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Fuse N, Sakurai M, Motoike IN, Kojima K, Takai-Igarashi T, Nakaya N, Tsuchiya N, Nakamura T, Ishikuro M, Obara T, Miyazawa A, Homma K, Ido K, Taira M, Kobayashi T, Shimizu R, Uruno A, Kodama EN, Suzuki K, Hamanaka Y, Tomita H, Sugawara J, Suzuki Y, Nagami F, Ogishima S, Katsuoka F, Minegishi N, Hozawa A, Kuriyama S, Yaegashi N, Kure S, Kinoshita K, Yamamoto M. Genome-wide Association Study of Axial Length in Population-based Cohorts in Japan. Ophthalmology Science 2022; 2:100113. [PMID: 36246171 PMCID: PMC9559092 DOI: 10.1016/j.xops.2022.100113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 01/07/2022] [Accepted: 01/07/2022] [Indexed: 11/20/2022]
Abstract
Purpose To elucidate the differences in ocular biometric parameters by generation and gender and to identify axial length (AL)-associated genetic variants in Japanese individuals, we analyzed Tohoku Medical Megabank Organization (ToMMo) Eye Study data. Design We designed the ToMMo Eye Study, examined AL variations, and conducted genome-wide association studies (GWASs). Participants In total, 33 483 participants aged > 18 years who were recruited into the community-based cohort (CommCohort) and the birth and three-generation cohort (BirThree Cohort) of the ToMMo Eye Study were examined. Methods Each participant was screened with an interview, ophthalmic examinations, and a microarray analysis. The GWASs were performed in 22 379 participants in the CommCohort (discovery stage) and 11 104 participants in the BirThree Cohort (replication stage). We evaluated the associations of single nucleotide polymorphisms (SNPs) with AL using a genome-wide significance threshold (5 × 10-8) in each stage of the study and in the subsequent meta-analysis. Main Outcome Measures We identified the association of SNPs with AL and distributions of AL in right and left eyes and individuals of different sexes and ages. Results In the discovery stage, the mean AL of the right eye (23.99 mm) was significantly greater than that of the left eye (23.95 mm). This difference was reproducible across sexes and ages. The GWASs revealed 703 and 215 AL-associated SNPs with genome-wide significance in the discovery and validation stages, respectively, and many of the SNPs in the discovery stage were replicated in the validation stage. Validated SNPs and their associated loci were meta-analyzed for statistical significance (P < 5 × 10-8). This study identified 1478 SNPs spread over 31 loci. Of the 31 loci, 5 are known AL loci, 15 are known refractive-error loci, 4 are known corneal-curvature loci, and 7 loci are newly identified loci that are not known to be associated with AL. Of note, some of them shared functional relationships with previously identified loci. Conclusions Our large-scale GWASs exploiting ToMMo Eye Study data identified 31 loci linked to variations in AL, 7 of which are newly reported in this article. The results revealed genetic heterogeneity and similarity in SNPs related to ethnic variations in AL.
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Tsuboi A, Matsui H, Shiraishi N, Murakami T, Otsuki A, Kawashima J, Kiyama T, Tamahara T, Goto M, Koyama S, Sugawara J, Kodama EN, Metoki H, Hozawa A, Kuriyama S, Tomita H, Kikuya M, Minegishi N, Suzuki K, Koshiba S, Tamiya G, Fuse N, Aoki Y, Takai-Igarashi T, Ogishima S, Nakamura T, Sakurai-Yageta M, Nagami F, Kinoshita K, Kure S, Shimizu R, Sasaki K, Yamamoto M. Design and Progress of Oral Health Examinations in the Tohoku Medical Megabank Project. TOHOKU J EXP MED 2021; 251:97-115. [PMID: 32581193 DOI: 10.1620/tjem.251.97] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to assess the long-term impact of the Great East Japan Earthquake on the oral health of disaster victims and to evaluate gene-environmental interactions in the development of major oral diseases and oral-systemic associations, the oral part of two large-scale genome cohort studies by the Tohoku Medical Megabank Organization (ToMMo), including the Community-based cohort (CommCohort) study and the Birth and Three-Generation cohort (BirThree) study, have been conducted. The study population comprised 32,185 subjects, including 16,886 participants in the CommCohort study and 15,299 participants in the BirThree cohort study, recruited from 2013 to 2017. The oral studies consist of a questionnaire regarding oral hygiene behavior, clinical examinations by dentists, and oral plaque and saliva sampling for microbiome analyses, which were carried out at seven community support centers in Miyagi prefecture. The median age of all participants was 55.0 years, and 66.1% of participants were women. Almost all participants reported that they brushed their teeth more than once a day. The median number of present teeth was 27.0, and the decayed, missing and filled tooth number was 16.0, with a significant difference according to age and sex. The median periodontal pocket and clinical attachment level was 2.48 mm and 4.00 mm, respectively. Periodontal parameters increased significantly according to age, except for the accumulation of dental calculus. The oral part of these extensive cross-sectional studies provides a unique and important platform for future studies on oral health and diseases that elicit through interactions with systemic diseases, lifestyles, life events and genetic backgrounds, and contributes to researches clarifying the long-term effects of disasters on oral health.
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Affiliation(s)
- Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Dentistry, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hiroyuki Matsui
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Dentistry, Tohoku University
| | | | - Takahisa Murakami
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Dentistry, Tohoku University.,Faculty of Medicine, Tohoku Medical and Pharmaceutical University
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | | | - Tomomi Kiyama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Dentistry, Tohoku University
| | - Toru Tamahara
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Dentistry, Tohoku University
| | - Maki Goto
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Eiichi N Kodama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Hirohito Metoki
- Tohoku Medical Megabank Organization, Tohoku University.,Faculty of Medicine, Tohoku Medical and Pharmaceutical University
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Masahiro Kikuya
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Teikyo University School of Medicine
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Center for Advanced Intelligence Project, RIKEN
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Information Sciences, Tohoku University
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | | | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Information Sciences, Tohoku University
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | | | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
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3
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Kuriyama S, Metoki H, Kikuya M, Obara T, Ishikuro M, Yamanaka C, Nagai M, Matsubara H, Kobayashi T, Sugawara J, Tamiya G, Hozawa A, Nakaya N, Tsuchiya N, Nakamura T, Narita A, Kogure M, Hirata T, Tsuji I, Nagami F, Fuse N, Arai T, Kawaguchi Y, Higuchi S, Sakaida M, Suzuki Y, Osumi N, Nakayama K, Ito K, Egawa S, Chida K, Kodama E, Kiyomoto H, Ishii T, Tsuboi A, Tomita H, Taki Y, Kawame H, Suzuki K, Ishii N, Ogishima S, Mizuno S, Takai-Igarashi T, Minegishi N, Yasuda J, Igarashi K, Shimizu R, Nagasaki M, Tanabe O, Koshiba S, Hashizume H, Motohashi H, Tominaga T, Ito S, Tanno K, Sakata K, Shimizu A, Hitomi J, Sasaki M, Kinoshita K, Tanaka H, Kobayashi T, Kure S, Yaegashi N, Yamamoto M. Cohort Profile: Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study): rationale, progress and perspective. Int J Epidemiol 2020; 49:18-19m. [PMID: 31504573 PMCID: PMC7124511 DOI: 10.1093/ije/dyz169] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/19/2019] [Indexed: 01/21/2023] Open
Affiliation(s)
- Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Hirohito Metoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,School of Medicine, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Masahiro Kikuya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,School of Medicine, Teikyo University, Tokyo, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Chizuru Yamanaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masato Nagai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hiroko Matsubara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,School of Health and Social Services, Saitama Prefectural University, Koshigaya, Japan
| | - Naho Tsuchiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takumi Hirata
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ichiro Tsuji
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Tomohiko Arai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoshio Kawaguchi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Higuchi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masaki Sakaida
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Department of Clinical Genetics, Ageo Central General Hospital, Ageo, Japan
| | - Noriko Osumi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Keiko Nakayama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kiyoshi Ito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Shinichi Egawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Koichi Chida
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Eiichi Kodama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tadashi Ishii
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan.,Graduate School of Dentistry, Tohou University, Sendai, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Yasuyuki Taki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan.,School of Medicine, The Jikei University, Tokyo, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Naoto Ishii
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Satoshi Mizuno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, Natori, Japan
| | - Kazuhiko Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Biosample Research Center, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hiroaki Hashizume
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hozumi Motohashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Teiji Tominaga
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Sadayoshi Ito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Kozo Tanno
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan.,School of Medicine, Iwate Medical University, Morioka, Japan
| | - Kiyomi Sakata
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan.,School of Medicine, Iwate Medical University, Morioka, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Jiro Hitomi
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan.,School of Medicine, Iwate Medical University, Morioka, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan.,School of Medicine, Iwate Medical University, Morioka, Japan.,Institute for Biomedical Science, Iwate Medical University, Yahaba, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Laboratory for Promotion of Medical Data Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tadao Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
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4
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Sakurai R, Ueki M, Makino S, Hozawa A, Kuriyama S, Takai-Igarashi T, Kinoshita K, Yamamoto M, Tamiya G. Outlier detection for questionnaire data in biobanks. Int J Epidemiol 2020; 48:1305-1315. [PMID: 30848787 DOI: 10.1093/ije/dyz012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Biobanks increasingly collect, process and store omics with more conventional epidemiologic information necessitating considerable effort in data cleaning. An efficient outlier detection method that reduces manual labour is highly desirable. METHOD We develop an unsupervised machine-learning method for outlier detection, namely kurPCA, that uses principal component analysis combined with kurtosis to ascertain the existence of outliers. In addition, we propose a novel regression adjustment approach to improve detection, namely the regression adjustment for data by systematic missing patterns (RAMP). RESULT Application to epidemiological record data in a large-scale biobank (Tohoku Medical Megabank Organization, Japan) shows that a combination of kurPCA and RAMP effectively detects known errors or inconsistent patterns. CONCLUSIONS We confirm through the results of the simulation and the application that our methods showed good performance. The proposed methods are useful for many practical analysis scenarios.
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Affiliation(s)
- Rieko Sakurai
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masao Ueki
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Satoshi Makino
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science (IRIDeS), Tohoku University, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Tokyo, Japan.,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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5
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Sakai K, Tanikawa C, Hirasawa A, Chiyoda T, Yamagami W, Kataoka F, Susumu N, Terao C, Kamatani Y, Takahashi A, Momozawa Y, Hirata M, Kubo M, Fuse N, Takai-Igarashi T, Shimizu A, Fukushima A, Kadota A, Arisawa K, Ikezaki H, Wakai K, Yamaji T, Sawada N, Iwasaki M, Tsugane S, Aoki D, Matsuda K. Identification of a novel uterine leiomyoma GWAS locus in a Japanese population. Sci Rep 2020; 10:1197. [PMID: 31988393 PMCID: PMC6985131 DOI: 10.1038/s41598-020-58066-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 12/12/2019] [Indexed: 12/26/2022] Open
Abstract
Uterine leiomyoma is one of the most common gynaecologic benign tumours, but its genetic basis remains largely unknown. Six previous GWAS identified 33 genetic factors in total. Here, we performed a two-staged GWAS using 13,746 cases and 70,316 controls from the Japanese population, followed by a replication analysis using 3,483 cases and 4,795 controls. The analysis identified 9 significant loci, including a novel locus on 12q23.2 (rs17033114, P = 6.12 × 10-25 with an OR of 1.177 (1.141-1.213), LINC00485). Subgroup analysis indicated that 5 loci (3q26.2, 5p15.33, 10q24.33, 11p15.5, 13q14.11) exhibited a statistically significant effect among multiple leiomyomas, and 2 loci (3q26.2, 10q24.33) exhibited a significant effect among submucous leiomyomas. Pleiotropic analysis indicated that all 9 loci were associated with at least one proliferative disease, suggesting the role of these loci in the common neoplastic pathway. Furthermore, the risk T allele of rs2251795 (3q26.2) was associated with longer telomere length in both normal and tumour tissues. Our findings elucidated the significance of genetic factors in the pathogenesis of leiomyoma.
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Affiliation(s)
- Kensuke Sakai
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Keio University School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Akira Hirasawa
- Keio University School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan.,Department of Clinical Genomic Medicine, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Tatsuyuki Chiyoda
- Keio University School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - Wataru Yamagami
- Keio University School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - Fumio Kataoka
- Keio University School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - Nobuyuki Susumu
- International University of Health and Welfare School of Medicine, Department of Obstetrics and Gynecology, Chiba, Japan
| | - Chikashi Terao
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | - Atsushi Takahashi
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.,Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | | | - Makoto Hirata
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Akimune Fukushima
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Aya Kadota
- Department of Health Science, Shiga University of Medical Science, Shiga, Japan
| | - Kokichi Arisawa
- Department of Preventive Medicine, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - Hiroaki Ikezaki
- Department of General Internal Medicine, Kyushu University Hospital, Fukuoka, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Daisuke Aoki
- Keio University School of Medicine, Department of Obstetrics and Gynecology, Tokyo, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.
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6
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Hozawa A, Tanno K, Nakaya N, Nakamura T, Tsuchiya N, Hirata T, Narita A, Kogure M, Nochioka K, Sasaki R, Takanashi N, Otsuka K, Sakata K, Kuriyama S, Kikuya M, Tanabe O, Sugawara J, Suzuki K, Suzuki Y, Kodama EN, Fuse N, Kiyomoto H, Tomita H, Uruno A, Hamanaka Y, Metoki H, Ishikuro M, Obara T, Kobayashi T, Kitatani K, Takai-Igarashi T, Ogishima S, Satoh M, Ohmomo H, Tsuboi A, Egawa S, Ishii T, Ito K, Ito S, Taki Y, Minegishi N, Ishii N, Nagasaki M, Igarashi K, Koshiba S, Shimizu R, Tamiya G, Nakayama K, Motohashi H, Yasuda J, Shimizu A, Hachiya T, Shiwa Y, Tominaga T, Tanaka H, Oyama K, Tanaka R, Kawame H, Fukushima A, Ishigaki Y, Tokutomi T, Osumi N, Kobayashi T, Nagami F, Hashizume H, Arai T, Kawaguchi Y, Higuchi S, Sakaida M, Endo R, Nishizuka S, Tsuji I, Hitomi J, Nakamura M, Ogasawara K, Yaegashi N, Kinoshita K, Kure S, Sakai A, Kobayashi S, Sobue K, Sasaki M, Yamamoto M. Study Profile of the Tohoku Medical Megabank Community-Based Cohort Study. J Epidemiol 2020; 31:65-76. [PMID: 31932529 PMCID: PMC7738642 DOI: 10.2188/jea.je20190271] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Background We established a community-based cohort study to assess the long-term impact of the Great East Japan Earthquake on disaster victims and gene-environment interactions on the incidence of major diseases, such as cancer and cardiovascular diseases. Methods We asked participants to join our cohort in the health check-up settings and assessment center based settings. Inclusion criteria were aged 20 years or over and living in Miyagi or Iwate Prefecture. We obtained information on lifestyle, effect of disaster, blood, and urine information (Type 1 survey), and some detailed measurements (Type 2 survey), such as carotid echography and calcaneal ultrasound bone mineral density. All participants agreed to measure genome information and to distribute their information widely. Results As a result, 87,865 gave their informed consent to join our study. Participation rate at health check-up site was about 70%. The participants in the Type 1 survey were more likely to have psychological distress than those in the Type 2 survey, and women were more likely to have psychological distress than men. Additionally, coastal residents were more likely to have higher degrees of psychological distress than inland residents, regardless of sex. Conclusion This cohort comprised a large sample size and it contains information on the natural disaster, genome information, and metabolome information. This cohort also had several detailed measurements. Using this cohort enabled us to clarify the long-term effect of the disaster and also to establish personalized prevention based on genome, metabolome, and other omics information.
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Affiliation(s)
- Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kozo Tanno
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Saitama Prefectural University
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Naho Tsuchiya
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Takumi Hirata
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kotaro Nochioka
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Ryohei Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Nobuyuki Takanashi
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Kotaro Otsuka
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Kiyomi Sakata
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Masahiro Kikuya
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Teikyo University School of Medicine
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Radiation Effects Research Foundation
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University.,Ageo Central General Hospital
| | - Eiichi N Kodama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Yohei Hamanaka
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hirohito Metoki
- Tohoku Medical Megabank Organization, Tohoku University.,Faculty of Medicine, Tohoku Medical and Pharmaceutical University
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kazuyuki Kitatani
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Setsunan University
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Mamoru Satoh
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,Institute for Biomedical Sciences, Iwate Medical University
| | - Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Dentistry, Tohoku University
| | - Shinichi Egawa
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Tadashi Ishii
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Kiyoshi Ito
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,International Research Institute of Disaster Science, Tohoku University
| | - Sadayoshi Ito
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Yasuyuki Taki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Institute of Development, Aging and Cancer, Tohoku University
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Naoto Ishii
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Graduate School of Information Sciences, Tohoku University.,Kyoto University Graduate School of Medicine Faculty of Medicine
| | - Kazuhiko Igarashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Center for Advanced Intelligence Project, RIKEN
| | - Keiko Nakayama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hozumi Motohashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Institute of Development, Aging and Cancer, Tohoku University
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Miyagi Cancer Center
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Yuh Shiwa
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Teiji Tominaga
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tokyo Medical and Dental University
| | - Kotaro Oyama
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Ryoichi Tanaka
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,The JIKEI University School of Medicine
| | - Akimune Fukushima
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Yasushi Ishigaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Tomoharu Tokutomi
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Noriko Osumi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | | | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Tomohiko Arai
- Tohoku Medical Megabank Organization, Tohoku University
| | | | | | | | - Ryujin Endo
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,Iwate Medical University School of Nursing
| | - Satoshi Nishizuka
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,Institute for Biomedical Sciences, Iwate Medical University
| | - Ichiro Tsuji
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Jiro Hitomi
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | | | - Kuniaki Ogasawara
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Information Sciences, Tohoku University
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Tohoku University Hospital, Tohoku University
| | | | | | | | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,Institute for Biomedical Sciences, Iwate Medical University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
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7
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Sakurai-Yageta M, Kawame H, Kuriyama S, Hozawa A, Nakaya N, Nagami F, Minegishi N, Ogishima S, Takai-Igarashi T, Danjoh I, Obara T, Ishikuro M, Kobayashi T, Aizawa Y, Ishihara R, Yamamoto M, Suzuki Y. A training and education program for genome medical research coordinators in the genome cohort study of the Tohoku Medical Megabank Organization. BMC Med Educ 2019; 19:297. [PMID: 31375111 PMCID: PMC6679441 DOI: 10.1186/s12909-019-1725-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Genome cohort studies are used to analyze interactions between genetic and environmental factors, providing valuable information for personalized healthcare. Large-scale and long-term cohort studies require a number of specially trained personnel, of whom those involved in obtaining informed consent play a vital role, especially during the initial phase of such studies. The Japanese Society of Human Genetics (JSHG) previously established a certification system for genome medical research coordinators (GMRCs) responsible for obtaining written consent via face-to-face explanation. Meanwhile, in the Tohoku Medical Megabank Organization (ToMMo), GMRCs are expected to play important roles not only in obtaining informed consent and conducting various assessments, but also in communicating with participants throughout the long-term follow-up. Based on the JSHG program, we therefore developed a specific education and training program for ToMMo GMRCs consisting of 17 lectures, one practical training session on the informed consent procedure, and written and interview examinations. Re-education workshops aimed at self-improvement are also carried out following certification. In this study, we evaluated the education and training program in terms of overall understanding, usefulness, and satisfaction using an anonymous questionnaire. METHODS An anonymous questionnaire addressing each aspect of the education and training program (understanding, usefulness, and satisfaction) was distributed among 152 qualified ToMMo GMRCs. Responses were received from 94 participants (61.8%). RESULTS There was a significant association between the level of overall understanding of lectures and medical qualification (nurse or clinical laboratory technologist), but not with age or educational background. The level of understanding and overall usefulness were lower in sessions related to genetics and epidemiology than those dealing with ToMMo practices. In the re-education workshops, GMRCs showed a preference for and hoped to learn more about both background knowledge and research progress in the ToMMo. CONCLUSIONS The results of our questionnaire suggest that not all ToMMo GMRCs are able to understand everything during the initial education and training program, especially in terms of genomic medicine. Continuous re-education is therefore vital in improving knowledge, skills and motivation, and preparing GMRCs for a specialist role in community-based personalized healthcare.
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Affiliation(s)
- Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
- International Research Institute of Disaster Science, 468-1 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8572 Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Yayoi Aizawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Rino Ishihara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575 Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573 Japan
- Ageo Central General Hospital, 1-10-10 Kashiwaza, Ageo, Saitama, 362-8588 Japan
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8
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Nagasaki M, Kuroki Y, Shibata TF, Katsuoka F, Mimori T, Kawai Y, Minegishi N, Hozawa A, Kuriyama S, Suzuki Y, Kawame H, Nagami F, Takai-Igarashi T, Ogishima S, Kojima K, Misawa K, Tanabe O, Fuse N, Tanaka H, Yaegashi N, Kinoshita K, Kure S, Yasuda J, Yamamoto M. Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing. Hum Genome Var 2019; 6:27. [PMID: 31231536 PMCID: PMC6555796 DOI: 10.1038/s41439-019-0057-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 01/28/2019] [Accepted: 03/15/2019] [Indexed: 12/14/2022] Open
Abstract
In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented. Here, we assembled a Japanese genome using single-molecule real-time sequencing data and characterized insertions found in the assembled genome. We identified 3691 insertions ranging from 100 bps to ~10,000 bps in the assembled genome relative to the international reference sequence (GRCh38). To validate and characterize these insertions, we mapped short-reads from 1070 Japanese individuals and 728 individuals from eight other populations to insertions integrated into GRCh38. With this result, we constructed JRGv1 (Japanese Reference Genome version 1) by integrating the 903 verified insertions, totaling 1,086,173 bases, shared by at least two Japanese individuals into GRCh38. We also constructed decoyJRGv1 by concatenating 3559 verified insertions, totaling 2,536,870 bases, shared by at least two Japanese individuals or by six other assemblies. This assembly improved the alignment ratio by 0.4% on average. These results demonstrate the importance of refining the reference assembly and creating a population-specific reference genome. JRGv1 and decoyJRGv1 are available at the JRG website. Researchers in Japan have assembled a Japanese reference genome, which includes sequences missing from the international reference genome, as well as others specific to East Asian populations. A team led by Masao Nagasaki and Masayuki Yamamoto sequenced a Japanese individual using a method, which produces longer sequences than previous technologies. Using this approach, they identified thousands of sequences spanning 2.5 million bases, which were absent in the international reference genome. Many of these were sequences able to move within the genome. They showed that the majority of these sequences are also present in early humans and chimpanzees, demonstrating that their absence from the current reference is due to deletions or limitations of earlier sequencing methodologies. In addition to providing a population-specific reference, these findings demonstrate the importance of continually improving the international reference genome.
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Affiliation(s)
- Masao Nagasaki
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yoko Kuroki
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,4Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Tomoko F Shibata
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takahiro Mimori
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,5International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hiroshi Kawame
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Soichi Ogishima
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Kazuharu Misawa
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Osamu Tanabe
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,6Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Hiroshi Tanaka
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Yaegashi
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,6Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,3Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Shiego Kure
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan.,6Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- 1Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,2Graduate School of Medicine, Tohoku University, Sendai, Japan
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9
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Yasuda J, Kinoshita K, Katsuoka F, Danjoh I, Sakurai-Yageta M, Motoike IN, Kuroki Y, Saito S, Kojima K, Shirota M, Saigusa D, Otsuki A, Kawashima J, Yamaguchi-Kabata Y, Tadaka S, Aoki Y, Mimori T, Kumada K, Inoue J, Makino S, Kuriki M, Fuse N, Koshiba S, Tanabe O, Nagasaki M, Tamiya G, Shimizu R, Takai-Igarashi T, Ogishima S, Hozawa A, Kuriyama S, Sugawara J, Tsuboi A, Kiyomoto H, Ishii T, Tomita H, Minegishi N, Suzuki Y, Suzuki K, Kawame H, Tanaka H, Taki Y, Yaegashi N, Kure S, Nagami F, Kosaki K, Sutoh Y, Hachiya T, Shimizu A, Sasaki M, Yamamoto M. Genome analyses for the Tohoku Medical Megabank Project towards establishment of personalized healthcare. J Biochem 2019; 165:139-158. [PMID: 30452759 DOI: 10.1093/jb/mvy096] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/10/2018] [Indexed: 12/29/2022] Open
Abstract
Personalized healthcare (PHC) based on an individual's genetic make-up is one of the most advanced, yet feasible, forms of medical care. The Tohoku Medical Megabank (TMM) Project aims to combine population genomics, medical genetics and prospective cohort studies to develop a critical infrastructure for the establishment of PHC. To date, a TMM CommCohort (adult general population) and a TMM BirThree Cohort (birth+three-generation families) have conducted recruitments and baseline surveys. Genome analyses as part of the TMM Project will aid in the development of a high-fidelity whole-genome Japanese reference panel, in designing custom single-nucleotide polymorphism (SNP) arrays specific to Japanese, and in estimation of the biological significance of genetic variations through linked investigations of the cohorts. Whole-genome sequencing from >3,500 unrelated Japanese and establishment of a Japanese reference genome sequence from long-read data have been done. We next aim to obtain genotype data for all TMM cohort participants (>150,000) using our custom SNP arrays. These data will help identify disease-associated genomic signatures in the Japanese population, while genomic data from TMM BirThree Cohort participants will be used to improve the reference genome panel. Follow-up of the cohort participants will allow us to test the genetic markers and, consequently, contribute to the realization of PHC.
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Affiliation(s)
- Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Japan.,Institute of Development, Aging, and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yoko Kuroki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,United Centers for Advanced Research and Translational Medicine
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Miho Kuriki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Molecular Hematology, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Tadashi Ishii
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Education and Support for Community Medicine, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, 468-1, Aramaki Aza Aoba, Aoba-ku, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Medical Data Science Promotion Office, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, Japan
| | - Yasuyuki Taki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Institute of Development, Aging, and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Obstetrics and Gynecology
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Pediatrics, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
| | | | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo, Japan
| | - Yoichi Sutoh
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center
| | - Tsuyoshi Hachiya
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center.,Division of Ultrahigh Field MRI, Institute for Biomedical Sciences Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1, Seiryo-Machi, Aoba-ku, Sendai, Japan
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10
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Miura E, Tsuchiya N, Igarashi Y, Arakawa R, Nikkuni E, Tamai T, Tabata M, Ohkouchi S, Irokawa T, Ogawa H, Takai-Igarashi T, Suzuki Y, Kuriyama S, Tamiya G, Hozawa A, Yamamoto M, Kurosawa H. Respiratory resistance among adults in a population-based cohort study in Northern Japan. Respir Investig 2019; 57:274-281. [PMID: 30770233 DOI: 10.1016/j.resinv.2018.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 12/14/2018] [Accepted: 12/21/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND Forced oscillation technique (FOT) is a noninvasive method used to measure respiratory system resistance (Rrs) and reactance (Xrs) during quiet breathing, which has been extensively studied in clinical settings. The distribution of measured FOT values was previously assessed in a community-based cohort study. In this study, we aimed to confirm the distribution of measured FOT values in a different cohort in order to investigate the relationship between these values and patient clinical and biological data. METHODS We reviewed FOT data and relevant patient clinical and biological information collected from the Community-Based Cohort Study (CommCohort Study), carried out between 2013 to 2016 as a part of the Tohoku Medical Megabank project (TMM). In total, 16,231 adults were enrolled in the study (Male/Female: 4886/11,345). RESULTS Significant gender differences were observed in distributions of Rrs and Xrs values at 5 Hz (termed R5 and X5, respectively). R5 values in males were lower than those in females, while X5 values in males were slightly less negative. High R5 values were strongly associated with high BMI, short height, smoking status in males, high serum IgE level, and high peripheral blood eosinophil count. CONCLUSION The present distribution values and their relation to clinical and biological data should provide useful insights for clinical settings and serve as a helpful guide in implementing FOT. Forced oscillation technique, respiratory system resistance, respiratory system reactance, gender difference, obesity.
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Affiliation(s)
- Emiri Miura
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan
| | - Naho Tsuchiya
- Tohoku University Tohoku Medical Megabank Organization, Japan
| | - Yu Igarashi
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan
| | - Ritsuko Arakawa
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan
| | - Etsuhiro Nikkuni
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan
| | - Tokiwa Tamai
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan; Center for Environmental Conservation and Research Safety, Tohoku University, Japan
| | | | - Shinya Ohkouchi
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan; Center for Environmental Conservation and Research Safety, Tohoku University, Japan
| | - Toshiya Irokawa
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan; Center for Environmental Conservation and Research Safety, Tohoku University, Japan
| | - Hiromasa Ogawa
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan; Center for Environmental Conservation and Research Safety, Tohoku University, Japan
| | | | - Yoichi Suzuki
- Tohoku University Tohoku Medical Megabank Organization, Japan
| | | | - Gen Tamiya
- Tohoku University Tohoku Medical Megabank Organization, Japan
| | - Atsushi Hozawa
- Tohoku University Tohoku Medical Megabank Organization, Japan
| | | | - Hajime Kurosawa
- Department of Occupational Health, Tohoku University Graduate School of Medicine, Japan; Tohoku University Tohoku Medical Megabank Organization, Japan; Center for Environmental Conservation and Research Safety, Tohoku University, Japan.
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11
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Tanikawa C, Kamatani Y, Toyoshima O, Sakamoto H, Ito H, Takahashi A, Momozawa Y, Hirata M, Fuse N, Takai-Igarashi T, Shimizu A, Sasaki M, Yamaji T, Sawada N, Iwasaki M, Tsugane S, Naito M, Hishida A, Wakai K, Furusyo N, Murakami Y, Nakamura Y, Imoto I, Inazawa J, Oze I, Sato N, Tanioka F, Sugimura H, Hirose H, Yoshida T, Matsuo K, Kubo M, Matsuda K. Genome-wide association study identifies gastric cancer susceptibility loci at 12q24.11-12 and 20q11.21. Cancer Sci 2018; 109:4015-4024. [PMID: 30281874 PMCID: PMC6272082 DOI: 10.1111/cas.13815] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022] Open
Abstract
Gastric cancer is the third leading cause of cancer mortality in Japan and worldwide. Although previous studies identify various genetic variations associated with gastric cancer, host genetic factors are largely unidentified. To identify novel gastric cancer loci in the Japanese population, herein, we carried out a large‐scale genome‐wide association study using 6171 cases and 27 178 controls followed by three replication analyses. Analysis using a total of 11 507 cases and 38 904 controls identified two novel loci on 12q24.11‐12 (rs6490061, P = 3.20 × 10−8 with an odds ratio [OR] of 0.905) and 20q11.21 (rs2376549, P = 8.11 × 10−10 with an OR of 1.109). rs6490061 is located at intron 19 of the CUX2 gene, and its expression was suppressed by Helicobacter pylori infection. rs2376549 is included within the gene cluster of DEFB families that encode antibacterial peptides. We also found a significant association of rs7849280 in the ABO gene locus on 9q34.2 (P = 2.64 × 10−13 with an OR of 1.148). CUX2 and ABO expression in gastric mucosal tissues was significantly associated with rs6490061 and rs7849280 (P = 0.0153 and 8.00 × 10−11), respectively. Our findings show the crucial roles of genetic variations in the pathogenesis of gastric cancer.
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Affiliation(s)
- Chizu Tanikawa
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | - Hiromi Sakamoto
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hidemi Ito
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan.,Department of Genomic Medicine, Research Institute, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Makoto Hirata
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Taiki Yamaji
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shoichiro Tsugane
- Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Mariko Naito
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan.,Department of Oral Epidemiology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Asahi Hishida
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Norihiro Furusyo
- Department of Environmental Medicine and Infectious Disease, Kyushu University, Fukuoka, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Nakamura
- Departments of Medicine and Surgery and Center for Personalized Therapeutics, The University of Chicago, Chicago, USA
| | - Issei Imoto
- Department of Human Genetics, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan.,Division of Molecular Genetics, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isao Oze
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Naomi Sato
- Department of Clinical Nursing, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Fumihiko Tanioka
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Shizuoka, Japan.,Division of Pathology, Iwata City Hospital, Shizuoka, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, Hamamatsu University School of Medicine, Shizuoka, Japan
| | | | - Teruhiko Yoshida
- Division of Genetics, National Cancer Center Research Institute, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Aichi, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan.,Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
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12
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Koshiba S, Motoike I, Saigusa D, Inoue J, Shirota M, Katoh Y, Katsuoka F, Danjoh I, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Ogishima S, Fuse N, Kure S, Tamiya G, Tanabe O, Yasuda J, Kinoshita K, Yamamoto M. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes Cells 2018; 23:406-417. [PMID: 29701317 DOI: 10.1111/gtc.12588] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 01/05/2023]
Abstract
Population-based prospective cohort studies are indispensable for modern medical research as they provide important knowledge on the influences of many kinds of genetic and environmental factors on the cause of disease. Although traditional cohort studies are mainly conducted using questionnaires and physical examinations, modern cohort studies incorporate omics and genomic approaches to obtain comprehensive physical information, including genetic information. Here, we report the design and midterm results of multi-omics analysis on population-based prospective cohort studies from the Tohoku Medical Megabank (TMM) Project. We have incorporated genomic and metabolomic studies in the TMM cohort study as both metabolome and genome analyses are suitable for high-throughput analysis of large-scale cohort samples. Moreover, an association study between the metabolome and genome show that metabolites are an important intermediate phenotype connecting genetic and lifestyle factors to physical and pathologic phenotypes. We apply our metabolome and genome analyses to large-scale cohort samples in the following studies.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasutake Katoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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13
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Takai-Igarashi T, Kinoshita K, Nagasaki M, Ogishima S, Nakamura N, Nagase S, Nagaie S, Saito T, Nagami F, Minegishi N, Suzuki Y, Suzuki K, Hashizume H, Kuriyama S, Hozawa A, Yaegashi N, Kure S, Tamiya G, Kawaguchi Y, Tanaka H, Yamamoto M. Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design. BMC Med Inform Decis Mak 2017; 17:100. [PMID: 28683736 PMCID: PMC5501115 DOI: 10.1186/s12911-017-0494-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 06/27/2017] [Indexed: 01/08/2023] Open
Abstract
Background With the goal of realizing genome-based personalized healthcare, we have developed a biobank that integrates personal health, genome, and omics data along with biospecimens donated by volunteers of 150,000. Such a large-scale of data integration involves obvious risks of privacy violation. The research use of personal genome and health information is a topic of global discussion with regard to the protection of privacy while promoting scientific advancement. The present paper reports on our plans, current attempts, and accomplishments in addressing security problems involved in data sharing to ensure donor privacy while promoting scientific advancement. Methods Biospecimens and data have been collected in prospective cohort studies with the comprehensive agreement. The sample size of 150,000 participants was required for multiple researches including genome-wide screening of gene by environment interactions, haplotype phasing, and parametric linkage analysis. Results We established the TohokuMedicalMegabank (TMM) data sharing policy: a privacy protection rule that requires physical, personnel, and technological safeguards against privacy violation regarding the use and sharing of data. The proposed policy refers to that of NCBI and that of the Sanger Institute. The proposed policy classifies shared data according to the strength of re-identification risks. Local committees organized by TMM evaluate re-identification risk and assign a security category to a dataset. Every dataset is stored in an assigned segment of a supercomputer in accordance with its security category. A security manager should be designated to handle all security problems at individual data use locations. The proposed policy requires closed networks and IP-VPN remote connections. Conclusion The mission of the biobank is to distribute biological resources most productively. This mission motivated us to collect biospecimens and health data and simultaneously analyze genome/omics data in-house. The biobank also has the mission of improving the quality and quantity of the contents of the biobank. This motivated us to request users to share the results of their research as feedback to the biobank. The TMM data sharing policy has tackled every security problem originating with the missions. We believe our current implementation to be the best way to protect privacy in data sharing. Electronic supplementary material The online version of this article (doi:10.1186/s12911-017-0494-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Naoki Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Sachiko Nagase
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Satoshi Nagaie
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Tomo Saito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Hiroaki Hashizume
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Yoshio Kawaguchi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Japan. .,Graduate School of Medicine, Tohoku University, Sendai, Japan.
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14
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Koshiba S, Motoike I, Kojima K, Hasegawa T, Shirota M, Saito T, Saigusa D, Danjoh I, Katsuoka F, Ogishima S, Kawai Y, Yamaguchi-Kabata Y, Sakurai M, Hirano S, Nakata J, Motohashi H, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Fuse N, Kiyomoto H, Sugawara J, Suzuki Y, Kure S, Yaegashi N, Tanabe O, Kinoshita K, Yasuda J, Yamamoto M. The structural origin of metabolic quantitative diversity. Sci Rep 2016; 6:31463. [PMID: 27528366 PMCID: PMC4985752 DOI: 10.1038/srep31463] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/18/2016] [Indexed: 12/21/2022] Open
Abstract
Relationship between structural variants of enzymes and metabolic phenotypes in human population was investigated based on the association study of metabolite quantitative traits with whole genome sequence data for 512 individuals from a population cohort. We identified five significant associations between metabolites and non-synonymous variants. Four of these non-synonymous variants are located in enzymes involved in metabolic disorders, and structural analyses of these moderate non-synonymous variants demonstrate that they are located in peripheral regions of the catalytic sites or related regulatory domains. In contrast, two individuals with larger changes of metabolite levels were also identified, and these individuals retained rare variants, which caused non-synonymous variants located near the catalytic site. These results are the first demonstrations that variant frequency, structural location, and effect for phenotype correlate with each other in human population, and imply that metabolic individuality and susceptibility for diseases may be elicited from the moderate variants and much more deleterious but rare variants.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Kaname Kojima
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Takanori Hasegawa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Tomo Saito
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yosuke Kawai
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sachiko Hirano
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junichi Nakata
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hozumi Motohashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Shigeo Kure
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579 Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Jun Yasuda
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan.,Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
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15
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Kuriyama S, Yaegashi N, Nagami F, Arai T, Kawaguchi Y, Osumi N, Sakaida M, Suzuki Y, Nakayama K, Hashizume H, Tamiya G, Kawame H, Suzuki K, Hozawa A, Nakaya N, Kikuya M, Metoki H, Tsuji I, Fuse N, Kiyomoto H, Sugawara J, Tsuboi A, Egawa S, Ito K, Chida K, Ishii T, Tomita H, Taki Y, Minegishi N, Ishii N, Yasuda J, Igarashi K, Shimizu R, Nagasaki M, Koshiba S, Kinoshita K, Ogishima S, Takai-Igarashi T, Tominaga T, Tanabe O, Ohuchi N, Shimosegawa T, Kure S, Tanaka H, Ito S, Hitomi J, Tanno K, Nakamura M, Ogasawara K, Kobayashi S, Sakata K, Satoh M, Shimizu A, Sasaki M, Endo R, Sobue K, Tohoku Medical Megabank Project Study Group T, Yamamoto M. The Tohoku Medical Megabank Project: Design and Mission. J Epidemiol 2016; 26:493-511. [PMID: 27374138 PMCID: PMC5008970 DOI: 10.2188/jea.je20150268] [Citation(s) in RCA: 202] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Great East Japan Earthquake (GEJE) and resulting tsunami of March 11, 2011 gave rise to devastating damage on the Pacific coast of the Tohoku region. The Tohoku Medical Megabank Project (TMM), which is being conducted by Tohoku University Tohoku Medical Megabank Organization (ToMMo) and Iwate Medical University Iwate Tohoku Medical Megabank Organization (IMM), has been launched to realize creative reconstruction and to solve medical problems in the aftermath of this disaster. We started two prospective cohort studies in Miyagi and Iwate Prefectures: a population-based adult cohort study, the TMM Community-Based Cohort Study (TMM CommCohort Study), which will recruit 80 000 participants, and a birth and three-generation cohort study, the TMM Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study), which will recruit 70 000 participants, including fetuses and their parents, siblings, grandparents, and extended family members. The TMM CommCohort Study will recruit participants from 2013 to 2016 and follow them for at least 5 years. The TMM BirThree Cohort Study will recruit participants from 2013 to 2017 and follow them for at least 4 years. For children, the ToMMo Child Health Study, which adopted a cross-sectional design, was also started in November 2012 in Miyagi Prefecture. An integrated biobank will be constructed based on the two prospective cohort studies, and ToMMo and IMM will investigate the chronic medical impacts of the GEJE. The integrated biobank of TMM consists of health and clinical information, biospecimens, and genome and omics data. The biobank aims to establish a firm basis for personalized healthcare and medicine, mainly for diseases aggravated by the GEJE in the two prefectures. Biospecimens and related information in the biobank will be distributed to the research community. TMM itself will also undertake genomic and omics research. The aims of the genomic studies are: 1) to construct an integrated biobank; 2) to return genomic research results to the participants of the cohort studies, which will lead to the implementation of personalized healthcare and medicine in the affected areas in the near future; and 3) to contribute the development of personalized healthcare and medicine worldwide. Through the activities of TMM, we will clarify how to approach prolonged healthcare problems in areas damaged by large-scale disasters and how useful genomic information is for disease prevention.
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Abstract
BACKGROUND In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will give periodontal researchers opportunities to elucidate pathways and mechanisms of periodontitis. An ontology for periodontitis can be a model for integration of large variety of factors relating to a complex disease such as chronic inflammation in different organs accompanied by bone remodeling and immune system disorders, which has recently been referred to as osteoimmunology. METHODS Terms characteristic of descriptions related to the onset and progression of periodontitis were manually extracted from 194 review articles and PubMed abstracts by experts in periodontology. We specified all the relations between the extracted terms and constructed them into an ontology for periodontitis. We also investigated matching between classes of our ontology and that of Gene Ontology Biological Process. RESULTS We developed an ontology for periodontitis called Periodontitis-Ontology (PeriO). The pathological progression of periodontitis is caused by complex, multi-factor interrelationships. PeriO consists of all the required concepts to represent the pathological progression and clinical treatment of periodontitis. The pathological processes were formalized with reference to Basic Formal Ontology and Relation Ontology, which accounts for participants in the processes realized by biological objects such as molecules and cells. We investigated the peculiarity of biological processes observed in pathological progression and medical treatments for the disease in comparison with Gene Ontology Biological Process (GO-BP) annotations. The results indicated that peculiarities of Perio existed in 1) granularity and context dependency of both the conceptualizations, and 2) causality intrinsic to the pathological processes. PeriO defines more specific concepts than GO-BP, and thus can be added as descendants of GO-BP leaf nodes. PeriO defines causal relationships between the process concepts, which are not shown in GO-BP. The difference can be explained by the goal of conceptualization: PeriO focuses on mechanisms of the pathogenic progress, while GO-BP focuses on cataloguing all of the biological processes observed in experiments. The goal of conceptualization in PeriO may reflect the domain knowledge where a consequence in the causal relationships is a primary interest. We believe the peculiarities can be shared among other diseases when comparing processes in disease against GO-BP. CONCLUSIONS This is the first open biomedical ontology of periodontitis capable of providing a foundation for an ontology-based model of aspects of molecular biology and pathological processes related to periodontitis, as well as its relations with systemic diseases. PeriO is available at http://bio-omix.tmd.ac.jp/periodontitis/.
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Affiliation(s)
- Asami Suzuki
- Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Bunkyō, Japan ; General Dentistry, The Nippon Dental University Hospital at Tokyo, Tokyo, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ; Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Bunkyō, Japan
| | - Jun Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ; School of Medicine, Tohoku University, Sendai, Japan
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ; Department of Computational Biology, Graduate School of Biomedical Science, Tokyo Medical and Dental University, Bunkyō, Japan
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17
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Sawai H, Takai-Igarashi T, Tanaka H. Identification of collaborative activities with oxidative phosphorylation in bipolar disorder. Bioinformation 2015; 11:207-16. [PMID: 26124562 PMCID: PMC4479050 DOI: 10.6026/97320630011207] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 01/14/2015] [Accepted: 01/15/2015] [Indexed: 01/01/2023] Open
Abstract
UNLABELLED Bipolar disorder (BD) is a psychiatric disease considered to polygenic with multiple factors in genetics, each of which is not dominant but collaborative during pathogenic progression. We describe a method that estimates the collaborative contribution to the disease between a certain well-studied pathway and the other candidate pathway using Gene Set Enrichment Analysis (GSEA). We describe a modified GSEA (improved derivation) to identify genes that are significantly and differentially expressed between disease and non-disease states and that are consistently co-expressed with a target pathway which is deeply related to disease etiology. The modified GSEA uses available gene expression data to identify molecular mechanism (ubiquitin-proteasome and inflammatory response) associated with the disease. We believe that this approach could reveal hidden relations between a certain well-studied pathway and the other candidate pathway known in literature. ABBREVIATIONS ATP5I - ATP synthase H+ transporting mitochondrial F0 complex subunit E, ATP5J - ATP synthase H+ transporting mitochondrial F0 complex subunit F6, BAD - Bcl-2-associated death promoter, BAX - Bcl-2-associated x protein, Bcl-2 - B-cell lymphoma 2, BDNF - brain derived neurotrophic factor, COX5B - Cytochrome c oxidase subunit Vb, COX7A2 - cytochrome c oxidase subunit VIIa polypeptide 2, DLK - dual leucine zipper-bearing kinase, GABA - Gamma aminobutyric acid, IL-8 - Interleukin 8, NDUFA1 - NADH dehydrogenase 1 alpha subcomplex 1, NDUFB2 - NADH dehydrogenase1 beta subcomplex 2, NDUFS4 - NADH dehydrogenase Fe-S protein 4, NGF - nerve growth factor, PPP2R5C - protein phosphatase 2 regulatory subunit B gamma, PSMA3 - proteasome subunit alpha type 3, PSMA7 - proteasome subunit alpha type 7, PSMB1 - proteasome subunit beta type 1, PSMB6 - proteasome subunit beta type 6, PSMB7 - proteasome subunit beta type 7, PSMC2 - proteasome 26S subunit ATPase 2, PSMC5 - proteasome 26S subunit ATPase 5, SLC6A4 - solute carrier family 6 member 4, TNFa - tumor necrosis factor a, UBE2A - ubiquitinconjugating enzyme E2A, UCRC - ubiquinol-cytochrome c reductase complex, UFC1 - ubiquitin-fold modifier conjugating enzyme 1, UQCRQ - ubiquinol-cytochrome c reductase complex III subunit VII, USP14 - ubiquitin specific protease 14.
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Affiliation(s)
- Hashime Sawai
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai Miyagi, 980-8573,Japan
| | - Hiroshi Tanaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai Miyagi, 980-8573,Japan ; Graduate School of Biomedical Science, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Hori-Tanaka Y, Yura K, Takai-Igarashi T, Tanaka H. Structural classification of steroid-binding sites on proteins by coarse-grained atomic environment and its correlation with their biological function. Steroids 2015; 96:81-8. [PMID: 25645710 DOI: 10.1016/j.steroids.2015.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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] [Received: 09/14/2014] [Revised: 12/22/2014] [Accepted: 01/19/2015] [Indexed: 11/19/2022]
Abstract
Steroid hormone is extensively used for transmitting variety of biological signals in organisms. Natural steroid hormone is synthesized from cholesterol in adrenal cortex and in sexual gland in vertebrates. Appropriately dosed synthetic steroid hormones can be used for medication. Despite their positive effects as medicine, they sometimes cause significant side effects due to their wide range of actions, and the studies for discovering the mechanisms of side effects were carried out aiming to reduce the side effects. The fundamental cause of the side effects seems to be interactions between the steroid and a non-target protein. To understand the possible range of interaction of steroid molecule, we gathered all the three-dimensional structures of protein-steroid complex determined by X-ray crystallography, compared the atomic environments of the steroid-binding sites in proteins and classified the pattern of steroid binding. Protein Data Bank contained 871 structures of steroid-protein complexes in 382 entries. For this study, we selected 832 steroid binding proteins. Using a newly developed method to describe the atomic environments of these steroid molecules and their function, we were able to separate the environments into six patterns. This classification had a potential to predict the function of function-unknown proteins with a co-crystallized steroid molecule. We speculated that the proteins grouped into the same pattern of nuclear receptors were the candidates of non-targeted proteins causing a side effect by a therapeutic prescription of steroid hormone.
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Affiliation(s)
- Yasuha Hori-Tanaka
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Kei Yura
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan; Center for Informational Biology, Ochanomizu University, 2-1-1, Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan; National Institute of Genetics, 1111, Yata, Mishima, Shizuoka 411-8540, Japan.
| | - Takako Takai-Igarashi
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hiroshi Tanaka
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan; Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
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19
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Ehara T, Kamei Y, Yuan X, Takahashi M, Kanai S, Tamura E, Tsujimoto K, Tamiya T, Nakagawa Y, Shimano H, Takai-Igarashi T, Hatada I, Suganami T, Hashimoto K, Ogawa Y. Ligand-activated PPARα-dependent DNA demethylation regulates the fatty acid β-oxidation genes in the postnatal liver. Diabetes 2015; 64:775-84. [PMID: 25311726 DOI: 10.2337/db14-0158] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 11/13/2022]
Abstract
The metabolic function of the liver changes sequentially during early life in mammals to adapt to the marked changes in nutritional environment. Accordingly, hepatic fatty acid β-oxidation is activated after birth to produce energy from breast milk lipids. However, how it is induced during the neonatal period is poorly understood. Here we show DNA demethylation and increased mRNA expression of the fatty acid β-oxidation genes in the postnatal mouse liver. The DNA demethylation does not occur in the fetal mouse liver under the physiologic condition, suggesting that it is specific to the neonatal period. Analysis of mice deficient in the nuclear receptor peroxisome proliferator-activated receptor α (PPARα) and maternal administration of a PPARα ligand during the gestation and lactation periods reveal that the DNA demethylation is PPARα dependent. We also find that DNA methylation of the fatty acid β-oxidation genes are reduced in the adult human liver relative to the fetal liver. This study represents the first demonstration that the ligand-activated PPARα-dependent DNA demethylation regulates the hepatic fatty acid β-oxidation genes during the neonatal period, thereby highlighting the role of a lipid-sensing nuclear receptor in the gene- and life-stage-specific DNA demethylation of a particular metabolic pathway.
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Affiliation(s)
- Tatsuya Ehara
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan Nutrition Research Department, Nutritional Science Institute, Morinaga Milk Industry Co. Ltd., Zama, Kanagawa, Japan
| | - Yasutomi Kamei
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Xunmei Yuan
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Mayumi Takahashi
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Sayaka Kanai
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Erina Tamura
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Kazutaka Tsujimoto
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Takashi Tamiya
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshimi Nakagawa
- Department of Internal Medicine (Metabolism and Endocrinology), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hitoshi Shimano
- Department of Internal Medicine (Metabolism and Endocrinology), Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Takako Takai-Igarashi
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Aoba-ku, Sendai, Miyagi, Japan
| | - Izuho Hatada
- Genome Science, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Takayoshi Suganami
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan Japan Science and Technology Agency, PRESTO, Goban-cho Chiyoda-ku, Tokyo, Japan
| | - Koshi Hashimoto
- Department of Preemptive Medicine and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshihiro Ogawa
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
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20
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Hatazawa Y, Tadaishi M, Nagaike Y, Morita A, Ogawa Y, Ezaki O, Takai-Igarashi T, Kitaura Y, Shimomura Y, Kamei Y, Miura S. PGC-1α-mediated branched-chain amino acid metabolism in the skeletal muscle. PLoS One 2014; 9:e91006. [PMID: 24638054 PMCID: PMC3956461 DOI: 10.1371/journal.pone.0091006] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 02/06/2014] [Indexed: 11/20/2022] Open
Abstract
Peroxisome proliferator-activated receptor (PPAR) γ coactivator 1α (PGC-1α) is a coactivator of various nuclear receptors and other transcription factors, which is involved in the regulation of energy metabolism, thermogenesis, and other biological processes that control phenotypic characteristics of various organ systems including skeletal muscle. PGC-1α in skeletal muscle is considered to be involved in contractile protein function, mitochondrial function, metabolic regulation, intracellular signaling, and transcriptional responses. Branched-chain amino acid (BCAA) metabolism mainly occurs in skeletal muscle mitochondria, and enzymes related to BCAA metabolism are increased by exercise. Using murine skeletal muscle overexpressing PGC-1α and cultured cells, we investigated whether PGC-1α stimulates BCAA metabolism by increasing the expression of enzymes involved in BCAA metabolism. Transgenic mice overexpressing PGC-1α specifically in the skeletal muscle had increased the expression of branched-chain aminotransferase (BCAT) 2, branched-chain α-keto acid dehydrogenase (BCKDH), which catabolize BCAA. The expression of BCKDH kinase (BCKDK), which phosphorylates BCKDH and suppresses its enzymatic activity, was unchanged. The amount of BCAA in the skeletal muscle was significantly decreased in the transgenic mice compared with that in the wild-type mice. The amount of glutamic acid, a metabolite of BCAA catabolism, was increased in the transgenic mice, suggesting the activation of muscle BCAA metabolism by PGC-1α. In C2C12 cells, the overexpression of PGC-1α significantly increased the expression of BCAT2 and BCKDH but not BCKDK. Thus, PGC-1α in the skeletal muscle is considered to significantly contribute to BCAA metabolism.
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Affiliation(s)
- Yukino Hatazawa
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory of Molecular Nutrition, Graduate School of Environmental and Life Science, Kyoto Prefectural University, Kyoto, Japan
| | - Miki Tadaishi
- Department of Food Function and Labeling, National Institute of Health and Nutrition, Tokyo, Japan
| | - Yuta Nagaike
- Laboratory of Nutritional Biochemistry, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Akihito Morita
- Laboratory of Nutritional Biochemistry, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yoshihiro Ogawa
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Osamu Ezaki
- Department of Human Health and Design, Showa Women's University, Tokyo, Japan
| | - Takako Takai-Igarashi
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yasuyuki Kitaura
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoshiharu Shimomura
- Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yasutomi Kamei
- Laboratory of Molecular Nutrition, Graduate School of Environmental and Life Science, Kyoto Prefectural University, Kyoto, Japan
- * E-mail: (YS); (SM)
| | - Shinji Miura
- Laboratory of Nutritional Biochemistry, Graduate School of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan
- * E-mail: (YS); (SM)
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21
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Iwasaki Y, Suganami T, Hachiya R, Shirakawa I, Kim-Saijo M, Tanaka M, Hamaguchi M, Takai-Igarashi T, Nakai M, Miyamoto Y, Ogawa Y. Activating transcription factor 4 links metabolic stress to interleukin-6 expression in macrophages. Diabetes 2014; 63:152-61. [PMID: 23990363 DOI: 10.2337/db13-0757] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [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: 11/13/2022]
Abstract
Chronic inflammation is a molecular element of the metabolic syndrome and type 2 diabetes. Saturated fatty acids (SFAs) are considered to be an important proinflammatory factor. However, it is still incompletely understood how SFAs induce proinflammatory cytokine expression. Hereby we report that activating transcription factor (ATF) 4, a transcription factor that is induced downstream of metabolic stresses including endoplasmic reticulum (ER) stress, plays critical roles in SFA-induced interleukin-6 (Il6) expression. DNA microarray analysis using primary macrophages revealed that the ATF4 pathway is activated by SFAs. Haploinsufficiency and short hairpin RNA-based knockdown of ATF4 in macrophages markedly inhibited SFA- and metabolic stress-induced Il6 expression. Conversely, pharmacological activation of the ATF4 pathway and overexpression of ATF4 resulted in enhanced Il6 expression. Moreover, ATF4 acts in synergy with the Toll-like receptor-4 signaling pathway, which is known to be activated by SFAs. At a molecular level, we found that ATF4 exerts its proinflammatory effects through at least two different mechanisms: ATF4 is involved in SFA-induced nuclear factor-κB activation; and ATF4 directly activates the Il6 promoter. These findings provide evidence suggesting that ATF4 links metabolic stress and Il6 expression in macrophages.
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Affiliation(s)
- Yorihiro Iwasaki
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
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22
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Takahashi M, Kamei Y, Ehara T, Yuan X, Suganami T, Takai-Igarashi T, Hatada I, Ogawa Y. Analysis of DNA methylation change induced by Dnmt3b in mouse hepatocytes. Biochem Biophys Res Commun 2013; 434:873-8. [PMID: 23611774 DOI: 10.1016/j.bbrc.2013.04.041] [Citation(s) in RCA: 13] [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: 03/30/2013] [Accepted: 04/07/2013] [Indexed: 01/25/2023]
Abstract
DNA methylation is a key epigenetic contributor to gene regulation in mammals. We have recently found that in the mouse liver, the promoter region of glycerol-3-phosphate acyltransferase 1, a rate-limiting enzyme of de novo lipogenesis, is regulated by DNA methylation, which is mediated by Dnmt3b, an enzyme required for the initiation of de novo methylation. In this study, using primary cultures of mouse hepatocytes with adenoviral overexpression of Dnmt3b, we characterized Dnmt3b-dependent DNA methylation on a genome-wide basis. A genome-wide DNA methylation analysis, called microarray-based integrated analysis of methylation by isoschizomers, identified 108 genes with Dnmt3b dependent DNA methylation. In DNA expression array analysis, expression of some genes with Dnmt3b-dependent DNA methylation was suppressed. Studies with primary mouse hepatocytes overexpressing Dnmt3b or Dnmt3a revealed that many genes with Dnmt3b-dependent methylation are not methylated by Dnmt3a, whereas those methylated by Dnmt3a are mostly methylated by Dnmt3b. Bioinformatic analysis showed that the CANAGCTG and CCGGWNCSC (N denotes A, T, G, or C; W denotes A or T; and S denotes C or G) sequences are enriched in genes methylated by overexpression of Dnmt3b and Dnmt3a, respectively. We also observed a large number of genes with Dnmt3b-dependent DNA methylation in primary cultures of mouse hepatocytes with adenoviral overexpression of Dnmt3, suggesting that Dnmt3b is an important DNA methyltransferase in primary mouse hepatocytes, targets specific genes, and potentially plays a role in vivo.
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Affiliation(s)
- Mayumi Takahashi
- Department of Organ Network and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Tokyo 136-8510, Japan.
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23
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Hatano A, Chiba H, Moesa HA, Taniguchi T, Nagaie S, Yamanegi K, Takai-Igarashi T, Tanaka H, Fujibuchi W. CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses. Database (Oxford) 2011; 2011:bar046. [PMID: 22039163 PMCID: PMC3204613 DOI: 10.1093/database/bar046] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
CELLPEDIA is a repository database for current knowledge about human cells. It contains various types of information, such as cell morphologies, gene expression and literature references. The major role of CELLPEDIA is to provide a digital dictionary of human cells for the biomedical field, including support for the characterization of artificially generated cells in regenerative medicine. CELLPEDIA features (i) its own cell classification scheme, in which whole human cells are classified by their physical locations in addition to conventional taxonomy; and (ii) cell differentiation pathways compiled from biomedical textbooks and journal papers. Currently, human differentiated cells and stem cells are classified into 2260 and 66 cell taxonomy keys, respectively, from which 934 parent-child relationships reported in cell differentiation or transdifferentiation pathways are retrievable. As far as we know, this is the first attempt to develop a digital cell bank to function as a public resource for the accumulation of current knowledge about human cells. The CELLPEDIA homepage is freely accessible except for the data submission pages that require authentication (please send a password request to cell-info@cbrc.jp). Database URL: http://cellpedia.cbrc.jp/
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Affiliation(s)
- Akiko Hatano
- Computational Biology Research Center, Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
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24
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Sugita S, Kamei Y, Akaike F, Suganami T, Kanai S, Hattori M, Manabe Y, Fujii N, Takai-Igarashi T, Tadaishi M, Oka JI, Aburatani H, Yamada T, Katagiri H, Kakehi S, Tamura Y, Kubo H, Nishida K, Miura S, Ezaki O, Ogawa Y. Increased systemic glucose tolerance with increased muscle glucose uptake in transgenic mice overexpressing RXRγ in skeletal muscle. PLoS One 2011; 6:e20467. [PMID: 21655215 PMCID: PMC3105070 DOI: 10.1371/journal.pone.0020467] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 04/26/2011] [Indexed: 01/27/2023] Open
Abstract
Background Retinoid X receptor (RXR) γ is a nuclear receptor-type transcription
factor expressed mostly in skeletal muscle, and regulated by nutritional
conditions. Previously, we established transgenic mice overexpressing
RXRγ in skeletal muscle (RXRγ mice), which showed lower blood
glucose than the control mice. Here we investigated their glucose
metabolism. Methodology/Principal Findings RXRγ mice were subjected to glucose and insulin tolerance tests, and
glucose transporter expression levels, hyperinsulinemic-euglycemic clamp and
glucose uptake were analyzed. Microarray and bioinformatics analyses were
done. The glucose tolerance test revealed higher glucose disposal in
RXRγ mice than in control mice, but insulin tolerance test revealed no
difference in the insulin-induced hypoglycemic response. In the
hyperinsulinemic-euglycemic clamp study, the basal glucose disposal rate was
higher in RXRγ mice than in control mice, indicating an
insulin-independent increase in glucose uptake. There was no difference in
the rate of glucose infusion needed to maintain euglycemia (glucose infusion
rate) between the RXRγ and control mice, which is consistent with the
result of the insulin tolerance test. Skeletal muscle from RXRγ mice
showed increased Glut1 expression, with increased glucose uptake, in an
insulin-independent manner. Moreover, we performed in vivo
luciferase reporter analysis using Glut1 promoter
(Glut1-Luc). Combination of RXRγ and PPARδ
resulted in an increase in Glut1-Luc activity in skeletal
muscle in vivo. Microarray data showed that RXRγ
overexpression increased a diverse set of genes, including glucose
metabolism genes, whose promoter contained putative PPAR-binding motifs. Conclusions/Significance Systemic glucose metabolism was increased in transgenic mice overexpressing
RXRγ. The enhanced glucose tolerance in RXRγ mice may be mediated at
least in part by increased Glut1 in skeletal muscle. These results show the
importance of skeletal muscle gene regulation in systemic glucose
metabolism. Increasing RXRγ expression may be a novel therapeutic
strategy against type 2 diabetes.
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Affiliation(s)
- Satoshi Sugita
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
| | - Yasutomi Kamei
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
- * E-mail:
| | - Fumiko Akaike
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
- Laboratory of Pharmacology, Faculty of
Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Takayoshi Suganami
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
| | - Sayaka Kanai
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
| | - Maki Hattori
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
- Laboratory of Pharmacology, Faculty of
Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Yasuko Manabe
- Graduate School of Human Health Sciences,
Tokyo Metropolitan University, Tokyo, Japan
| | - Nobuharu Fujii
- Graduate School of Human Health Sciences,
Tokyo Metropolitan University, Tokyo, Japan
| | - Takako Takai-Igarashi
- Department of Bioinformatics, Graduate School
of Biomedical Science, Tokyo Medical and Dental University, Tokyo,
Japan
| | - Miki Tadaishi
- Nutritional Science Program, National
Institute of Health and Nutrition, Tokyo, Japan
- Department of Nutritional Science, Faculty of
Applied Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Jun-Ichiro Oka
- Laboratory of Pharmacology, Faculty of
Pharmaceutical Sciences, Tokyo University of Science, Chiba, Japan
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and
Technology, University of Tokyo, Tokyo, Japan
| | - Tetsuya Yamada
- Department of Metabolic Diseases, Center for
Metabolic Diseases, Tohoku University Graduate School of Medicine, Miyagi,
Japan
| | - Hideki Katagiri
- Department of Metabolic Diseases, Center for
Metabolic Diseases, Tohoku University Graduate School of Medicine, Miyagi,
Japan
| | - Saori Kakehi
- Department of Medicine, Metabolism and
Endocrinology, School of Medicine, Juntendo University, Tokyo, Japan
| | - Yoshifumi Tamura
- Department of Medicine, Metabolism and
Endocrinology, School of Medicine, Juntendo University, Tokyo, Japan
- Sportology Center, Juntendo University,
Tokyo, Japan
| | | | | | - Shinji Miura
- Nutritional Science Program, National
Institute of Health and Nutrition, Tokyo, Japan
| | - Osamu Ezaki
- Nutritional Science Program, National
Institute of Health and Nutrition, Tokyo, Japan
| | - Yoshihiro Ogawa
- Department of Molecular Medicine and
Metabolism, Medical Research Institute, Tokyo Medical and Dental University,
Tokyo, Japan
- Global Center of Excellence Program,
International Research Center for Molecular Science in Tooth and Bone Diseases,
Medical Research Institute, Tokyo Medical and Dental University, Tokyo,
Japan
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25
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Takai-Igarashi T, Akasaka R, Suzuki K, Furukawa T, Yoshida M, Inoue K, Maruyama T, Maejima T, Bando M, Takasaki M, Sakota M, Eguchi M, Konagaya A, Matsuura H, Suzumura T, Tanaka H. On experiences of i2b2 (Informatics for integrating biology and the bedside) database with Japanese clinical patients' data. Bioinformation 2011; 6:86-90. [PMID: 21544172 PMCID: PMC3082863 DOI: 10.6026/97320630006086] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 11/23/2022] Open
Abstract
Informatics for Integrating Biology and the Bedside (i2b2) is a database system to facilitate sharing and reuse of clinical patients' data collected in individual hospitals. The i2b2 provides an ontology based object-oriented database system with highly simple and flexible database schema which enables us to integrate clinical patients' data from different laboratories and different hospitals. 392 patients' data including carcinoma and non-carcinoma specimens from cancer patients are transported from the Integrated Clinical Omics Database (iCOD) to the i2b2 database for a feasibility study to check applicability of i2b2 ontology and database schema on Japanese clinical patients' data. No modification is required for the i2b2 data model to deal with Japanese characters. Some modification of ontology is required to integrate biomedical information extracted from the cancer patients' data. We believe that the i2b2 system will be practical infrastructure to integrate Japanese clinical databases if appropriate disease ontology for Japanese patients is provided.
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26
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Kishimoto T, Kondo J, Takai-Igarashi T, Tanaka H. Accurate mass comparison coupled with two endopeptidases enables identification of protein termini. Proteomics 2011; 11:485-9. [DOI: 10.1002/pmic.201000537] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/20/2010] [Accepted: 11/10/2010] [Indexed: 11/05/2022]
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27
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Takai-Igarashi T. Ontology based standardization of petri net modeling for signaling pathways. Stud Health Technol Inform 2011; 162:122-129. [PMID: 21685568] [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: 05/30/2023]
Abstract
Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.
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Affiliation(s)
- Takako Takai-Igarashi
- Graduate School of Information Science and Technology, University of Tokyo, 7-3-1, Hongou, Bunkyou-ku, Tokyo 113-0033, Japan, E-mail:
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28
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Suzuki A, Takai-Igarashi T, Numabe Y, Tanaka H. Development of a database and ontology for pathogenic pathways in periodontitis. In Silico Biol 2009; 9:233-243. [PMID: 20109153] [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: 05/28/2023]
Abstract
It is getting familiar that pathway information greatly contributes to elucidate the molecular basis of human disease with large-scale biological data. We developed a pathway database for molecular pathology in periodontitis named 'Pathogenic Pathway Database for Periodontitis'. Periodontitis is an inflammation disease in periodontal tissue and associated with an increased health risk of angina, myocardial infarction, and fetal cardiovascular events. Despite accumulation of biomedical research on periodontitis pathology at the molecular level, there has been no systematization for biological pathways in periodontitis. We checked 185 reference papers and extracted causal relationships among molecules as well as pathways representing molecular etiology. We also built an ontology that systematizes conceptual terms associated with the pathways. Besides pathways, our ontology provides cellular and tissue specific contextual information that is required to represent pathology at the cellular and tissue specific levels. We implemented in our database an integrated viewer for the association between pathways and ontology. Pathogenic Pathway Database for Periodontitis is freely available at http://bio-omix.tmd.ac.jp/disease/perio/.
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Affiliation(s)
- Asami Suzuki
- General Dentistry, The Nippon Dental University Hospital at Tokyo, Tokyo, Japan
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Takai-Igarashi T. Ontology based standardization of Petri net modeling for signaling pathways. In Silico Biol 2005; 5:529-36. [PMID: 16268794] [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: 05/05/2023]
Abstract
Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.
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Affiliation(s)
- Takako Takai-Igarashi
- Graduate School of Information Science and Technology, University of Tokyo, 7-3-1, Hongou, Bunkyou-ku, Tokyo 113-0033, Japan.
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Takai-Igarashi T, Mizoguchi R. Ontological integration of data models for cell signaling pathways by defining a factor of causality called 'signal'. Genome Inform 2004; 15:255-65. [PMID: 15706511] [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: 05/01/2023]
Abstract
Databases have collected masses of information concerning cell signaling pathways that includes information on pathways, molecular interactions as well as molecular complexes. However we have no general data model to represent comprehensive properties of cell signaling pathways, so that this type of information has been represented by two different data models that we call 'binary relation' and 'state transition'. The disagreement between the existing models derives from lack of consensus about a factor of causality in reactions in cell signaling pathways, which is often called 'signal'. We developed an ontology named CSNO (Cell Signaling Networks Ontology) based on device ontology. As device ontology is a research product of knowledge engineering, CSNO is the first application of it to biological knowledge. CSNO defines the factor of causality called 'signal', offers an integrative viewpoint for the two different data models, explicates intrinsic distinctions between signaling and metabolic pathways, and eliminates ambiguity from representation of complex molecules.
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Affiliation(s)
- Takako Takai-Igarashi
- Computer Science, Graduate School of Information Science and Technology, University of Tokyo, 7-3-1 Hongou, Bunkyou-ku, Tokyo 113-0033, Japan.
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Takai-Igarashi T, Mizoguchi R. Cell signaling networks ontology. In Silico Biol 2004; 4:81-7. [PMID: 15089755] [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: 04/29/2023]
Abstract
Although databases for cell signaling pathways include numbers of reaction data of the pathways, the reaction data cannot be used yet to deduce biological functions from them. For the deduction, we need systematic and consistent interpretation of biological functions of reactions in cell signaling pathways in the context of "information transmission". To address this issue, we have developed a functional ontology for cell signaling pathways, Cell Signaling Network Ontology (CSN-Ontology), which provides framework for the functional interpretation presenting some important concepts as information, selectivity, movability, and signaling rules including passage of time.
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Affiliation(s)
- Takako Takai-Igarashi
- Computer Science, Graduate School of Information Science and Technology, University of Tokyo.
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Takai-Igarashi T, Kaminuma T. A pathway finding system for the cell signaling networks database. In Silico Biol 2001; 1:129-46. [PMID: 11471234] [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: 02/20/2023]
Abstract
We report on a knowledge-based pathway-finding system that builds on the cell-signaling networks database, CSNDB, which we developed previously. This new system, PaF-CSNDB, uses a general inference engine to apply rules for finding and coupling pathways between or around specific biomolecules from the CSNDB database. We show how PaF-CSNDB finds relationships in a large but fragmented collection of cell-signaling knowledge by filtering out and composing together those sections of pathways specified from an extensive and complex set of binary or pair-wise cell-signaling reactions.
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Affiliation(s)
- T Takai-Igarashi
- Division of Chem-Bio Informatics, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158, Japan.
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Affiliation(s)
- Kotoko Nakata
- Division of Chem-Bio Informatics, National Institute of Health Sciences
| | | | - Kyoko Toda
- Division of Chem-Bio Informatics, National Institute of Health Sciences
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Affiliation(s)
| | - Kotoko Nakata
- Division of Chem-Bio Informatics, National Institute of Health Sciences
| | - Tatsuya Nakano
- Division of Chem-Bio Informatics, National Institute of Health Sciences
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Affiliation(s)
- Kotoko Nakata
- Division of Chem-Bio Informatics, National Institute of Health Sciences
| | | | - Tatsuya Nakano
- Division of Chem-Bio Informatics, National Institute of Health Sciences
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Abstract
The so called endocrine disruptors have become an important working hypothesis for a wide range of toxicology researchers. This hypothesis has also attracted those who have worked on designer estrogens or selective estrogen receptor modulators. Already numbers of substances have been identified as such chemicals, but there remain a large number of chemicals waiting to be tested for their endocrine modulating capabilities. Because of the time and costs required for wet lab tests, it is unrealistic to apply these kinds of tests to all such suspicious or probable chemicals. Thus some theoretical methods must be developed for this purpose. However the conventional QSAR (quantitative structure activity relationships) approach is of limited relevance to this problem, because these methods do not take detailed mechanisms of molecular interactions in biological systems into account. Thus we have developed a database complex system that enables one to trace molecular interactions triggered by interaction of receptors with xenobiotic chemicals. The main components of this database complex are a potential endocrine disruptor database, a receptor database, a cell signaling networks database, a transcription factor database, and an affinity binding database based on modes of actions.
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Affiliation(s)
- T Kaminuma
- Division of Chem-Bio Informatics, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo, Japan.
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Abstract
We developed a data and knowledge base for cellular signal transduction in human cells, to make this rapidly growing information available. The database includes all the biological properties of cellular signal transduction, including biological reactions that transfer cellular signals and molecular attributes characterized by sequences, structures, and functions. Since the database is based on the object-oriented technique, highly flexible methods of data definition and modification are necessary to handle this diverse and complex biological information. The database includes attractive graphical representations of signaling cascades and the three-dimensional structure of molecules. The database is a novel application of ACEDB, which was the database originally developed to store the C. elegans genome. The database can be accessed through the Internet at http://geo.nihs.go.jp/csndb.html.
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Affiliation(s)
- T Takai-Igarashi
- Division of Chem-Bio Informatics, National Institute of Health Sciences, Setagaya, Tokyo, Japan.
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