1
|
Sato M, Hishinuma E, Matsukawa N, Shima Y, Saigusa D, Motoike IN, Kogure M, Nakaya N, Hozawa A, Kuriyama S, Yamamoto M, Koshiba S, Kinoshita K. Dietary habits and plasma lipid concentrations in a general Japanese population. Metabolomics 2024; 20:34. [PMID: 38441752 PMCID: PMC10914877 DOI: 10.1007/s11306-024-02087-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/02/2024] [Indexed: 03/07/2024]
Abstract
INTRODUCTION Accumulating data on the associations between food consumption and lipid composition in the body is essential for understanding the effects of dietary habits on health. OBJECTIVES As part of omics research in the Tohoku Medical Megabank Community-Based Cohort Study, this study sought to reveal the dietary impact on plasma lipid concentration in a Japanese population. METHODS We conducted a correlation analysis of food consumption and plasma lipid concentrations measured using mass spectrometry, for 4032 participants in Miyagi Prefecture, Japan. RESULTS Our analysis revealed 83 marked correlations between six food categories and the concentrations of plasma lipids in nine subclasses. Previously reported associations, including those between seafood consumption and omega-3 fatty acids, were validated, while those between dairy product consumption and odd-carbon-number fatty acids (odd-FAs) were validated for the first time in an Asian population. Further analysis suggested that dairy product consumption is associated with odd-FAs via sphingomyelin (SM), which suggests that SM is a carrier of odd-FAs. These results are important for understanding odd-FA metabolism with regards to dairy product consumption. CONCLUSION This study provides insight into the dietary impact on plasma lipid concentration in a Japanese population.
Collapse
Affiliation(s)
- Mitsuharu Sato
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Yoshiko Shima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, 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
| | - 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, 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
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
| |
Collapse
|
2
|
Aoki YI, Taguchi K, Anzawa H, Kawashima J, Ishida N, Otuki A, Hasegawa A, Baird L, Suzuki T, Motoike IN, Ohneda K, Kumada K, Katsuoka F, Kinoshita K, Yamamoto M. Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals. J Biochem 2024:mvae008. [PMID: 38268329 DOI: 10.1093/jb/mvae008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/29/2023] [Indexed: 01/26/2024] Open
Abstract
Whole blood transcriptome analysis is a valuable approach in medical research, primarily due to the ease of sample collection and the richness of the information obtained. Since the expression profile of individual genes in the analysis is influenced by medical traits and demographic attributes such as age and gender, there has been a growing demand for a comprehensive database for blood transcriptome analysis. Here, we performed whole blood RNA sequencing (RNA-seq) analysis on 576 participants stratified by age (20-30s and 60-70s) and gender from cohorts of the Tohoku Medical Megabank (TMM). A part of female segment included pregnant women. We did not exclude the globin gene family in our RNA-seq study, which enabled us to identify instances of hereditary persistence of fetal hemoglobin based on the HBG1 and HBG2 expression information. Comparing stratified populations allowed us to identify groups of genes associated with age-related changes and gender differences. We also found that the immune response status, particularly measured by neutrophil-to-lymphocyte ratio (NLR), strongly influences the diversity of individual gene expression profiles in whole blood transcriptome analysis. This stratification has resulted in a dataset that will be highly beneficial for future whole blood transcriptome analysis in the Japanese population.
Collapse
Affiliation(s)
- Yu-Ichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University
| | - Keiko Taguchi
- Tohoku Medical Megabank Organization, Tohoku University
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | - Hayato Anzawa
- Tohoku Medical Megabank Organization, Tohoku University
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University
| | | | - Noriko Ishida
- Tohoku Medical Megabank Organization, Tohoku University
| | - Akihito Otuki
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Liam Baird
- Tohoku Medical Megabank Organization, Tohoku University
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | | | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University
| | - Kinuko Ohneda
- Tohoku Medical Megabank Organization, Tohoku University
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | | |
Collapse
|
3
|
Hishinuma E, Shimada M, Matsukawa N, Shima Y, Li B, Motoike IN, Shibuya Y, Hagihara T, Shigeta S, Tokunaga H, Saigusa D, Kinoshita K, Koshiba S, Yaegashi N. Identification of predictive biomarkers for endometrial cancer diagnosis and treatment response monitoring using plasma metabolome profiling. Cancer Metab 2023; 11:16. [PMID: 37821929 PMCID: PMC10568780 DOI: 10.1186/s40170-023-00317-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Endometrial cancer (EMC) is the most common female genital tract malignancy with an increasing prevalence in many countries including Japan, a fact that renders early detection and treatment necessary to protect health and fertility. Although early detection and treatment are necessary to further improve the prognosis of women with endometrial cancer, biomarkers that accurately reflect the pathophysiology of EMC patients are still unclear. Therefore, it is clinically critical to identify biomarkers to assess diagnosis and treatment efficacy to facilitate appropriate treatment and development of new therapies for EMC. METHODS In this study, wide-targeted plasma metabolome analysis was performed to identify biomarkers for EMC diagnosis and the prediction of treatment responses. The absolute quantification of 628 metabolites in plasma samples from 142 patients with EMC was performed using ultra-high-performance liquid chromatography with tandem mass spectrometry. RESULTS The concentrations of 111 metabolites increased significantly, while the concentrations of 148 metabolites decreased significantly in patients with EMC compared to healthy controls. Specifically, LysoPC and TGs, including unsaturated fatty acids, were reduced in patients with stage IA EMC compared to healthy controls, indicating that these metabolic profiles could be used as early diagnostic markers of EMC. In contrast, blood levels of amino acids such as histidine and tryptophan decreased as the risk of recurrence increased and the stages of EMC advanced. Furthermore, a marked increase in total TG and a decrease in specific TGs and free fatty acids including polyunsaturated fatty acids levels were observed in patients with EMC. These results suggest that the polyunsaturated fatty acids in patients with EMC are crucial for disease progression. CONCLUSIONS Our data identified specific metabolite profiles that reflect the pathogenesis of EMC and showed that these metabolites correlate with the risk of recurrence and disease stage. Analysis of changes in plasma metabolite profiles could be applied for the early diagnosis and monitoring of the course of treatment of EMC patients.
Collapse
Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Muneaki Shimada
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan.
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan.
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Yoshiko Shima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Bin Li
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, 980-8579, Japan
| | - Yusuke Shibuya
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Tatsuya Hagihara
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Shogo Shigeta
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Hideki Tokunaga
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, 173-8605, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, 980-8579, Japan
| | - Seizo Koshiba
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Nobuo Yaegashi
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| |
Collapse
|
4
|
Taira M, Mugikura S, Mori N, Hozawa A, Saito T, Nakamura T, Kiyomoto H, Kobayashi T, Ogishima S, Nagami F, Uruno A, Shimizu R, Kobayashi T, Yasuda J, Kure S, Sakurai M, Motoike IN, Kumada K, Nakaya N, Obara T, Oba K, Sekiguchi A, Thyreau B, Mutoh T, Takano Y, Abe M, Maikusa N, Tatewaki Y, Taki Y, Yaegashi N, Tomita H, Kinoshita K, Kuriyama S, Fuse N, Yamamoto M. Tohoku Medical Megabank Brain Magnetic Resonance Imaging Study: Rationale, Design, and Background. JMA J 2023; 6:246-264. [PMID: 37560377 PMCID: PMC10407421 DOI: 10.31662/jmaj.2022-0220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/24/2023] [Indexed: 08/11/2023] Open
Abstract
The Tohoku Medical Megabank Brain Magnetic Resonance Imaging Study (TMM Brain MRI Study) was established to collect multimodal information through neuroimaging and neuropsychological assessments to evaluate the cognitive function and mental health of residents who experienced the Great East Japan Earthquake (GEJE) and associated tsunami. The study also aimed to promote advances in personalized healthcare and medicine related to mental health and cognitive function among the general population. We recruited participants for the first (baseline) survey starting in July 2014, enrolling individuals who were participating in either the TMM Community-Based Cohort Study (TMM CommCohort Study) or the TMM Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study). We collected multiple magnetic resonance imaging (MRI) sequences, including 3D T1-weighted sequences, magnetic resonance angiography (MRA), diffusion tensor imaging (DTI), pseudo-continuous arterial spin labeling (pCASL), and three-dimensional fluid-attenuated inversion recovery (FLAIR) sequences. To assess neuropsychological status, we used both questionnaire- and interview-based rating scales. The former assessments included the Tri-axial Coping Scale, Impact of Event Scale in Japanese, Profile of Mood States, and 15-item Depression, Anxiety, and Stress Scale, whereas the latter assessments included the Mini-Mental State Examination, Japanese version. A total of 12,164 individuals were recruited for the first (baseline) survey, including those unable to complete all assessments. In parallel, we returned the MRI results to the participants and subsequently shared the MRI data through the TMM Biobank. At present, the second (first follow-up) survey of the study started in October 2019 is underway. In this study, we established a large and comprehensive database that included robust neuroimaging data as well as psychological and cognitive assessment data. In combination with genomic and omics data already contained in the TMM Biobank database, these data could provide new insights into the relationships of pathological processes with neuropsychological disorders, including age-related cognitive impairment.
Collapse
Affiliation(s)
- Makiko Taira
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Shunji Mugikura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Naoko Mori
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomo Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hideyasu Kiyomoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tadao Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- 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
| | - 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
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Miyagi Cancer Center, Natori, 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
- Miyagi Children's Hospital, Sendai, Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kentaro Oba
- 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
| | - Atsushi Sekiguchi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Benjamin Thyreau
- 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
| | - Tatsushi Mutoh
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Yuji Takano
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
- University of Human Environments, Matsuyama, Japan
| | - Mitsunari Abe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Tokyo, Japan
- Graduate School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Norihide Maikusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Tokyo, Japan
- Graduate School of Art and Science, University of Tokyo, Tokyo, Japan
| | - Yasuko Tatewaki
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, 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
| | - 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
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, 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
- The United Centers for Advanced Research and Translational Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| |
Collapse
|
5
|
Hishinuma E, Shimada M, Matsukawa N, Li B, Motoike IN, Hagihara T, Shigeta S, Tokunaga H, Saigusa D, Kinoshita K, Koshiba S, Yaegashi N. Identification of predictive biomarkers for diagnosis and radiation sensitivity of uterine cervical cancer using wide-targeted metabolomics. J Obstet Gynaecol Res 2023. [PMID: 37291943 DOI: 10.1111/jog.15709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/28/2023] [Indexed: 06/10/2023]
Abstract
AIM Uterine cervical cancer (UCC) is the fourth most common cancer in women, responsible for more than 300 000 deaths worldwide. Its early detection, by cervical cytology, and prevention, by vaccinating against human papilloma virus, greatly contribute to reducing cervical cancer mortality in women. However, penetration of the effective prevention of UCC in Japan remains low. Plasma metabolome analysis is widely used for biomarker discovery and the identification of cancer-specific metabolic pathways. Here, we aimed to identify predictive biomarkers for the diagnosis and radiation sensitivity of UCC using wide-targeted plasma metabolomics. METHODS We analyzed 628 metabolites in plasma samples obtained from 45 patients with UCC using ultra-high-performance liquid chromatography with tandem mass spectrometry. RESULTS The levels of 47 metabolites were significantly increased and those of 75 metabolites were significantly decreased in patients with UCC relative to healthy controls. Increased levels of arginine and ceramides, and decreased levels of tryptophan, ornithine, glycosylceramides, lysophosphatidylcholine, and phosphatidylcholine were characteristic of patients with UCC. Comparison of metabolite profiles in groups susceptible and non-susceptible to radiation therapy, a treatment for UCC, revealed marked variations in polyunsaturated fatty acid, nucleic acid, and arginine metabolism in the group not susceptible to treatment. CONCLUSIONS Our findings suggest that the metabolite profile of patients with UCC may be an important indicator for distinguishing these patients from healthy cohorts, and may also be useful for predicting sensitivity to radiotherapy.
Collapse
Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Muneaki Shimada
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Bin Li
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Tatsuya Hagihara
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shogo Shigeta
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hideki Tokunaga
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Yaegashi
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| |
Collapse
|
6
|
Watarai G, Suzuki J, Motoike IN, Sakurai M, Ikeda R, Kawase T, Kinoshita K, Hozawa A, Kuriyama S, Fuse N, Yamamoto M, Katori Y. Relationship between age-related hearing loss and consumption of coffee and tea. Geriatr Gerontol Int 2023; 23:453-456. [PMID: 37132547 DOI: 10.1111/ggi.14589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/10/2023] [Accepted: 04/15/2023] [Indexed: 05/04/2023]
Affiliation(s)
- Gosuke Watarai
- Department of Otolaryngology, Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Jun Suzuki
- Department of Otolaryngology, Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ryoukichi Ikeda
- Department of Otolaryngology-Head and Neck Surgery, Iwate Medical University, Iwate, Japan
| | - Tetsuaki Kawase
- Department of Otolaryngology, Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
- Laboratory of Rehabilitative Auditory Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yukio Katori
- Department of Otolaryngology, Head and Neck Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
7
|
Sato S, Yu Z, Sakai M, Motoike IN, Saigusa D, Hirayama R, Kikuchi Y, Abe T, Kinoshita K, Koshiba S, Tomita H. Decreased β-hydroxybutyrate and ketogenic amino acid levels in depressed human adults. Eur J Neurosci 2023; 57:1018-1032. [PMID: 36750311 DOI: 10.1111/ejn.15931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023]
Abstract
β-hydroxybutyrate (BHB) is a major ketone body synthesized mainly in the liver mitochondria and is associated with stress and severity of depression in humans. It is known to alleviate depressive-like behaviors in mouse models of depression. In this study, plasma BHB, ketogenic and glucogenic amino acids selected from the Tohoku Medical Megabank Project Community-Based Cohort Study were analysed and measured using nuclear magnetic resonance spectroscopy. The Center for Epidemiologic Studies Depression Scale (CES-D) was utilized to select adult participants with depressive symptoms (CES-D ≥ 16; n = 5722) and control participants (CES-D < 16; n = 18,150). We observed significantly reduced plasma BHB, leucine, and tryptophan levels in participants with depressive symptoms. Using social defeat stress (SDS) mice models, we found that BHB levels in mice sera increased after acute SDS, but showed no change after chronic SDS, which differed from human plasma results. Furthermore, acute SDS increased mitochondrial BHB levels in the prefrontal cortex at 6 h. In contrast, chronic SDS significantly increased the amount of food intake but reduced hepatic mitochondrial BHB levels in mice. Moreover, gene transcriptions of voltage-dependent anion-selective channel 1 (Vdac1) and monocarboxylic acid transporter 1 (Mct1), major molecules relevant to mitochondrial biogenesis and BHB transporter, significantly decreased in the liver and PFC after chronic SDS exposure. These results provide evidence that hepatic and prefrontal mitochondrial biogenesis plays an important role in BHB synthesis under chronic stress and in humans with depressive symptoms.
Collapse
Affiliation(s)
- Shiho Sato
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Mai Sakai
- Department of Psychiatric Nursing, Graduate School of Health Science, Tohoku University, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryo Hirayama
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takaaki Abe
- Department of Biomedical Engineering Regenerative and Biomedical Engineering Medical Science, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Preventive Medicine and Epidemiology, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Psychiatry, Tohoku University Hospital, Sendai, Japan
| |
Collapse
|
8
|
Tatara Y, Yamazaki H, Katsuoka F, Chiba M, Saigusa D, Kasai S, Nakamura T, Inoue J, Aoki Y, Shoji M, Motoike IN, Tamada Y, Hashizume K, Shoji M, Kinoshita K, Murashita K, Nakaji S, Yamamoto M, Itoh K. Multiomics and artificial intelligence enabled peripheral blood-based prediction of amnestic mild cognitive impairment. Curr Res Transl Med 2023; 71:103367. [PMID: 36446162 DOI: 10.1016/j.retram.2022.103367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 03/28/2022] [Revised: 08/03/2022] [Accepted: 10/20/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Since dementia is preventable with early interventions, biomarkers that assist in diagnosing early stages of dementia, such as mild cognitive impairment (MCI), are urgently needed. METHODS Multiomics analysis of amnestic MCI (aMCI) peripheral blood (n = 25) was performed covering the transcriptome, microRNA, proteome, and metabolome. Validation analysis for microRNAs was conducted in an independent cohort (n = 12). Artificial intelligence was used to identify the most important features for predicting aMCI. FINDINGS We found that hsa-miR-4455 is the best biomarker in all omics analyses. The diagnostic index taking a ratio of hsa-miR-4455 to hsa-let-7b-3p predicted aMCI patients against healthy subjects with 97% overall accuracy. An integrated review of multiomics data suggested that a subset of T cells and the GCN (general control nonderepressible) pathway are associated with aMCI. INTERPRETATION The multiomics approach has enabled aMCI biomarkers with high specificity and illuminated the accompanying changes in peripheral blood. Future large-scale studies are necessary to validate candidate biomarkers for clinical use.
Collapse
Affiliation(s)
- Yota Tatara
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Hiromi Yamazaki
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Mitsuru Chiba
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shuya Kasai
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Tomohiro Nakamura
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Division of Personalized Prevention and Epidemiology, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jin Inoue
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Miho Shoji
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yoshinori Tamada
- Innovation Center for Health Promotion, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Katsuhito Hashizume
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Mikio Shoji
- Department of Neurology, Gunma University Hospital, 3-39-15 Showamachi, Maebashi, Gunma 371-8511, Japan; Department of Neurology, Dementia Research Center, Geriatrics Research Institute and Hospital, 3-26-8 Ootomo-machi, Maebashi, Gunma 371-0847 Japan; COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Koichi Murashita
- COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Shigeyuki Nakaji
- Department of Social Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan.
| |
Collapse
|
9
|
Sato S, Imaeda T, Mugikura S, Mori N, Takanashi M, Hayakawa K, Saito T, Taira M, Narita A, Kogure M, Chiba I, Hatanaka R, Nakaya K, Kanno I, Ishiwata R, Nakamura T, Motoike IN, Nakaya N, Koshiba S, Kinoshita K, Kuriyama S, Ogishima S, Nagami F, Fuse N, Hozawa A. Association Between Olfactory Test Data with Multiple Levels of Odor Intensity and Suspected Cognitive Impairment: A Cross-Sectional Study. J Alzheimers Dis 2023; 95:1469-1480. [PMID: 37718802 DOI: 10.3233/jad-230318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 09/19/2023]
Abstract
BACKGROUND Olfactory function decline has recently been reported to be associated with a risk of cognitive impairment. Few population-based studies have included younger adults when examining the association between olfactory test data with multiple odor intensities and suspected cognitive impairment. OBJECTIVE We investigated the association between high-resolution olfactory test data with fewer odors and suspected cognitive impairments. We also examined the differences between older and younger adults in this association. METHODS The Japanese version of the Montreal Cognitive Assessment (MoCA-J) was administered to 1,450 participants, with three odor-intensity-level olfactometry using six different odors. Logistic regressions to discriminate suspected cognitive impairment were conducted to examine the association, adjusted for age, sex, education duration, and smoking history. Data were collected from the Program by Tohoku University Tohoku Medical Megabank Organization, with an additional olfactory test conducted between 2019 and 2021. RESULTS We generally observed that the lower the limit of distinguishable odor intensity was, the higher the MoCA-J score was. The combination of spearmint and stuffy socks contributed most to the distinction between suspected and unsuspected cognitive impairment. Furthermore, the association was significant in women aged 60-74 years (adjusted odds ratio 0.881, 95% confidence interval [0.790, 0.983], p = 0.024). CONCLUSIONS The results indicate an association between the limit of distinguishable odor intensity and cognitive function. The olfactory test with multiple odor intensity levels using fewer odors may be applicable for the early detection of mild cognitive impairment, especially in older women aged 60-74 years.
Collapse
Affiliation(s)
- Shuichi Sato
- Toyota Central Research and Development Laboratories, Inc., Nagakute, Japan
| | - Takao Imaeda
- Toyota Central Research and Development Laboratories, Inc., Nagakute, Japan
| | - Shunji Mugikura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoko Mori
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Akita University Graduate School of Medicine, Akita, Japan
| | - Masaki Takanashi
- Toyota Central Research and Development Laboratories, Inc., Nagakute, Japan
| | - Kazumi Hayakawa
- Toyota Central Research and Development Laboratories, Inc., Nagakute, Japan
| | - Tomo Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Makiko Taira
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ippei Chiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Rieko Hatanaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kumi Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikumi Kanno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryosuke Ishiwata
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Information Sciences, Sendai, Japan
- Institute of Development, Aging, and Cancer, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
10
|
Yu Z, Matsukawa N, Saigusa D, Motoike IN, Ono C, Okamura Y, Onuma T, Takahashi Y, Sakai M, Kudo H, Obara T, Murakami K, Shirota M, Kikuchi S, Kobayashi N, Kikuchi Y, Sugawara J, Minegishi N, Ogishima S, Kinoshita K, Yamamoto M, Yaegashi N, Kuriyama S, Koshiba S, Tomita H. Plasma metabolic disturbances during pregnancy and postpartum in women with depression. iScience 2022; 25:105666. [PMID: 36505921 PMCID: PMC9732390 DOI: 10.1016/j.isci.2022.105666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/17/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Examining plasma metabolic profiling during pregnancy and postpartum could help clinicians understand the risk factors for postpartum depression (PPD) development. This analysis targeted paired plasma metabolites in mid-late gestational and 1 month postpartum periods in women with (n = 209) or without (n = 222) PPD. Gas chromatogram-mass spectrometry was used to analyze plasma metabolites at these two time points. Among the 170 objected plasma metabolites, principal component analysis distinguished pregnancy and postpartum metabolites but failed to discriminate women with and without PPD. Compared to women without PPD, those with PPD exhibited 37 metabolites with disparate changes during pregnancy and the 1-month postpartum period and an enriched citrate cycle. Machine learning and multivariate statistical analysis identified two or three compounds that could be potential biomarkers for PPD prediction during pregnancy. Our findings suggest metabolic disturbances in women with depression and may help to elucidate metabolic processes associated with PPD development.
Collapse
Affiliation(s)
- Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Corresponding author
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University
| | - Ikuko N. Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Chiaki Ono
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasunobu Okamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Innovations in Next-Generation Medicine, Advanced Research Center, Tohoku University, Sendai, Japan
| | - Tomomi Onuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yuta Takahashi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Mai Sakai
- Department of Disaster Psychiatry, International Research Institute for Disaster Science, Tohoku University, Sendai, Japan
| | - Hisaaki Kudo
- Department of Biobank Life Science, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Keiko Murakami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matusyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Saya Kikuchi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Natsuko Kobayashi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Department of Biobank Life Science, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Division of Disaster Public Health, International Research Institute for Disaster Science, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Disaster Psychiatry, International Research Institute for Disaster Science, Tohoku University, Sendai, Japan
| |
Collapse
|
11
|
Hirose W, Horiuchi M, Li D, Motoike IN, Zhang L, Nishi H, Taniyama Y, Kamei T, Suzuki M, Kinoshita K, Katsuoka F, Taguchi K, Yamamoto M. Selective Elimination of NRF2-Activated Cells by Competition With Neighboring Cells in the Esophageal Epithelium. Cell Mol Gastroenterol Hepatol 2022; 15:153-178. [PMID: 36115578 PMCID: PMC9672893 DOI: 10.1016/j.jcmgh.2022.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS NF-E2-related factor 2 (NRF2) is a transcription factor that regulates cytoprotective gene expression in response to oxidative and electrophilic stresses. NRF2 activity is mainly controlled by Kelch-like ECH-associated protein 1 (KEAP1). Constitutive NRF2 activation by NRF2 mutations or KEAP1 dysfunction results in a poor prognosis for esophageal squamous cell carcinoma (ESCC) through the activation of cytoprotective functions. However, the detailed contributions of NRF2 to ESCC initiation or promotion have not been clarified. Here, we investigated the fate of NRF2-activated cells in the esophageal epithelium. METHODS We generated tamoxifen-inducible, squamous epithelium-specific Keap1 conditional knockout (Keap1-cKO) mice in which NRF2 was inducibly activated in a subset of cells at the adult stage. Histologic, quantitative reverse-transcription polymerase chain reaction, single-cell RNA-sequencing, and carcinogen experiments were conducted to analyze the Keap1-cKO esophagus. RESULTS KEAP1-deleted/NRF2-activated cells and cells with normal NRF2 expression (KEAP1-normal cells) coexisted in the Keap1-cKO esophageal epithelium in approximately equal numbers, and NRF2-activated cells formed dysplastic lesions. NRF2-activated cells exhibited weaker attachment to the basement membrane and gradually disappeared from the epithelium. In contrast, neighboring KEAP1-normal cells exhibited accelerated proliferation and started dominating the epithelium but accumulated DNA damage that triggered carcinogenesis upon carcinogen exposure. CONCLUSIONS Constitutive NRF2 activation promotes the selective elimination of epithelial cells via cell competition, but this competition induces DNA damage in neighboring KEAP1-normal cells, which predisposes them to chemical-induced ESCC.
Collapse
Affiliation(s)
- Wataru Hirose
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Makoto Horiuchi
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Donghan Li
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ikuko N. Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Lin Zhang
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Hafumi Nishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yusuke Taniyama
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Kamei
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mikiko Suzuki
- Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Information Sciences, Tohoku University, Sendai, Japan,Advanced Research Center for Innovations in Next Generation Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Advanced Research Center for Innovations in Next Generation Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Keiko Taguchi
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Advanced Research Center for Innovations in Next Generation Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Advanced Research Center for Innovations in Next Generation Medicine (INGEM), Tohoku University, Sendai, Japan.
| |
Collapse
|
12
|
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.
Collapse
|
13
|
Yamada M, Motoike IN, Kojima K, Fuse N, Hozawa A, Kuriyama S, Katsuoka F, Tadaka S, Shirota M, Sakurai M, Nakamura T, Hamanaka Y, Suzuki K, Sugawara J, Ogishima S, Uruno A, Kodama EN, Fujino N, Numakura T, Ichikawa T, Mitsune A, Ohe T, Kinoshita K, Ichinose M, Sugiura H, Yamamoto M. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Commun Biol 2021; 4:1288. [PMID: 34782693 PMCID: PMC8593164 DOI: 10.1038/s42003-021-02813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
Lung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.
Collapse
Affiliation(s)
- Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yohei Hamanaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiichi N Kodama
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadahisa Numakura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Ichikawa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumi Mitsune
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ohe
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | | | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
| |
Collapse
|
14
|
Saigusa D, Hishinuma E, Matsukawa N, Takahashi M, Inoue J, Tadaka S, Motoike IN, Hozawa A, Izumi Y, Bamba T, Kinoshita K, Ekroos K, Koshiba S, Yamamoto M. Comparison of Kit-Based Metabolomics with Other Methodologies in a Large Cohort, towards Establishing Reference Values. Metabolites 2021; 11:652. [PMID: 34677367 PMCID: PMC8538467 DOI: 10.3390/metabo11100652] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic profiling is an omics approach that can be used to observe phenotypic changes, making it particularly attractive for biomarker discovery. Although several candidate metabolites biomarkers for disease expression have been identified in recent clinical studies, the reference values of healthy subjects have not been established. In particular, the accuracy of concentrations measured by mass spectrometry (MS) is unclear. Therefore, comprehensive metabolic profiling in large-scale cohorts by MS to create a database with reference ranges is essential for evaluating the quality of the discovered biomarkers. In this study, we tested 8700 plasma samples by commercial kit-based metabolomics and separated them into two groups of 6159 and 2541 analyses based on the different ultra-high-performance tandem mass spectrometry (UHPLC-MS/MS) systems. We evaluated the quality of the quantified values of the detected metabolites from the reference materials in the group of 2541 compared with the quantified values from other platforms, such as nuclear magnetic resonance (NMR), supercritical fluid chromatography tandem mass spectrometry (SFC-MS/MS) and UHPLC-Fourier transform mass spectrometry (FTMS). The values of the amino acids were highly correlated with the NMR results, and lipid species such as phosphatidylcholines and ceramides showed good correlation, while the values of triglycerides and cholesterol esters correlated less to the lipidomics analyses performed using SFC-MS/MS and UHPLC-FTMS. The evaluation of the quantified values by MS-based techniques is essential for metabolic profiling in a large-scale cohort.
Collapse
Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.T.); (Y.I.); (T.B.)
| | - Jin Inoue
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Ikuko N. Motoike
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan;
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.T.); (Y.I.); (T.B.)
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.T.); (Y.I.); (T.B.)
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, 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
| | - Kim Ekroos
- Lipidomics Consulting Ltd., 02230 Espoo, Finland;
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| |
Collapse
|
15
|
Hakamata M, Hokari S, Ohshima Y, Kagami M, Saito S, Motoike IN, Abe T, Aoki N, Hayashi M, Watanabe S, Koya T, Kikuchi T. Chronic Hypercapnic Respiratory Failure in an Adult Patient with Silver-Russell Syndrome. Intern Med 2021; 60:1921-1926. [PMID: 33518558 PMCID: PMC8263195 DOI: 10.2169/internalmedicine.5479-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
A 31-year-old woman who was clinically diagnosed with Silver-Russell syndrome (SRS) in childhood was admitted with complaints of dyspnea. She had hypercapnic respiratory failure accompanied by nocturnal hypoventilation. Computed tomography revealed systemic muscle atrophy and superior mesenteric artery syndrome; however, the bilateral lung fields were normal. She was treated with nocturnal noninvasive positive pressure ventilation and showed improvement of respiratory failure. In this case, loss of methylation on chromosome 11p15 and maternal uniparental disomy of chromosome 7, which are the common causes of SRS, were not detected. This is a rare case of adult SRS manifesting as chronic hypercapnic respiratory failure.
Collapse
Affiliation(s)
- Mariko Hakamata
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Satoshi Hokari
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Yasuyoshi Ohshima
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Japan
| | - Sakae Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan
- Department of Molecular Network Analysis, Tohoku University Graduate School of Medicine, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Japan
- Department of Systems Bioinformatics, Tohoku University Graduate School of Information Sciences, Japan
| | - Taiki Abe
- Department of Medical Genetics, Tohoku University School of Medicine, Japan
| | - Nobumasa Aoki
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Masachika Hayashi
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Satoshi Watanabe
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Toshiyuki Koya
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| | - Toshiaki Kikuchi
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Japan
| |
Collapse
|
16
|
Sakurai-Yageta M, Kumada K, Gocho C, Makino S, Uruno A, Tadaka S, Motoike IN, Kimura M, Ito S, Otsuki A, Narita A, Kudo H, Aoki Y, Danjoh I, Yasuda J, Kawame H, Minegishi N, Koshiba S, Fuse N, Tamiya G, Yamamoto M, Kinoshita K. Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs. J Biochem 2021; 170:399-410. [PMID: 34131746 PMCID: PMC8510329 DOI: 10.1093/jb/mvab060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023] Open
Abstract
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.
Collapse
Affiliation(s)
- Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Chinatsu Gocho
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akira Uruno
- 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
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Masae Kimura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shin Ito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akihito Otsuki
- 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
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jun Yasuda
- 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
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, 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
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, 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
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, 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
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| |
Collapse
|
17
|
Shido K, Kojima K, Shirota M, Yamasaki K, Motoike IN, Hozawa A, Ogishima S, Minegishi N, Tanno K, Katsuoka F, Tamiya G, Aiba S, Yamamoto M, Kinoshita K. GWAS Identified IL4R and the Major Histocompatibility Complex Region as the Associated Loci of Total Serum IgE Levels in 9,260 Japanese Individuals. J Invest Dermatol 2021; 141:2749-2752. [PMID: 33864772 DOI: 10.1016/j.jid.2021.02.762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 02/17/2021] [Accepted: 02/22/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Kosuke Shido
- Department of Dermatology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Division of Interdisciplinary Medical Science, Graduate School of Medicine, Tohoku University, Sendai, Japan; Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Kenshi Yamasaki
- Department of Dermatology, Graduate School of Medicine, Tohoku University, Sendai, Japan.
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Kozo Tanno
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; RIKEN Center for Advanced Intelligence Project, Tokyo, Japan; Department of Statistical Genetics and Genomics, Graduate School of Medicine, Tohoku University, Sendai, Japan; Department of AI and Innovative Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Setsuya Aiba
- Department of Dermatology, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan; Department of Medical Biochemistry, 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; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan; Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| |
Collapse
|
18
|
Hisahara S, Nishiyama A, Tsuda E, Suzuki S, Matsumura A, Ishikawa A, Sakurai A, Motoike IN, Aoki M, Aoki Y, Shimohama S. Possible Somatic Mosaicism of Novel FUS Variant in Familial Amyotrophic Lateral Sclerosis. Neurol Genet 2021; 7:e552. [PMID: 33987464 PMCID: PMC8112850 DOI: 10.1212/nxg.0000000000000552] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Shin Hisahara
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Ayumi Nishiyama
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Emiko Tsuda
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Syuuichirou Suzuki
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Akihiro Matsumura
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Aki Ishikawa
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Akihiro Sakurai
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Masashi Aoki
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Yoko Aoki
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| | - Shun Shimohama
- Department of Neurology (S.H., S. Suzuki, A.M., S. Shimohama), School of Medicine, Sapporo Medical University, Japan; Department of Neurology (A.N., M.A.), Tohoku University School of Medicine, Sendai, Japan; Department of Neurology (E.T.), Sapporo Shirakabadai Hospital, Japan; Department of Medical Genetics and Genomics (A.I., A.S.), School of Medicine, Sapporo Medical University, Japan; Tohoku Medical Megabank Organization (I.N.M.), Tohoku University Graduate School of Information Sciences, Sendai, Japan; and Department of Medical Genetics (Y.A.), Tohoku University School of Medicine, Sendai, Japan
| |
Collapse
|
19
|
Tadaka S, Hishinuma E, Komaki S, Motoike IN, Kawashima J, Saigusa D, Inoue J, Takayama J, Okamura Y, Aoki Y, Shirota M, Otsuki A, Katsuoka F, Shimizu A, Tamiya G, Koshiba S, Sasaki M, Yamamoto M, Kinoshita K. jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population. Nucleic Acids Res 2021; 49:D536-D544. [PMID: 33179747 PMCID: PMC7779038 DOI: 10.1093/nar/gkaa1034] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022] Open
Abstract
In the Tohoku Medical Megabank project, genome and omics analyses of participants in two cohort studies were performed. A part of the data is available at the Japanese Multi Omics Reference Panel (jMorp; https://jmorp.megabank.tohoku.ac.jp) as a web-based database, as reported in our previous manuscript published in Nucleic Acid Research in 2018. At that time, jMorp mainly consisted of metabolome data; however, now genome, methylome, and transcriptome data have been integrated in addition to the enhancement of the number of samples for the metabolome data. For genomic data, jMorp provides a Japanese reference sequence obtained using de novo assembly of sequences from three Japanese individuals and allele frequencies obtained using whole-genome sequencing of 8,380 Japanese individuals. In addition, the omics data include methylome and transcriptome data from ∼300 samples and distribution of concentrations of more than 755 metabolites obtained using high-throughput nuclear magnetic resonance and high-sensitivity mass spectrometry. In summary, jMorp now provides four different kinds of omics data (genome, methylome, transcriptome, and metabolome), with a user-friendly web interface. This will be a useful scientific data resource on the general population for the discovery of disease biomarkers and personalized disease prevention and early diagnosis.
Collapse
Affiliation(s)
- Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shohei Komaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Daisuke Saigusa
- 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
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jun Takayama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yasunobu Okamura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, 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
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Akihito Otsuki
- 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
| | - Fumiki Katsuoka
- 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
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
- Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
| | - Gen Tamiya
- 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
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
- Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba-cho, Shiwa-gun, Iwate 028-3694, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, 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
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| |
Collapse
|
20
|
Koshiba S, Motoike IN, Saigusa D, Inoue J, Aoki Y, Tadaka S, Shirota M, Katsuoka F, Tamiya G, Minegishi N, Fuse N, Kinoshita K, Yamamoto M. Identification of critical genetic variants associated with metabolic phenotypes of the Japanese population. Commun Biol 2020; 3:662. [PMID: 33177615 PMCID: PMC7659008 DOI: 10.1038/s42003-020-01383-5] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
We performed a metabolome genome-wide association study for the Japanese population in the prospective cohort study of Tohoku Medical Megabank. By combining whole-genome sequencing and nontarget metabolome analyses, we identified a large number of novel associations between genetic variants and plasma metabolites. Of the identified metabolite-associated genes, approximately half have already been shown to be involved in various diseases. We identified metabolite-associated genes involved in the metabolism of xenobiotics, some of which are from intestinal microorganisms, indicating that the identified genetic variants also markedly influence the interaction between the host and symbiotic bacteria. We also identified five associations that appeared to be female-specific. A number of rare variants that influence metabolite levels were also found, and combinations of common and rare variants influenced the metabolite levels more profoundly. These results support our contention that metabolic phenotyping provides important insights into how genetic and environmental factors provoke human diseases.
Collapse
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.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Ikuko N 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
| | - 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
| | - Jin Inoue
- 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
| | - Yuichi Aoki
- 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
| | - Shu Tadaka
- 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
| | - 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
| | - 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
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Gen Tamiya
- 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
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, 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
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, 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
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), 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
| | - 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.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| |
Collapse
|
21
|
Takahashi Y, Ueki M, Yamada M, Tamiya G, Motoike IN, Saigusa D, Sakurai M, Nagami F, Ogishima S, Koshiba S, Kinoshita K, Yamamoto M, Tomita H. Improved metabolomic data-based prediction of depressive symptoms using nonlinear machine learning with feature selection. Transl Psychiatry 2020; 10:157. [PMID: 32427830 PMCID: PMC7237664 DOI: 10.1038/s41398-020-0831-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
To solve major limitations in algorithms for the metabolite-based prediction of psychiatric phenotypes, a novel prediction model for depressive symptoms based on nonlinear feature selection machine learning, the Hilbert-Schmidt independence criterion least absolute shrinkage and selection operator (HSIC Lasso) algorithm, was developed and applied to a metabolomic dataset with the largest sample size to date. In total, 897 population-based subjects were recruited from the communities affected by the Great East Japan Earthquake; 306 metabolite features (37 metabolites identified by nuclear magnetic resonance measurements and 269 characterized metabolites based on the intensities from mass spectrometry) were utilized to build prediction models for depressive symptoms as evaluated by the Center for Epidemiologic Studies-Depression Scale (CES-D). The nested fivefold cross-validation was used for developing and evaluating the prediction models. The HSIC Lasso-based prediction model showed better predictive power than the other prediction models, including Lasso, support vector machine, partial least squares, random forest, and neural network. L-leucine, 3-hydroxyisobutyrate, and gamma-linolenyl carnitine frequently contributed to the prediction. We have demonstrated that the HSIC Lasso-based prediction model integrating nonlinear feature selection showed improved predictive power for depressive symptoms based on metabolome data as well as on risk metabolites based on nonlinear statistics in the Japanese population. Further studies should use HSIC Lasso-based prediction models with different ethnicities to investigate the generality of each risk metabolite for predicting depressive symptoms.
Collapse
Affiliation(s)
- Yuta Takahashi
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
| | - Masao Ueki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Makoto Yamada
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Gen Tamiya
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute for Development Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
| |
Collapse
|
22
|
Saigusa D, Motoike IN, Saito S, Zorzi M, Aoki Y, Kitamura H, Suzuki M, Katsuoka F, Ishii H, Kinoshita K, Motohashi H, Yamamoto M. Impacts of NRF2 activation in non-small-cell lung cancer cell lines on extracellular metabolites. Cancer Sci 2020; 111:667-678. [PMID: 31828882 PMCID: PMC7004536 DOI: 10.1111/cas.14278] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [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: 08/23/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 01/09/2023] Open
Abstract
Aberrant activation of NRF2 is as a critical prognostic factor that drives the malignant progression of various cancers. Cancer cells with persistent NRF2 activation heavily rely on NRF2 activity for therapeutic resistance and aggressive tumorigenic capacity. To clarify the metabolic features of NRF2-activated lung cancers, we conducted targeted metabolomic (T-Met) and global metabolomic (G-Met) analyses of non-small-cell lung cancer (NSCLC) cell lines in combination with exome and transcriptome analyses. Exome analysis of 88 cell lines (49 adenocarcinoma, 14 large cell carcinoma, 15 squamous cell carcinoma and 10 others) identified non-synonymous mutations in the KEAP1, NRF2 and CUL3 genes. Judging from the elevated expression of NRF2 target genes, these mutations are expected to result in the constitutive stabilization of NRF2. Out of the 88 cell lines, 52 NSCLC cell lines (29 adenocarcinoma, 10 large cell carcinoma, 9 squamous cell carcinoma and 4 others) were subjected to T-Met analysis. Classification of the 52 cell lines into three groups according to the NRF2 target gene expression enabled us to draw typical metabolomic signatures induced by NRF2 activation. From the 52 cell lines, 18 NSCLC cell lines (14 adenocarcinoma, 2 large cell carcinoma, 1 squamous cell carcinoma and 1 others) were further chosen for G-Met and detailed transcriptome analyses. G-Met analysis of their culture supernatants revealed novel metabolites associated with NRF2 activity, which may be potential diagnostic biomarkers of NRF2 activation. This study also provides useful information for the exploration of new metabolic nodes for selective toxicity towards NRF2-activated NSCLC.
Collapse
Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Sakae Saito
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Michael Zorzi
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Hiroshi Kitamura
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Mikiko Suzuki
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Hozumi Motohashi
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| |
Collapse
|
23
|
Tadaka S, Saigusa D, Motoike IN, Inoue J, Aoki Y, Shirota M, Koshiba S, Yamamoto M, Kinoshita K. jMorp: Japanese Multi Omics Reference Panel. Nucleic Acids Res 2019; 46:D551-D557. [PMID: 29069501 PMCID: PMC5753289 DOI: 10.1093/nar/gkx978] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [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: 08/10/2017] [Accepted: 10/10/2017] [Indexed: 12/12/2022] Open
Abstract
We developed jMorp, a new database containing metabolome and proteome data for plasma obtained from >5000 healthy Japanese volunteers from the Tohoku Medical Megabank Cohort Study, which is available at https://jmorp.megabank.tohoku.ac.jp. Metabolome data were measured by proton nuclear magnetic resonance (NMR) and liquid chromatography–mass spectrometry (LC–MS), while proteome data were obtained by nanoLC–MS. We released the concentration distributions of 37 metabolites identified by NMR, distributions of peak intensities of 257 characterized metabolites by LC–MS, and observed frequencies of 256 abundant proteins. Additionally, correlation networks for the metabolites can be observed using an interactive network viewer. Compared with some existing databases, jMorp has some unique features: (i) Metabolome data were obtained using a single protocol in a single institute, ensuring that measurement biases were significantly minimized; (ii) The database contains large-scale data for healthy volunteers with various health records and genome data and (iii) Correlations between metabolites can be easily observed using the graphical viewer. Metabolites data are becoming important intermediate markers for evaluating the health states of humans, and thus jMorp is an outstanding resource for a wide range of researchers, particularly those in the fields of medical science, applied molecular biology, and biochemistry.
Collapse
Affiliation(s)
- Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki aza Aoba, Aoba-ku, Miyagi 980-8579, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki aza Aoba, Aoba-ku, Miyagi 980-8579, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki aza Aoba, Aoba-ku, Miyagi 980-8579, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki aza Aoba, Aoba-ku, Miyagi 980-8579, Japan.,Institute of Development, Aging and Cancer, Tohoku University, 4-1, Seiryo-machi, Aoba-ku, Miyagi 980-8575, Japan
| |
Collapse
|
24
|
Kiniwa Y, Yasuda J, Saito S, Saito R, Motoike IN, Danjoh I, Kinoshita K, Fuse N, Yamamoto M, Okuyama R. Identification of genetic alterations in extramammary Paget disease using whole exome analysis. J Dermatol Sci 2019; 94:229-235. [DOI: 10.1016/j.jdermsci.2019.03.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Sato K, Saigusa D, Saito R, Fujioka A, Nakagawa Y, Nishiguchi KM, Kokubun T, Motoike IN, Maruyama K, Omodaka K, Shiga Y, Uruno A, Koshiba S, Yamamoto M, Nakazawa T. Metabolomic changes in the mouse retina after optic nerve injury. Sci Rep 2018; 8:11930. [PMID: 30093719 PMCID: PMC6085332 DOI: 10.1038/s41598-018-30464-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 03/04/2018] [Accepted: 07/20/2018] [Indexed: 12/12/2022] Open
Abstract
In glaucoma, although axonal injury drives retinal ganglion cell (RGC) death, little is known about the underlying pathomechanisms. To provide new mechanistic insights and identify new biomarkers, we combined latest non-targeting metabolomics analyses to profile altered metabolites in the mouse whole retina 2, 4, and 7 days after optic nerve crush (NC). Ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry and liquid chromatography Fourier transform mass spectrometry covering wide spectrum of metabolites in combination highlighted 30 metabolites that changed its concentration after NC. The analysis displayed similar changes for purine nucleotide and glutathione as reported previously in another animal model of axonal injury and detected multiple metabolites that increased after the injury. After studying the specificity of the identified metabolites to RGCs in histological sections using imaging mass spectrometry, two metabolites, i.e., L-acetylcarnitine and phosphatidylcholine were increased not only preceding the peak of RGC death in the whole retina but also at the RGC layer (2.3-fold and 1.2-fold, respectively). These phospholipids propose novel mechanisms of RGC death and may serve as early biomarkers of axonal injury. The combinatory metabolomics analyses promise to illuminate pathomechanisms, reveal biomarkers, and allow the discovery of new therapeutic targets of glaucoma.
Collapse
Affiliation(s)
- Kota Sato
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Department of Ophthalmic imaging and information analytics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan.,LEAP, Japan Agency for Medical Research and Development (AMED), Chiyoda, Tokyo, Japan
| | - Ritsumi Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Amane Fujioka
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yurika Nakagawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Koji M Nishiguchi
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Taiki Kokubun
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuichi Maruyama
- Department of Innovative Visual Science, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kazuko Omodaka
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Department of Ophthalmic imaging and information analytics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yukihiro Shiga
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan. .,Department of Ophthalmic imaging and information analytics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan. .,Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan. .,Department of Retinal Disease Control, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
| |
Collapse
|
27
|
Yasuda J, Katsuoka F, Danjoh I, Kawai Y, Kojima K, Nagasaki M, Saito S, Yamaguchi-Kabata Y, Tadaka S, Motoike IN, Kumada K, Sakurai-Yageta M, Tanabe O, Fuse N, Tamiya G, Higasa K, Matsuda F, Yasuda N, Iwasaki M, Sasaki M, Shimizu A, Kinoshita K, Yamamoto M. Regional genetic differences among Japanese populations and performance of genotype imputation using whole-genome reference panel of the Tohoku Medical Megabank Project. BMC Genomics 2018; 19:551. [PMID: 30041597 PMCID: PMC6057088 DOI: 10.1186/s12864-018-4942-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [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: 04/04/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022] Open
Abstract
Background Genotype imputation from single-nucleotide polymorphism (SNP) genotype data using a haplotype reference panel consisting of thousands of unrelated individuals from populations of interest can help to identify strongly associated variants in genome-wide association studies. The Tohoku Medical Megabank (TMM) project was established to support the development of precision medicine, together with the whole-genome sequencing of 1070 human genomes from individuals in the Miyagi region (Northeast Japan) and the construction of the 1070 Japanese genome reference panel (1KJPN). Here, we investigated the performance of 1KJPN for genotype imputation of Japanese samples not included in the TMM project and compared it with other population reference panels. Results We found that the 1KJPN population was more similar to other Japanese populations, Nagahama (south-central Japan) and Aki (Shikoku Island), than to East Asian populations in the 1000 Genomes Project other than JPT, suggesting that the large-scale collection (more than 1000) of Japanese genomes from the Miyagi region covered many of the genetic variations of Japanese in mainland Japan. Moreover, 1KJPN outperformed the phase 3 reference panel of the 1000 Genomes Project (1KGPp3) for Japanese samples, and IKJPN showed similar imputation rates for the TMM and other Japanese samples for SNPs with minor allele frequencies (MAFs) higher than 1%. Conclusions 1KJPN covered most of the variants found in the samples from areas of the Japanese mainland outside the Miyagi region, implying 1KJPN is representative of the Japanese population’s genomes. 1KJPN and successive reference panels are useful genome reference panels for the mainland Japanese population. Importantly, the addition of whole genome sequences not included in the 1KJPN panel improved imputation efficiencies for SNPs with MAFs under 1% for samples from most regions of the Japanese archipelago. Electronic supplementary material The online version of this article (10.1186/s12864-018-4942-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jun Yasuda
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.
| | - Fumiki Katsuoka
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Inaho Danjoh
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Yosuke Kawai
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.,Present address: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, 113-0033, Tokyo, Japan
| | - Kaname Kojima
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Masao Nagasaki
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Sakae Saito
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Yumi Yamaguchi-Kabata
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Shu Tadaka
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Ikuko N Motoike
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Kazuki Kumada
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Mika Sakurai-Yageta
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Osamu Tanabe
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Nobuo Fuse
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Gen Tamiya
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan
| | - Koichiro Higasa
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Sakyo-ku, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, 606-8501, Sakyo-ku, Japan
| | - Nobufumi Yasuda
- Department of Public Health, Kochi University Medical School, Nankoku-shi, 783-8505, Kochi, Japan
| | - Motoki Iwasaki
- Division of Epidemiology, Center for Public Health Sciences, National Cancer Center, Tokyo, 104-0045, Chuo-ku, Japan
| | - Makoto Sasaki
- Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan.,Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 2-1-1 Nishitokuta, Yahaba, Shiwa, Iwate, 028-3694, Japan
| | - Kengo Kinoshita
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan.,Graduate School of Information Sciences, Tohoku University, Aoba-ku, Sendai, 980-8579, Miyagi, Japan
| | - Masayuki Yamamoto
- Sendai, Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Tohoku Medical Megabank, Tohoku University, Sendai, 980-8573, Miyagi, Japan. .,Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Aoba-ku, Sendai, 980-8575, Miyagi, Japan.
| |
Collapse
|
28
|
Saigusa D, Okamura Y, Motoike IN, Katoh Y, Kurosawa Y, Saijyo R, Koshiba S, Yasuda J, Motohashi H, Sugawara J, Tanabe O, Kinoshita K, Yamamoto M. Establishment of Protocols for Global Metabolomics by LC-MS for Biomarker Discovery. PLoS One 2016; 11:e0160555. [PMID: 27579980 PMCID: PMC5006994 DOI: 10.1371/journal.pone.0160555] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 07/20/2016] [Indexed: 01/04/2023] Open
Abstract
Metabolomics is a promising avenue for biomarker discovery. Although the quality of metabolomic analyses, especially global metabolomics (G-Met) using mass spectrometry (MS), largely depends on the instrumentation, potential bottlenecks still exist at several basic levels in the metabolomics workflow. Therefore, we established a precise protocol initially for the G-Met analyses of human blood plasma to overcome some these difficulties. In our protocol, samples are deproteinized in a 96-well plate using an automated liquid-handling system, and conducted either using a UHPLC-QTOF/MS system equipped with a reverse phase column or a LC-FTMS system equipped with a normal phase column. A normalization protocol of G-Met data was also developed to compensate for intra- and inter-batch differences, and the variations were significantly reduced along with our normalization, especially for the UHPLC-QTOF/MS data with a C18 reverse-phase column for positive ions. Secondly, we examined the changes in metabolomic profiles caused by the storage of EDTA-blood specimens to identify quality markers for the evaluation of the specimens’ pre-analytical conditions. Forty quality markers, including lysophospholipids, dipeptides, fatty acids, succinic acid, amino acids, glucose, and uric acid were identified by G-Met for the evaluation of plasma sample quality and established the equation of calculating the quality score. We applied our quality markers to a small-scale study to evaluate the quality of clinical samples. The G-Met protocols and quality markers established here should prove useful for the discovery and development of biomarkers for a wider range of diseases.
Collapse
Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
- CREST, Japan Agency for Medical Research and Development (AMED), Chiyoda, Tokyo, Japan
- * E-mail: (DS); (MY)
| | - Yasunobu Okamura
- Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Ikuko N. Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Yasutake Katoh
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yasuhiro Kurosawa
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Reina Saijyo
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Jun Yasuda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Hozumi Motohashi
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Junichi Sugawara
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Osamu Tanabe
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Department of Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
- * E-mail: (DS); (MY)
| |
Collapse
|
29
|
Motoike IN, Matsumoto M, Danjoh I, Katsuoka F, Kojima K, Nariai N, Sato Y, Yamaguchi-Kabata Y, Ito S, Kudo H, Nishijima I, Nishikawa S, Pan X, Saito R, Saito S, Saito T, Shirota M, Tsuda K, Yokozawa J, Igarashi K, Minegishi N, Tanabe O, Fuse N, Nagasaki M, Kinoshita K, Yasuda J, Yamamoto M. Validation of multiple single nucleotide variation calls by additional exome analysis with a semiconductor sequencer to supplement data of whole-genome sequencing of a human population. BMC Genomics 2014; 15:673. [PMID: 25109789 PMCID: PMC4138778 DOI: 10.1186/1471-2164-15-673] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 08/01/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Validation of single nucleotide variations in whole-genome sequencing is critical for studying disease-related variations in large populations. A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously. RESULTS Here, we analyzed 12 independent Japanese genomes using two next-generation sequencing platforms: the Illumina HiSeq 2500 platform for whole-genome sequencing (average depth 32.4×), and the Ion Proton semiconductor sequencer for whole exome sequencing (average depth 109×). Single nucleotide polymorphism (SNP) calls based on the Illumina Human Omni 2.5-8 SNP chip data were used as the reference. We compared the variant calls for the 12 samples, and found that the concordance between the two next-generation sequencing platforms varied between 83% and 97%. CONCLUSIONS Our results show the versatility and usefulness of the combination of exome sequencing with whole-genome sequencing in studies of human population genetics and demonstrate that combining data from multiple sequencing platforms is an efficient approach to validate and supplement SNP calls.
Collapse
Affiliation(s)
- Ikuko N Motoike
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mitsuyo Matsumoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Inaho Danjoh
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Fumiki Katsuoka
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaname Kojima
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Naoki Nariai
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yukuto Sato
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Yumi Yamaguchi-Kabata
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Shin Ito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hisaaki Kudo
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Ichiko Nishijima
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Satoshi Nishikawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Xiaoqing Pan
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Rumiko Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Sakae Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Tomo Saito
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Matsuyuki Shirota
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />United Centers for Advanced Research and Translational Medicine, Tohoku University Graduate School of Medicine, 1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Kaoru Tsuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Junji Yokozawa
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kazuhiko Igarashi
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| | - Naoko Minegishi
- />Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Osamu Tanabe
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Nobuo Fuse
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Kengo Kinoshita
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi, 980-8579 Japan
- />Institute of Development, Aging, and Cancer, Tohoku University, 4-1 Seiryo-machi, Aoba-ku Sendai, Sendai, 980-8575 Japan
| | - Jun Yasuda
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- />Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
- />Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, 980-8575 Japan
| |
Collapse
|
30
|
Tsuchiya M, Hashimoto M, Takenaka Y, Motoike IN, Yoshikawa K. Global genetic response in a cancer cell: self-organized coherent expression dynamics. PLoS One 2014; 9:e97411. [PMID: 24831017 PMCID: PMC4022610 DOI: 10.1371/journal.pone.0097411] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/18/2014] [Indexed: 12/19/2022] Open
Abstract
Understanding the basic mechanism of the spatio-temporal self-control of genome-wide gene expression engaged with the complex epigenetic molecular assembly is one of major challenges in current biological science. In this study, the genome-wide dynamical profile of gene expression was analyzed for MCF-7 breast cancer cells induced by two distinct ErbB receptor ligands: epidermal growth factor (EGF) and heregulin (HRG), which drive cell proliferation and differentiation, respectively. We focused our attention to elucidate how global genetic responses emerge and to decipher what is an underlying principle for dynamic self-control of genome-wide gene expression. The whole mRNA expression was classified into about a hundred groups according to the root mean square fluctuation (rmsf). These expression groups showed characteristic time-dependent correlations, indicating the existence of collective behaviors on the ensemble of genes with respect to mRNA expression and also to temporal changes in expression. All-or-none responses were observed for HRG and EGF (biphasic statistics) at around 10–20 min. The emergence of time-dependent collective behaviors of expression occurred through bifurcation of a coherent expression state (CES). In the ensemble of mRNA expression, the self-organized CESs reveals distinct characteristic expression domains for biphasic statistics, which exhibits notably the presence of criticality in the expression profile as a route for genomic transition. In time-dependent changes in the expression domains, the dynamics of CES reveals that the temporal development of the characteristic domains is characterized as autonomous bistable switch, which exhibits dynamic criticality (the temporal development of criticality) in the genome-wide coherent expression dynamics. It is expected that elucidation of the biophysical origin for such critical behavior sheds light on the underlying mechanism of the control of whole genome.
Collapse
Affiliation(s)
- Masa Tsuchiya
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, School of Media and Governance, Keio University, Fujisawa, Japan
- * E-mail: (MT); (KY)
| | - Midori Hashimoto
- Graduate School of Frontier Science, The University of Tokyo, Kashiwa, Japan
| | - Yoshiko Takenaka
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Ikuko N. Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
- * E-mail: (MT); (KY)
| |
Collapse
|
31
|
Obayashi T, Okamura Y, Ito S, Tadaka S, Motoike IN, Kinoshita K. COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. Nucleic Acids Res 2012. [PMID: 23203868 PMCID: PMC3531062 DOI: 10.1093/nar/gks1014] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [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
Coexpressed gene databases are valuable resources for identifying new gene functions or functional modules in metabolic pathways and signaling pathways. Although coexpressed gene databases are a fundamental platform in the field of plant biology, their use in animal studies is relatively limited. The COXPRESdb (http://coxpresdb.jp) provides coexpression relationships for multiple animal species, as comparisons of coexpressed gene lists can enhance the reliability of gene coexpression determinations. Here, we report the updates of the database, mainly focusing on the following two points. First, we updated our coexpression data by including recent microarray data for the previous seven species (human, mouse, rat, chicken, fly, zebrafish and nematode) and adding four new species (monkey, dog, budding yeast and fission yeast), along with a new human microarray platform. A reliability scoring function was also implemented, based on coexpression conservation to filter out coexpression with low reliability. Second, the network drawing function was updated, to implement automatic cluster analyses with enrichment analyses in Gene Ontology and in cis elements, along with interactive network analyses with Cytoscape Web. With these updates, COXPRESdb will become a more powerful tool for analyses of functional and regulatory networks of genes in a variety of animal species.
Collapse
Affiliation(s)
- Takeshi Obayashi
- Graduate School of Information Sciences, Tohoku University, Sendai 980-8679, Japan
| | | | | | | | | | | |
Collapse
|
32
|
Suematsu NJ, Sato T, Motoike IN, Kashima K, Nakata S. Density wave propagation of a wave train in a closed excitable medium. Phys Rev E Stat Nonlin Soft Matter Phys 2011; 84:046203. [PMID: 22181241 DOI: 10.1103/physreve.84.046203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Indexed: 05/31/2023]
Abstract
A wave train in an excitable reaction-diffusion medium shows a variety of spatiotemporal patterns as a result of interactions between the individual waves. In this paper, we report a novel spatiotemporal pattern in a wave train in a closed excitable medium. We carried out experiments using a photosensitive Belousov-Zhabotinsky reaction with Ru(bpy)(3)(2+) as a catalyst and a numerical calculation using the FitzHugh-Nagumo equation. A wave train was locally distributed as an initial condition and the number of waves was systematically varied. In both the experiment and numerical calculation, density wave propagation was formed in a wave train during relaxation with a large number of waves. Our results suggest that density wave propagation originates from inhibitory interaction between the waves.
Collapse
Affiliation(s)
- Nobuhiko J Suematsu
- Graduate School of Advanced Mathematical Sciences, Meiji University, 1-1-1 Higashimita, Tamaku, Kawasaki 214-8571, Japan.
| | | | | | | | | |
Collapse
|
33
|
Motoike IN, Takigawa-Imamura H. Branching pattern formation that reflects the history of signal propagation. Phys Rev E Stat Nonlin Soft Matter Phys 2010; 82:046205. [PMID: 21230363 DOI: 10.1103/physreve.82.046205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 08/06/2010] [Indexed: 05/30/2023]
Abstract
In living organisms, branching structures are often observed in open systems. During the process of structure formation/deformation, signal propagation can be observed. Branching paths often deform depending on the history of signal propagation. To gain a better understanding of the process of pattern formation that results in characteristic geometrical paths, we adopt a system in which the dynamics of path formation are correlated with signal propagation. This model involves both branch-generation dynamics and signal-propagation dynamics, and we introduced positive feedback between these two dynamic processes. We studied the geometrical properties of path deformation and the pattern of signal propagation using a discretized reaction-diffusion model. The proposed model can qualitatively reproduce different branching patterns and means of signal propagation. One remarkable result is that the mutual interaction of these two dynamic processes leads to autonomous wave generation, similar to a pacemaker or the generation of spiral waves. Because the autonomous wave generation in the signal is spontaneous, the shapes of the branching paths become distorted. We discuss the correlation between path deformation and signal propagation as a first step in understanding signal processing for such complex deformable paths.
Collapse
Affiliation(s)
- Ikuko N Motoike
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan.
| | | |
Collapse
|
34
|
Motoike IN, Nakata S, Iguchi Y, Takemura KK, Hayashi K, Yoshikawa K. Apex of a V-shaped cut field acts as a pacemaker on an oscillatory system. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
35
|
Suzuki Y, Takayama T, Motoike IN, Asai T. A reaction-diffusion model performing stripe- and spot-image restoration and its LSI implementation. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/ecjc.20243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
36
|
Ichino T, Igarashi Y, Motoike IN, Yoshikawa K. Different operations on a single circuit: Field computation on an excitable chemical system. J Chem Phys 2003. [DOI: 10.1063/1.1565103] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
37
|
Motoike IN, Yoshikawa K, Iguchi Y, Nakata S. Real-time memory on an excitable field. Phys Rev E Stat Nonlin Soft Matter Phys 2001; 63:036220. [PMID: 11308754 DOI: 10.1103/physreve.63.036220] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2000] [Indexed: 05/23/2023]
Abstract
Recently, we proposed a novel method for computing logic operations based on the time-sequential information in a geometrically arranged excitable field. As an extension of this study, in the present article we describe a strategy for creating real-time memory. Using a numerical simulation, we show that input pulse trains can be stored as a sequence of rotating traveling waves in a circular excitable field, by using its characteristics as a diode due to spatially asymmetric arrangement. Furthermore, through an experiment on an excitable chemical reaction, we demonstrate that this real-time memory actually works in the real world.
Collapse
Affiliation(s)
- I N Motoike
- Department of Physics, Graduate School of Science, Kyoto University & CREST, Kyoto 606-8502, Japan
| | | | | | | |
Collapse
|