10, 2017.01, Background: The evolutionary dynamics of repeat sequences is quite complex, with some duplicates never
having differentiated from each other. Two models can explain the complex evolutionary process for repeated
genes—concerted and birth-and-death, of which the latter is driven by duplications maintained by selection.
Copy number variations caused by random duplications and losses in repeat regions may modulate molecular
pathways and therefore affect phenotypic characteristics in a population, resulting in individuals that are able to
adapt to new environments. In this study, we investigated the filaggrin gene (FLG), which codes for filaggrin—an
important component of the outer layers of mammalian skin—and contains tandem repeats that exhibit copy
number variation between and within species. To examine which model best fits the evolutionary pathway for
the complete tandem repeats within a single exon of FLG, we determined the repeat sequences in crab-eating
macaque (Macaca fascicularis), orangutan (Pongo abelii), gorilla (Gorilla gorilla), and chimpanzee (Pan troglodytes)
and compared these with the sequence in human (Homo sapiens).
Results: In this study we compared concerted and birth-and-death evolution models, commonly used for gene
copies. We found that there is high nucleotide diversity between filaggrin repeat regions, which fits the birth-anddeath
model. Phylogenetic analyses also suggested that independent duplication events created the repeat sequences
in crab-eating macaques and orangutans, while different duplication and loss events created the repeats in gorillas,
chimpanzees, and humans. Comparison of the repeat sequences detected purifying selection within species and
lineage-specific duplications across species. We also found variation in the length of the repeated region within
species such as chimpanzee and crab-eating macaque.
Conclusions: We conclude that the copy number variation in the repeat sequences of FLG between primates
may be a consequence of species-specific divergence and expansion.
Keywords: Filaggrin, Copy number variation, Birth-and-death evolution, Duplication/loss.
33. Shiroh Miura, Takuya Morikawa, Ryuta Fujioka, Kengo Kosaka, Kohei Yamada, Kazuhito Noda, Gohsuke Hattori, Manabu Motomura, Takayuki Taniwaki, Hiroki Shibata, A novel frameshift mutation of DDHD1 in a Japanese patient with autosomal recessive spastic paraplegia., European Journal of Medical Genetics, 10.1016/j.ejmg.2016.05.010, 59, 8, 413-416, 2016.05, Spastic paraplegia (SPG) type 28 is an autosomal recessive SPG caused by mutations in the DDHD1 gene. We examined a Japanese 54-years-old male patient with autosomal recessive SPG. His parents were consanguineous. He needed a wheelchair for transfer due to spastic paraplegia. There was a history of operations for bilateral hallux valgus, thoracic ossification of the yellow ligament, bilateral carpal tunnel syndrome, bilateral ankle contracture, and lumbar spinal canal stenosis. He noticed gait disturbance at age 14. He used a cane for walking in his 40s. On neurological examination, he showed hyperreflexia, spasticity, and weakness in the lower extremities and bilateral Babinski reflexes. Urinary dysfunctions and impaired vibration sense in the lower limbs were observed. By exome sequencing analysis using Agilent SureSelect and Illumina MiSeq, we identified 17,248 homozygous nucleotide variants in the patient. Through the examination of 48 candidate genes known to be responsible for autosomal recessive SPG, we identified a novel homozygous 4-bp deletion, c.914_917delGTAA, p.Ser305Ilefs*2 in exon2 of the DDHD1 gene encoding phosphatidic acid-preferring phospholipase A1 (PA-PLA1). The mutation is expected to cause a frameshift generating a premature stop codon 3-bp downstream from the deletion. In consequence, the DDHD domain that is known to be critical for PLA1 activity is completely depleted in the mutated DDHD1 protein, predicted to be a functionally null mutation of the DDHD1 gene. By Sanger sequencing, we confirmed that both parents are heterozygous for the mutation. This variation was not detected in 474 Japanese control subjects as well as the data of the 1,000G Project. We conclude that the novel mutation in DDHD1 is the causative variant for the SPG28 patient that is the first record of the disease in Japanese population..
34. Hiroki Shibata, Takahito Chijiwa, Shosaku Hattori, Koki Terada, Motonori Ohno, Yasuyuki Fukumaki, The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands., Molecular Phylogenetics and Evolution, 10.1016/j.ympev.2016.04.027, 101, 91-100, 2016.04, There are four Habu species currently recognized in Japan: Protobothrops flavoviridis from the Amami Islands and the Okinawa Islands, P. tokarensis from the Tokara Islands, P. elegans from the Yaeyama Islands and Ovophis okinabvensis from the Amami Islands and the Okinawa Islands. To clarify their taxonomic positions, we determined the complete mitochondria genome sequence (approx. 17 kb) from two specimens from two different islands each for P. flavoviridis, P. tokarensis and P. elegans as well as one specimen of O. okinavensis and reconstructed the molecular phylogeny of Protobothrops using the published sequences of related species. The maximum likelihood tree showed four major species groups within Protbothrops: Group I consisting of P. cornutus, P. dabieshanensis, P. jerdonii and P. xiangchengensis; Group II consisting of P. flavoviridis and P. tokarensis; Group III consisting of P. maolensis, P. mucrosquamatus and P. elegans; Group IV consisting of P. himalayanus and P. kaubacki. Since we observed an unexpected divergence and the paraphyly of the two samples of P. flavoviridis collected from different islands, Amami-Oshima and Okinawajima within the Group II, we expanded the analysis by increasing the number of P. flavoviridis and P. tokarensis collected from 10 islands: Amami-Oshima (5 specimens), Kakeromajima (4) and Tokunoshima (4) from the Amami Islands, Okinawajima (4), Iheyajima (4), Iejima (4), Tokashikijima (4) and Kumejima (4) from the Okinawa Islands, Kodakarajima (P. tokarensis) (4) and Takarajima (P. tokarensis) (4) from the Tokara Islands. The maximum likelihood tree of the 44 samples replicated the significant divergence of P. flavoviridis between the Amami Clade including Amami-Oshima, Kakeromajima and Tokunoshima and the Okinawa Clade including Okinawajima, Iheyajima, Iejima, Tokashikijima and Kumejima. The Amami Clade also include all specimens from the Tokara Islands currently known as an independent species, P. tokarensis, suggesting the paraphyly of the taxon, P. flavoviridis. In contrast, we observed a distinct lineage of the two specimens from the Yaeyama Islands, supporting the validity of the taxon, P. elegans as an independent species. By MCMC method, we estimated the divergence time between the Amami Clade and the Okinawa Clade to be 6.51 MYA, suggesting that the vicariance of the two clades preceded the geological separation of the Amami Islands and the Okinawa Islands (~1.5 MYA). As expected from the limited mobility of terrestrial reptiles including snakes, we observed high genetic divergence in Habu mtDNA among Japanese subtropical island populations..
35. 藤岡竜太, 三浦史郎, 貴田浩志, 柴田弘紀, SPTBN2にミスセンス変異を認めた脊髄小脳失調症, 別府大学短期大学紀要, 35, 11-16, 2016.02, 本研究は、日本人の脊髄小脳失調症 (Spinocerebellar ataxia: SCA)症例の遺伝解析研究である。本症例は臨床的にSCAタイプ5に矛盾せず、頭部MRI画像では小脳萎縮が認められ、脳幹は保たれていた。遺伝学的解析により、SCA5の原因遺伝子であるβ-IIIスペクトリン遺伝子(SPTBN2)の新規非同義変異(c.924 G>C, p. E308D)が認められた。その遺伝子は細胞骨格たんぱく質をコードして 11番染色体に位置しており、E308Dの変異はホットスポットに局在していた。日本人健常者507人を検討した結果、9人が同様の変異を有していた。したがって、SCA5の責任遺伝子内のミスセンス変異であるE308Dが責任変異ではない可能性が示唆された。.
36. Ken Sano, Shiroh Miura, Toshiya Fujiwara, Ryuta Fujioka, Akiko Yorita, Kazuhito Noda, Hiroshi Kida, Koichi Azuma, Shinjiro Kaieda, Ken Yamamoto, Takayuki Taniwaki, Yasuyuki Fukumaki, Hiroki Shibata, A novel missense mutation of RYR1 in familial idiopathic hyper CK-emia, Journal of Neurological Sciences, 10.1016/j.jns.2015.06.035, 356, 1-2, 142-147, 2015.09, Persistent elevation of serum creatine kinase (CK) without any symptoms has been called idiopathic hyper CKemia
(IHCK).We examined a four-generation Japanese pedigree of familial IHCK. Themultipoint linkage analysis
of the pedigree showed seven clear peaks of logarithm of odds (LOD) scores (>1.4). By the exome sequencing
followed bymultiple filtering processes,we identified one novel heterozygous nonsynonymous single nucleotide
variant (SNV), c.7034GNC, p.S2345T in the ryanodine receptor 1 gene, RYR1 cosegregated with IHCK in the pedigree.
Mutation Taster predicted this substitution as “disease causing” (p = 0.999). The PolyPhen-2 and PANTHER
subPSEC scores for the substitution are 0.911 (possibly damaging) and−3.56 (probably damaging), respectively.
We confirmed the absence of the SNV in 511 healthy Japanese individuals excluding the possibility of a normal
variant with a very low frequency. Immunohistochemistry andWestern blotting of biopsy samples consistently
showed the expression level of RYR1 reduced in the patient. In real-time RT-PCR, the mRNA expression level of
RYR1 was also significantly reduced in the patient (p = 0.009). These results suggest that the novel
nonsynonymous SNV contribute to the vulnerability of the RYR1 protein through the dominant negative effect.
We conclude that the SNV in the RYR1 gene is one of the responsible genes of IHCK..
37. Naoki Kubo, Hidehiro Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Sato Tetsuya, Hidetoshi Sone, Yasuyuki Sato, Shin-ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Tomohiro Kono, Kazuyuki Ohbo, Hiroyuki Sasaki, DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis., BMC Genomics, 10.1186/s12864-015-1833-5, 16, 1, 624-624, 2015.08, Background: In the male germline, neonatal prospermatogonia give rise to spermatogonia, which include stem cell
population (undifferentiated spermatogonia) that supports continuous spermatogenesis in adults. Although the levels of
DNA methyltransferases change dynamically in the neonatal and early postnatal male germ cells, detailed genome-wide
DNA methylation profiles of these cells during the stem cell formation and differentiation have not been reported.
Results: To understand the regulation of spermatogonial stem cell formation and differentiation, we examined the DNA
methylation and gene expression dynamics of male mouse germ cells at the critical stages: neonatal prospermatogonia,
and early postntal (day 7) undifferentiated and differentiating spermatogonia. We found large partially methylated
domains similar to those found in cancer cells and placenta in all these germ cells, and high levels of non-CG
methylation and 5-hydroxymethylcytosines in neonatal prospermatogonia. Although the global CG methylation levels
were stable in early postnatal male germ cells, and despite the reported scarcity of differential methylation in the adult
spermatogonial stem cells, we identified many regions showing stage-specific differential methylation in and around
genes important for stem cell function and spermatogenesis. These regions contained binding sites for specific
transcription factors including the SOX family members.
Conclusions: Our findings show a distinctive and dynamic regulation of DNA methylation during spermatogonial stem
cell formation and differentiation in the neonatal and early postnatal testes. Furthermore, we revealed a unique
accumulation and distribution of non-CG methylation and 5hmC marks in neonatal prospermatogonia. These findings
contrast with the reported scarcity of differential methylation in adult spermatogonial stem cell differentiation and
represent a unique phase of male germ cell development..
38. Kazuaki Yamaguchi, Takahito Chijiwa, Naoki Ikeda, Hiroki Shibata, Yasuyuki Fukumaki, Naoko Oda-Ueda, Shosaku Hattori, Motonori Ohno, The finding of a group IIE phospholipase A2 gene in a specified segment of Protobothrops flavoviridis genome and its possible evolutionary relationship to group IIA phospholipase A2 genes., Toxins, 10.3390/toxins6123471, 6, 3471-3487, 2014.12.
39. Hiroki Shibata, Ken Yamamoto, Zhu Sun, Akira Oka, Hidetoshi Inoko, Tadao Arinami, Toshiya Inada, Hiroshi Ujike, Masanari Itokawa, Mamoru Tochigi, Yuichiro Watanabe, Toshiyuki Someya, Hiroshi Kunugi, Tatsuyo Suzuki, Nakao Iwata, Norio Ozaki, Yasuyuki Fukumaki, Genome-wide association study of schizophrenia using microsatellite markers in the Japanese population., Psychiatr Genetics, 23, 3, 117-123, 2013.06, OBJECTIVES: To search for schizophrenia susceptibility loci, we carried out a case-control study using 28601 microsatellite markers distributed across the entire genome.
MATERIALS AND METHODS: To control the highly multiple testing, we designed three sequential steps of screening using three independent sets of pooled samples, followed by the confirmatory step using an independent sample set (>2200 case-control pairs).
RESULTS: The first screening using pooled samples of 157 case-control pairs showed 2966 markers to be significantly associated with the disorder (PCONCLUSION: Genome-wide association study using microsatellite markers suggested SLC23A3, CNPPD1, and FAM134A genes as candidates for schizophrenia susceptibility in the Japanese population..
40. Satoshi Kusuda, Yuichirou Yasukawa, Hiroki Shibata, Tomomi Saito, Osamu Doi, Yutaka Ohya, Norio Yoshizaki, Diversity in the matrix structure of eggshells in the testudines (reptilia)., Zoological Science, 30, 5, 366-8374, 2013.05, The eggshells of 56 chelonians were examined by electron microscopy and X-ray diffractometry. They were classified into six types in terms of the matrix structure of their calcareous layer; type I was composed of a thin calcareous layer with minerals in an amorphous structure; type II with shell units composed of mammillary cores calcified with aragonite crystals; type III with shell units composed of mammillary cores, plus a single palisade layer also calcified with aragonite crystals, and with each shell unit separated; type IV with shell units the same as type III, but tightly packed together; type V with shell units composed of mammillary cores plus two palisade layers; and type VI with a cuticle layer calcified with calcite crystals over the same structure as that of type V. X-ray diffraction analyses at the outer surface of eggshells showed a gradual change in crystal disposition from the random disposition of type II to the single direction-oriented disposition of type V. The shell height was approximately parallel to the development of the palisade-layer matrix. The limiting membrane of all eggshell types was perforated with canals and that of type I was partially missing. Type I had a parchment shell, types II and III had a pliable shell (some were rigid) and types IV to VI had rigid shells. The present study showed that the hardness of eggshells can be determined by the composition of the shell matrices, as shell matrices are the framework for mineralization..
41. Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H., Crohn’s disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation., Mol Biol Evol. , 156, 7, 850-858, 2012.01, Risk alleles for complex diseases are spread widely throughout human populations. However, little is known about the geographic distribution of risk allele frequencies, which may contribute to geographic differences in disease susceptibility and prevalence. Here we focus on Crohn’s disease (CD) as a model for the evolutionary study of complex disease alleles. Recent genome-wide association studies and classical linkage analyses have identified more than 70 susceptible genomic regions for CD in Europeans, but only a few have been confirmed in non-European populations. Our analysis of eight European-specific susceptibility genes using HapMap data shows that at the NOD2 locus the CD-risk alleles are linked with a haplotype specific to CEU at a frequency that is significantly higher compared to the entire genome. We subsequently examined nine global populations and found that the CD-risk alleles spread through hitchhiking with a high-frequency haplotype (H1) exclusive to Europeans. To examine the neutrality of NOD2, we performed phylogenetic network analyses, coalescent simulation, protein structural prediction, characterization of mutation patterns, and estimations of population growth and time to most recent common ancestor (TMRCA). We found that while H1 was significantly prevalent in European populations, the H1 TMRCA predated human migration out of Africa. H1 is likely to have undergone negative selection because (i) the root of H1 genealogy is defined by a pre-existing amino acid substitution that causes serious conformational changes to the NOD2 protein, (ii) the haplotype has almost become extinct in Africa, and (iii) the haplotype has not been affected by the recent European expansion reflected in the other haplotypes. Nevertheless, H1 has survived in European populations, suggesting that the haplotype is advantageous to the populations. We propose that several CD-risk alleles, which destabilize and disrupt the NOD2 protein, have been maintained by natural selection on standing variation because the deleterious haplotype of NOD2 is advantageous in diploid individuals due to heterozygote advantage and/or intergenic interactions..
42. Deng X, Takaki H, Wang L, Kuroki T, Nakahara T, Hashimoto K, Ninomiya H, Arinami T, Inada T, Ujike H, Itokawa M, Tochigi M, Watanabe Y, Someya T, Kunugi H, Iwata N, Ozaki N, Shibata H, Fukumaki Y., Positive association of phencyclidine-responsive genes, PDE4A and PLAT, with schizophrenia., Am J Med Genet Neuropsychiatr Genet., 156, 7, 850-858, 2011.09, Spastic paraplegia type 4 (SPG4) is the most common autosomal dominant hereditary SPG caused by mutations in the SPAST gene. We studied the four- generation pedigree of a Japanese family with autosomal dominant hereditary SPG both clinically and genetically. Twelve available family members (ten affected; two unaffected) and two spouses were enrolled in the study. The clinical features were hyperreflexia in all four limbs, spasticity of the lower extremities, impaired vibration sense, mild cognitive impairment confirmed by the Wechsler Adult Intelligence Scale—Third Edition, and peripheral neuropathy confirmed by neurophysiological examinations. All four female patients experienced miscarriages. The cerebrospinal fluid tau levels were mildly increased in two of three patients examined. Linkage analyses revealed the highest logarithm of odds score of 2.64 at 2p23-p21 where the SPAST gene is located. Mutation scanning of the entire exonic regions of the SPAST gene by direct sequencing revealed no mutations. Exonic copy number analysis by real- time quantitative polymerase chain reaction revealed hetero- zygous deletion of exons 1 to 4 of the SPAST gene. Breakpoint analysis showed that the centromeric breakpoint was located within intron 4 of SPAST while the telomeric breakpoint was located within intron 3 of the neighboring DPY30 gene, causing a deletion of approximately 70 kb ranging from exons 1 to 3 of DPY30 to exons 1 to 4 of SPAST. To our knowledge, this is the first report of SPG4 associated with partial deletions of both the SPAST and DPY30 genes. The partial heterozygous deletion of DPY30 could modify the phenotypic expression of SPG4 patients with this pedigree..
43. Shiroh Miura, Hiroki Shibata, Hiroshi Kida, Kazuhito Noda, Takayuki Toyama, Naoka Iwasaki, Akiko Iwaki, Mitsuyoshi Ayabe, Hisamichi Aizawa, Takayuki Taniwaki, Yasuyuki Fukumaki., Partial SPAST and DPY30 deletions in a Japanese spastic paraplegia type 4 family., Neurogenetics, 12 (1): 25-31, 2010.09, [URL], Spastic paraplegia type 4 (SPG4) is the most common autosomal dominant hereditary SPG caused by mutations in the SPAST gene. We studied the four- generation pedigree of a Japanese family with autosomal dominant hereditary SPG both clinically and genetically. Twelve available family members (ten affected; two unaffected) and two spouses were enrolled in the study. The clinical features were hyperreflexia in all four limbs, spasticity of the lower extremities, impaired vibration sense, mild cognitive impairment confirmed by the Wechsler Adult Intelligence Scale—Third Edition, and peripheral neuropathy confirmed by neurophysiological examinations. All four female patients experienced miscarriages. The cerebrospinal fluid tau levels were mildly increased in two of three patients examined. Linkage analyses revealed the highest logarithm of odds score of 2.64 at 2p23-p21 where the SPAST gene is located. Mutation scanning of the entire exonic regions of the SPAST gene by direct sequencing revealed no mutations. Exonic copy number analysis by real- time quantitative polymerase chain reaction revealed hetero- zygous deletion of exons 1 to 4 of the SPAST gene. Breakpoint analysis showed that the centromeric breakpoint was located within intron 4 of SPAST while the telomeric breakpoint was located within intron 3 of the neighboring DPY30 gene, causing a deletion of approximately 70 kb ranging from exons 1 to 3 of DPY30 to exons 1 to 4 of SPAST. To our knowledge, this is the first report of SPG4 associated with partial deletions of both the SPAST and DPY30 genes. The partial heterozygous deletion of DPY30 could modify the phenotypic expression of SPG4 patients with this pedigree..
44. Hiroki Goto, Kazunori Watanabe, Naozumi Araragi, Rui Kageyama, Kunika Tanaka, Yoko Kuroki, Atsushi Toyoda, Masahira Hattori, Yoshiyuki Sakaki, Asao Fujiyama, Yasuyuki Fukumaki, Hiroki Shibata., The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor family., BMC Evolutionary Biology., 9: 224, 2009.09, [URL], Background: The glutamate receptors (GluRs) play a vital role in the mediation of excitatory synaptic transmission in the central nervous system. To clarify the evolutionary dynamics and mechanisms of the GluR genes in the lineage leading to humans, we determined the complete sequences of the coding regions and splice sites of 26 chimpanzee GluR genes.
Results: We found that all of the reading frames and splice sites of these genes reported in humans were completely conserved in chimpanzees, suggesting that there were no gross structural changes in humans after their divergence from the human-chimpanzee common ancestor. We observed low KA/KS ratios in both humans and chimpanzees, and we found no evidence of accelerated evolution. We identified 30 human-specific "fixed" amino acid substitutions in the GluR genes by analyzing 80 human samples of seven different populations worldwide. Grantham's distance analysis showed that GRIN2C and GRIN3A are the most and the second most diverged GluR genes between humans and chimpanzees. However, most of the substitutions are non-radical and are not clustered in any particular region. Protein motif analysis assigned 11 out of these 30 substitutions to functional regions. Two out of these 11 substitutions, D71G in GRIN3A and R727H in GRIN3B, caused differences in the functional assignments of these genes between humans and other apes.
Conclusion: We conclude that the GluR genes did not undergo drastic changes such as accelerated evolution in the human lineage after the divergence of chimpanzees. However, there remains a possibility that two human-specific "fixed" amino acid substitutions, D71G in GRIN3A and R727H in GRIN3B, are related to human-specific brain function.
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45. Hiroki Shibata, Ayako Tani, Tomoyuki Chikuhara, Rumiko Kikuta, Mayumi Sakai, Hideaki Ninomiya, Nobutada Tashiro, Nakao Iwata, Norio Ozaki and Yasuyuki Fukumaki. , Association study of polymorphisms in the group III metabotropic glutamate receptor genes, GRM4 and GRM7, with schizophrenia. , Psychiatric Res. , 167:88-96., 2009.04, Based on the hypothesis that a glutamatergic dysfunction is involved in the pathophysiology of schizophrenia, we have been conducting systematic studies on the association between glutamate receptor genes and schizophrenia. Here we report association studies of schizophrenia with polymorphisms in group III metabotropic glutamate receptor genes, GRM4 and GRM7. We selected 8 and 43 common SNPs distributed in the entire gene regions of GRM4 (> 111 kb) and GRM7 (> 900 kb), respectively. We scanned significant associations with schizophrenia using 100 case-control pairs of Japanese. We identified two neighboring SNPs (rs12491620 and rs1450099) in GRM7 showing highly significant haplotype association with schizophrenia surviving the FDR correction. We then performed additional typing of the two SNPs using the expanded sample set (404 cases and 420 controls) and confirmed the significant association with the disease. We conclude that at least one susceptibility locus for schizophrenia is located within or nearby GRM7, whereas GRM4 is unlikely to be a major susceptibility gene for schizophrenia in the Japanese population..
46. Shinsaku Arai, Hiroki Shibata, Mayumi Sakai, Hideaki Ninomiya, Nakao Iwata, Norio Ozaki, Yasuyuki Fukumaki., Association analysis of the glutamic acid decarboxylase 2 and the glutamine synthetase genes (GAD2, GLUL) with schizophrenia., Psychiatric Genet., 19 (1): 6-13., 2009.02.
47. Shiroh Miura, Hiroki Shibata, Hiroshi Kida, Kazuhito Noda, Ken Yamamoto, Akiko Iwaki, Mitsuyoshi Ayabe, Hisamichi Aizawa, Takayuki Taniwaki, Yasuyuki Fukumaki, Hereditary motor and sensory neuropathy with proximal dominancy in the lower extremities, urinary disturbance, and paroxysmal dry cough., Journal of the Neurological Sciences. , 273(1-2): 88-92., 2008.10, We studied a four-generation pedigree of a Japanese family with hereditary neuropathy to elucidate the genetic basis of this disease. Twelve members of the family were enrolled in this study. The clinical features were neurogenic muscle weakness with proximal dominancy in the lower extremities, sensory involvement, areflexia, fine postural tremors, painful muscle cramps, elevated creatine kinase levels, recurrent paroxysmal dry cough, and neurogenic bladder. We performed a genome-wide search using genetic loci spaced at about 13 Mb intervals. Although nine chromosomes (1, 3, 4, 5, 6, 10, 17, 19, and 22) had at least one region in which the logarithm of odds (LOD) score was over 1.0, no loci fulfilled the criteria for significant evidence of linkage. Moreover, we analyzed an extra 14 markers on 3p12–q13 (the locus of hereditary motor and sensory neuropathy, proximal dominant form) and an extra five markers on 3p22–p24 (the locus of hereditary sensory neuropathy with chronic cough) and observed LOD scores of b−3 on both 3p12–q13 and 3p22–p24. Mutation scanning of the entire coding regions of the MPZ and PMP22 genes revealed no mutations. We conclude that the disorder described here is a newly classified hereditary motor and sensory neuropathy with autosomal dominant inheritance.
.
48. Deng X, Sagata N, Takeuchi N, Tanaka M, Ninomiya H, Iwata N, Ozaki N, Shibata H, Fukumaki Y., Association study of polymorphisms in the neutral amino acid transporter genes SLC1A4, SLC1A5 and the glycine transporter genes SLC6A5, SLC6A9 with schizophrenia., BMC Psychiatry, 8, 1, 58, 2008.07.
49. Iwaki A, Kawano Y, Miura S, Shibata H, Matsuse D, Li W, Furuya H, Ohyagi Y, Taniwaki T, Kira J, Fukumaki Y. , Heterozygous deletion of ITPR1, but not SUMF1 in spinocerebellar ataxia type 16. , J Med Genet , 45(1): 32-5., 2008.01.
50. Deng X, Shibata H, Takeuchi N, Rachi S, Sakai M, Ninomiya H, Iwata N, Ozaki N, and Fukumaki Y., Association study of polymorphisms in the glutamate transporter genes SLC1A1, SLC1A3 and SLC1A6 with schizophrenia., Neuropsychiatric Genetics, 2007.04.
51. Miura S, Shibata H, Furuya H, Ohyagi Y, Osoegawa M, Miyoshi Y, Matsunaga Y, Shibata A, Matsumoto N, Iwaki, Taniwaki T, Kikuchi H, Kira J and Fukumaki Y., The CNTN4 locus at 3p26 is a candidate gene of SCA16, Neurology, 67(7):1236-41, 2006.10.
52. Shibata H, Aramaki T, Sakai M, Ninomiya H, Tashiro N, Iwata N, Ozaki N and Fukumaki Y., Association study of polymorphisms in the GluR7, KA1 and KA2 kainate receptor genes (GRIK3, GRIK4, GRIK5) with schizophrenia., Psychiatry Res., 141: 39-51, 2006.01.
53. The Japanese Schizophrenia Sib-Pair Linkage Group (JSSLG)., Genome-wide high-density SNP linkage analysis of 236 Japanese families supports the existence of schizophrenia loci on chromosomes 1p, 14q and 20p., Am J Hum Genet., 77: 937-944, 2005.12.
54. Makino C, Shibata H, Ninomiya H, Tashiro N, Fukumaki Y., Identification of single-nucleotide polymorphisms in the human N-methyl-D-aspartate receptor subunit NR2D gene, GRIN2D, and association study with schizophrenia., Psychiatr Genet., 10.1097/00041444-200509000-00014, 15, 3, 215-221, 15 (3): 215-221., 2005.09.
55. Lee HJ, Song JY, Kim JW, Jin S-Y, Mi Hong S, Park JK, Chung J-H, Shibata H and Fukumaki Y., Association Study of polymorphisms in synaptic vesicle-associated genes, SYN2 and CPLX2, with schizophrenia., Behav Brain Funct, 1:15, 2005.08.
56. Deng XD, Shibata H, Ninomiya H, Tashiro N, Iwata N, Ozaki N and Fukumaki Y., Association study of polymorphisms in the excitatory amino acid transporter 2 gene (SLC1A2) with schizophrenia., BMC Psychiatry, 10.1186/1471-244X-4-21, 4, 4(1): 21, 2004.08.
57. Takaki H, Kikuta R, Shibata H, Ninomiya H, Tashiro N and Fukumaki Y., Positive associations of polymorphisms in the metabotropic glutamate receptor type 8 gene (GRM8) with schizophrenia., Am J Med Genet., 10.1002/ajmg.b.20108, 128B, 1, 6-14, 128B: 6-14., 2004.07.
58. The Japanese Schizophrenia Sib-pair Linkage Group., Initial genome-wide scan for linkage with schizophrenia in the Japanese Schizophrenia Sib-pair Linkage Group (JSSLG) families., Am J Med Genet., 10.1002/ajmg.b.20022, 120B, 1, 22-28, 120B(1): 22-8., 2003.07.
59. Fujii Y, Shibata H, Kikuta R, Makino C, Tani A, Hirata N, Shibata A, Ninomiya H, Tashiro N, Fukumaki Y., Positive associations of polymorphisms in the metabotropic glutamate receptor type 3 gene (GRM3) with schizophrenia., Psychiatric Genetics., 10.1097/01.ypg.0000056682.82896.b0, 13, 2, 71-76, 13(2):71-6., 2003.06.
60. Makino C, Fujii Y, Kikuta R, Hirata N, Tani A, Shibata A, Ninomiya H, Tashiro N, Shibata H, Fukumaki Y., Positive association of the AMPA receptor subunit GluR4 gene (GRIA4) haplotype with schizophrenia: linkage disequilibrium mapping using SNPs evenly distributed across the gene region., Am J Med Genet., 10.1002/ajmg.b.10041, 116B, 1, 17-22, 116B (1): 17-22., 2003.01.
61. Shibata H, Shibata A, Ninomiya H, Tashiro N, Fukumaki Y., Association study of polymorphisms in the GluR6 kainate receptor gene (GRIK2) with schizophrenia., Psychiatry Res., 10.1016/S0165-1781(02)00231-7, 113, 1-2, 59-67, 113(1-2): 59-67., 2002.12.
62. Tani A, Kikuta R, Itoh K, Joo A, Shibata H, Ninomiya H, Tashiro N and Fukumaki Y., Polymorphism analysis of upstream regions of the human N-methyl-D-aspartate receptor subunit NR1 gene (GRIN1): implications for schizophrenia., Schizophr Research, 10.1016/S0920-9964(02)00161-5, 58, 1, 83-86, 58 (1):83-86., 2002.11.
63. Shibata H, Joo A, Fujii Y, Tani A, Makino C, Hirata N, Kikuta R, Ninomiya H, Tashiro N, Fukumaki Y., Association study of polymorphisms in the coding region of the GluR5 kainate receptor gene (GRIK1) with schizophrenia., Psychiatric Genetics, 10.1097/00041444-200109000-00005, 11, 3, 139-144, 11 (3): 139-144., 2001.09.
64. Kiehl TR, Shibata H, Huynh DP, Vo T, Pulst SM., Identification and expression of a mouse ortholog of A2BP1., Mammalian Genome., 12 (8): 595-601., 2001.08.
65. Mitsuyasu H, Hirata N, Sakai Y, Shibata H, Takeda Y, Ninomiya H, Kawasaki H, Tashiro N, Fukumaki Y., Association analysis of polymorphisms in the upstream region of the human dopamine D4 receptor gene (DRD4) with schizophrenia and personality traits., J Hum Genet, 10.1007/s100380170120, 46, 1, 26-31, 46 (1): 26-31 (2001)., 2001.01.
66. Joo A, Shibata H, Ninomiya H, Kawasaki H, Tashiro N, Fukumaki Y., Structure and polymorphisms of the human metabotropic glutamate receptor type 2 gene (GRM2): analysis of association with schizophrenia., Molecular Psychiatry, 10.1038/sj.mp.4000841, 6, 2, 186-192, 6 (2): 186-192., 2001.03.
67. Kiehl TR, Shibata H, Pulst SM., The ortholog of human ataxin-2 is essential for early embryonic patterning in C. elegans., Journal of Molecular Neuroscience, 10.1385/JMN:15:3:231, 15, 3, 231-241, 15 (3): 231-241 (2000)., 2000.08.
68. Sakai Y, Kobayashi S, Shibata H, Furuumi H, Endo T, Fucharoen S, Hamano S, Acharya GP, Kawasaki T, Fukumaki Y., Molecular analysis of a-thalassemia in Nepal: correlation with malaria endemicity., Journal of Human Genetics, 10.1007/s100380050198, 45, 3, 127-132, 45 (3): 127-132 (2000)., 2000.01.
69. Shibata H, Huynh DP, Pulst SM., A novel protein with RNA binding motif binds to C-terminal ataxin-2., Human Molecular Genetics, 9 (9): 1303-1313., 2000.05.
70. Nechiporuk T, Nechiporuk A, Sahba S, Figueroa KP, Shibata H, Chen X-N, Korenberg J R, de Jong P, Pulst SM., A high resolution PAC and BAC map of the SCA2 region., Genomics, 44 (3): 321-329., 1997.09.
71. Okuyama E, Shibata H, Tachida H, Yamazaki T., Molecular evolution of the 5'-flanking regions of the duplicated Amy genes in Drosophila melanogaster species subgroup., Molecular Biology and Evolution, 13, 4, 574-583, 13 (4): 574-583., 1996.04.
72. Shibata H, Tahira T, Hayashi K., RNA-primed PCR., Genome Research, 10.1101/gr.5.4.400, 5, 4, 400-403, 5 (4): 400-403., 1995.11.
73. Shibata H, Yamazaki T., Molecular evolution of the duplicated Amy locus in the Drosophila melanogaster species subgroup: concerted evolution only in coding region and an excess of nonsynonymous substitutions in speciation., Genetics, 141, 1, 223-236, 141 (1): 223-236., 1995.09.
74. Inomata N, Shibata H, Okuyama E and Yamazaki T., Evolutionary relationship and sequence variation of a-amylase variants encoded by duplicated genes in the Amy locus of Drosophila melanogaster., Genetics, 141, 1, 237-244, 141 (1): 237-244., 1995.09.
75. Shibata H, Yamazaki T., A comparative study of the enzymological features of a-amylase in the Drosophila melanogaster species subgroup., Japan Journal of Genetics, 10.1266/jjg.69.251, 69, 3, 251-258, 69 (3): 251-258., 1994.06.

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