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Sakurai M, Motoike IN, Hishinuma E, Aoki Y, Tadaka S, Kogure M, Orui M, Ishikuro M, Obara T, Nakaya N, Kumada K, Hozawa A, Kuriyama S, Yamamoto M, Koshiba S, Kinoshita K. Identifying critical age and gender-based metabolomic shifts in a Japanese population of the Tohoku Medical Megabank cohort. Sci Rep 2024; 14:15681. [PMID: 38977808 PMCID: PMC11231361 DOI: 10.1038/s41598-024-66180-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding the physiological changes associated with aging and the associated disease risks is essential to establish biomarkers as indicators of biological aging. This study used the NMR-measured plasma metabolome to calculate age-specific metabolite indices. In doing so, the scope of the study was deliberately simplified to capture general trends and insights into age-related changes in metabolic patterns. In addition, changes in metabolite concentrations with age were examined in detail, with the period from 55-59 to 60-64 years being a period of significant metabolic change, particularly in men, and from 45-49 to 50-54 years in females. These results illustrate the different variations in metabolite concentrations by sex and provide new insights into the relationship between age and metabolic diseases.
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Affiliation(s)
- 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
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masatsugu Orui
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Tohoku University, Sendai, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation 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.
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Kiuchi S, Nakaya K, Cooray U, Takeuchi K, Motoike IN, Nakaya N, Taki Y, Koshiba S, Mugikura S, Osaka K, Hozawa A. A principal component analysis of metabolome and cognitive decline among Japanese older adults: cross-sectional analysis using Tohoku Medical Megabank Cohort Study. J Epidemiol 2024:JE20240099. [PMID: 38972731 DOI: 10.2188/jea.je20240099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024] Open
Abstract
BackgroundDementia is the leading cause of disability and imposes a significant burden on society. Previous studies have suggested an association between metabolites and cognitive decline. Although the metabolite composition differs between Western and Asian populations, studies targeting Asian populations remain scarce.MethodsThis cross-sectional study used data from a cohort survey of community-dwelling older adults aged ≥ 60 years living in Miyagi, Japan, conducted by Tohoku Medical Megabank Organization between 2013 and 2016. Forty-three metabolite variables quantified using nuclear magnetic resonance spectroscopy were used as explanatory variables. Dependent variable was the presence of cognitive decline (≤ 23 points), assessed by the Mini-Mental State Examination. Principal component (PC) analysis was performed to reduce the dimensionality of metabolite variables, followed by logistic regression analysis to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for cognitive decline.ResultsA total of 2,940 participants were included (men: 49.0%, mean age: 67.6 years). Among them, 1.9% showed cognitive decline. The first 12 PC components (PC1-PC12) accounted for 71.7% of the total variance. Multivariate analysis showed that PC1, which mainly represented essential amino acids, was associated with lower odds of cognitive decline (OR = 0.89; 95% CI, 0.80-0.98). PC2, which mainly included ketone bodies, was associated with cognitive decline (OR = 1.29; 95% CI, 1.11-1.51). PC3, which included amino acids, was associated with lower odds of cognitive decline (OR = 0.81; 95% CI, 0.66-0.99).ConclusionAmino acids are protectively associated with cognitive decline, whereas ketone metabolites are associated with higher odds of cognitive decline.
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Affiliation(s)
- Sakura Kiuchi
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
| | - Kumi Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
- Division of Epidemiology, School of Public Health, Graduate School of Medicine, Tohoku University
| | - Upul Cooray
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
- National Dental Research Institute Singapore, National Dental Centre Singapore
| | - Kenji Takeuchi
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
- Division of Statistics and Data Science, Liaison Center for Innovative Dentistry, Tohoku University Graduate School of Dentistry
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
- Division of Health Behavioral Epidemiology, Tohoku University Graduate School of Medicine
| | - Yasuyuki Taki
- Department of Aging Research and Geriatric Medicine, Institute of Development, Aging and Cancer, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | - Shunji Mugikura
- Tohoku Medical Megabank Organization, Tohoku University
- Department of Diagnostic Radiology, Graduate School of Medicine, Tohoku University
| | - Ken Osaka
- Department of International and Community Oral Health, Tohoku University Graduate School of Dentistry
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University
- Division of Epidemiology, School of Public Health, Graduate School of Medicine, Tohoku University
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3
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Chioccioli S, Rocchetti G, Ruzzolini J, Urciuoli S, Vitali F, Bartolucci G, Pallecchi M, Caderni G, De Filippo C, Nediani C, Lucini L. Changes in Faecal Microbiota Profile and Plasma Biomarkers following the Administration of an Antioxidant Oleuropein-Rich Leaf Extract in a Rat Model Mimicking Colorectal Cancer. Antioxidants (Basel) 2024; 13:724. [PMID: 38929163 PMCID: PMC11200411 DOI: 10.3390/antiox13060724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Oleuropein (OLE), a phenolic compound particularly abundant in the olive leaves, has been reported to have beneficial activities against colorectal cancer (CRC). In vitro studies suggested that these latter could be due to a modulation of the intestinal microbiota. Aiming to evaluate if OLE could affect the intestinal microbiota and the plasma metabolome, an antioxidant oleuropein-rich leaf extract (ORLE) was administered for one week to PIRC rats (F344/NTac-Apcam1137), a genetic model mimicking CRC. ORLE treatment significantly modulated the gut microbiota composition. Plasma metabolomic profiles revealed a significant predictive ability for amino acids, medium-chain fatty acids, and aldehydes. Pathway analysis revealed a significant decrease in phosphatidylcholine accumulation (LogFC = -1.67) in PIRC rats. These results suggest a significant effect of ORLE administration on faecal microbiota profiles and plasma metabolomes, thereby offering new omics-based insights into its protective role in CRC progression.
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Affiliation(s)
- Sofia Chioccioli
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Gabriele Rocchetti
- Department of Animal Science, Food and Nutrition, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Jessica Ruzzolini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy;
| | - Silvia Urciuoli
- PhytoLab (Pharmaceutical, Cosmetic, Food Supplement Technology and Analysis)-DiSIA, Department of Statistics, Informatics, Applications “Giuseppe Parenti”, Scientific and Technological Pole, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Moruzzi, 1, 56124 Pisa, Italy
- Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA), Via di Lanciola 12/A, 50125 Florence, Italy
| | - Gianluca Bartolucci
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Marco Pallecchi
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Giovanna Caderni
- Department of Neurosciences, Psychology, Drug Research and Child Health (NEUROFARBA), University of Florence, 50134 Florence, Italy; (S.C.); (G.B.); (G.C.)
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Moruzzi, 1, 56124 Pisa, Italy
| | - Chiara Nediani
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy;
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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Nakai T, Saigusa D, Kato K, Fukuuchi T, Koshiba S, Yamamoto M, Suzuki N. The drug-specific properties of hypoxia-inducible factor-prolyl hydroxylase inhibitors in mice reveal a significant contribution of the kidney compared to the liver to erythropoietin induction. Life Sci 2024; 346:122641. [PMID: 38614299 DOI: 10.1016/j.lfs.2024.122641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/13/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024]
Abstract
AIMS Kidney disease often leads to anemia due to a defect in the renal production of the erythroid growth factor erythropoietin (EPO), which is produced under the positive regulation of hypoxia-inducible transcription factors (HIFs). Chemical compounds that inhibit HIF-prolyl hydroxylases (HIF-PHs), which suppress HIFs, have been developed to reactivate renal EPO production in renal anemia patients. Currently, multiple HIF-PH inhibitors, in addition to conventional recombinant EPO reagents, are used for renal anemia treatment. This study aimed to elucidate the therapeutic mechanisms and drug-specific properties of HIF-PH inhibitors. METHODS AND KEY FINDINGS Gene expression analyses and mass spectrometry revealed that HIF-PH inhibitors (daprodustat, enarodustat, molidustat, and vadadustat) alter Epo gene expression levels in the kidney and liver in a drug-specific manner, with different pharmacokinetics in the plasma and urine after oral administration to mice. The drug specificity revealed the dominant contribution of EPO induction in the kidneys rather than in the liver to plasma EPO levels after HIF-PH inhibitor administration. We also found that several HIF-PH inhibitors directly induce duodenal gene expression related to iron intake, while these drugs indirectly suppress hepatic hepcidin expression to mobilize stored iron for hemoglobin synthesis through induction of the EPO-erythroferrone axis. SIGNIFICANCE Renal EPO induction is the major target of HIF-PH inhibitors for their therapeutic effects on erythropoiesis. Additionally, the drug-specific properties of HIF-PH inhibitors in EPO induction and iron metabolism have been shown in mice, providing useful information for selecting the proper HIF-PH inhibitor for each renal anemia patient.
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Affiliation(s)
- Taku Nakai
- Applied Oxygen Physiology Project, New Industry Creation Hatchery Center, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Kaga 2-11-1, Itabashi-ku, Tokyo 173-8605, Japan
| | - Koichiro Kato
- Applied Oxygen Physiology Project, New Industry Creation Hatchery Center, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Tomoko Fukuuchi
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Kaga 2-11-1, Itabashi-ku, Tokyo 173-8605, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; The 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 Biochemistry and Molecular Biology, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Norio Suzuki
- Applied Oxygen Physiology Project, New Industry Creation Hatchery Center, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
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5
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Šofranko J, Gondáš E, Murín R. Application of the Hydrophilic Interaction Liquid Chromatography (HILIC-MS) Novel Protocol to Study the Metabolic Heterogeneity of Glioblastoma Cells. Metabolites 2024; 14:297. [PMID: 38921432 PMCID: PMC11205371 DOI: 10.3390/metabo14060297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Glioblastoma is a highly malignant brain tumor consisting of a heterogeneous cellular population. The transformed metabolism of glioblastoma cells supports their growth and division on the background of their milieu. One might hypothesize that the transformed metabolism of a primary glioblastoma could be well adapted to limitations in the variety and number of substrates imported into the brain parenchyma and present it their microenvironment. Additionally, the phenotypic heterogeneity of cancer cells could promote the variations among their metabolic capabilities regarding the utilization of available substrates and release of metabolic intermediates. With the aim to identify the putative metabolic footprint of different types of glioblastoma cells, we exploited the possibility for separation of polar and ionic molecules present in culture media or cell lysates by hydrophilic interaction liquid chromatography (HILIC). The mass spectrometry (MS) was then used to identify and quantify the eluted compounds. The introduced method allows the detection and quantification of more than 150 polar and ionic metabolites in a single run, which may be present either in culture media or cell lysates and provide data for polaromic studies within metabolomics. The method was applied to analyze the culture media and cell lysates derived from two types of glioblastoma cells, T98G and U118. The analysis revealed that even both types of glioblastoma cells share several common metabolic aspects, and they also exhibit differences in their metabolic capability. This finding agrees with the hypothesis about metabolic heterogeneity of glioblastoma cells. Furthermore, the combination of both analytical methods, HILIC-MS, provides a valuable tool for metabolomic studies based on the simultaneous identification and quantification of a wide range of polar and ionic metabolites-polaromics.
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Affiliation(s)
- Jakub Šofranko
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4D, 036 01 Martin, Slovakia
| | - Eduard Gondáš
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4D, 036 01 Martin, Slovakia
| | - Radovan Murín
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4D, 036 01 Martin, Slovakia
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Xiao Z, Yu S, Zhang D, Li C. UHPLC-qTOF-MS-Based Nontargeted Metabolomics to Characterize the Effects of Capsaicin on Plasma and Skin Metabolic Profiles of C57BL/6 Mice-An In vivo Experimental Study. Drug Des Devel Ther 2024; 18:719-729. [PMID: 38476205 PMCID: PMC10929253 DOI: 10.2147/dddt.s423974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Background Capsaicin is the main compound found in chili pepper and has complex pharmacologic effects. This study aimed to elucidate the mechanism of the effect of capsaicin on physiological processes by analyzing changes in metabolites and metabolic pathways. Methods Female C57BL/6 mice were divided into two groups(n = 10/group) and fed with capsaicin-soybean oil solution(group T) or soybean oil(group C) for 6 weeks. Ultra-high performance liquid chromatography/quadrupole time-of-flight mass spectrometry (UHPLC-qTOF-MS) based metabolomics was undertaken to assess plasma and skin metabolic profile changes and identify differential metabolites through multivariate analysis. Results According to the OPLS-DA score plots, the plasma and skin metabolic profiles in the group T and group C were significantly separated. In plasma, 38 significant differential metabolites were identified. KEGG pathway enrichment analysis revealed that the most significant plasma metabolic pathways included pyruvate metabolism and ABC transporters. In skin, seven significant differential metabolites were found. Four metabolic pathways with p values < 0.05 were detected, including sphingolipid metabolism, sphingolipid signaling pathway, apoptosis, and necroptosis. Conclusion These findings will provide metabolomic insights to assess the physiological functions of capsaicin and contribute to a better understanding of the potential effects of a capsaicin-rich diet on health.
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Affiliation(s)
- Zhen Xiao
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
- Department of Dermatology, Taiyuan Central Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Simin Yu
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Deng Zhang
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
| | - Chunming Li
- Department of Dermatology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, People’s Republic of China
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Nishiumi S, Yokoyama T, Ojima N. User-friendly relative quantification procedure for gas chromatography/mass spectrometry-based plasma metabolome analysis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2024; 38:e9683. [PMID: 38212648 DOI: 10.1002/rcm.9683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/20/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024]
Abstract
RATIONALE Recently, metabolome analysis has been applied to a variety of research fields, but differences between batches or facilities can cause discrepancies in the results of such analyses. To resolve these issues using comprehensive metabolome analysis, in which it is difficult to perform quantitative analyses of all detected metabolites, internal standard compounds are used to obtain relative metabolite levels. This study investigated gas chromatography/mass spectrometry-based plasma metabolome analysis methods that are superior to relative quantification using internal standard compounds. METHODS In experiment I, four analyses were performed under different analytical conditions at one facility, and then the data from the four analyses were compared. In experiment II, the same samples were analyzed at three facilities, and then the data from the three facilities were compared. RESULTS Regarding the relative values obtained through comparisons with the internal standard compound, differences in the analytical results were observed among the four analytical conditions in experiment I and among the three facilities in experiment II, and the differences observed among the three facilities (experiment II) were larger. When correction was performed using plasma as a quality control, which is the procedure suggested in this study, these differences were markedly ameliorated. CONCLUSION The suggested procedure involves the analysis of a plasma standard as a quality control for each batch and the calculation of relative target plasma to quality-control plasma values for each metabolite. This is an easy and low-cost method and could be readily employed by researchers during comprehensive plasma metabolome analysis.
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Affiliation(s)
- Shin Nishiumi
- Department of Omics Medicine, Hyogo Medical University, Nishinomiya, Japan
- Department of Biosphere Sciences, School of Human Sciences, Kobe College, Nishinomiya, Japan
| | - Tomonori Yokoyama
- Department of Omics Medicine, Hyogo Medical University, Nishinomiya, Japan
- Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
| | - Noriyuki Ojima
- Department of Omics Medicine, Hyogo Medical University, Nishinomiya, Japan
- Analytical and Measuring Instruments Division, Shimadzu Corporation, Kyoto, Japan
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Rashad S, Al-Mesitef S, Mousa A, Zhou Y, Ando D, Sun G, Fukuuchi T, Iwasaki Y, Xiang J, Byrne SR, Sun J, Maekawa M, Saigusa D, Begley TJ, Dedon PC, Niizuma K. Translational response to mitochondrial stresses is orchestrated by tRNA modifications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580389. [PMID: 38405984 PMCID: PMC10888749 DOI: 10.1101/2024.02.14.580389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Mitochondrial stress and dysfunction play important roles in many pathologies. However, how cells respond to mitochondrial stress is not fully understood. Here, we examined the translational response to electron transport chain (ETC) inhibition and arsenite induced mitochondrial stresses. Our analysis revealed that during mitochondrial stress, tRNA modifications (namely f5C, hm5C, queuosine and its derivatives, and mcm5U) dynamically change to fine tune codon decoding, usage, and optimality. These changes in codon optimality drive the translation of many pathways and gene sets, such as the ATF4 pathway and selenoproteins, involved in the cellular response to mitochondrial stress. We further examined several of these modifications using targeted approaches. ALKBH1 knockout (KO) abrogated f5C and hm5C levels and led to mitochondrial dysfunction, reduced proliferation, and impacted mRNA translation rates. Our analysis revealed that tRNA queuosine (tRNA-Q) is a master regulator of the mitochondrial stress response. KO of QTRT1 or QTRT2, the enzymes responsible for tRNA-Q synthesis, led to mitochondrial dysfunction, translational dysregulation, and metabolic alterations in mitochondria-related pathways, without altering cellular proliferation. In addition, our analysis revealed that tRNA-Q loss led to a domino effect on various tRNA modifications. Some of these changes could be explained by metabolic profiling. Our analysis also revealed that utilizing serum deprivation or alteration with Queuine supplementation to study tRNA-Q or stress response can introduce various confounding factors by altering many other tRNA modifications. In summary, our data show that tRNA modifications are master regulators of the mitochondrial stress response by driving changes in codon decoding.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shadi Al-Mesitef
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Abdulrahman Mousa
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuan Zhou
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daisuke Ando
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurology, Tohoku university Graduate school of Medicine, Sendai, Japan
| | - Guangxin Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Tomoko Fukuuchi
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yuko Iwasaki
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Jingdong Xiang
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
| | - Shane R Byrne
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Codomax Inc, 17 Briden St STE 219, Worcester, MA 01605
| | - Jingjing Sun
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, Albany, NY, USA
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, MA, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance IRG, Campus for Research Excellence and Technological Enterprise, Singapore
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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Sun Y, Saito K, Ushiki A, Abe M, Saito Y, Kashiwada T, Horimasu Y, Gemma A, Tatsumi K, Hattori N, Tsushima K, Takemoto K, Ishikawa R, Momiyama T, Matsuyama SI, Arakawa N, Akane H, Toyoda T, Ogawa K, Sato M, Takamatsu K, Mori K, Nishiya T, Izumi T, Ohno Y, Saito Y, Hanaoka M. Identification of kynurenine and quinolinic acid as promising serum biomarkers for drug-induced interstitial lung diseases. Respir Res 2024; 25:31. [PMID: 38221627 PMCID: PMC10788992 DOI: 10.1186/s12931-023-02653-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 12/24/2023] [Indexed: 01/16/2024] Open
Abstract
BACKGROUND Drug-induced interstitial lung disease (DILD) is a lung injury caused by various types of drugs and is a serious problem in both clinical practice and drug development. Clinical management of the condition would be improved if there were DILD-specific biomarkers available; this study aimed to meet that need. METHODS Biomarker candidates were identified by non-targeted metabolomics focusing on hydrophilic molecules, and further validated by targeted approaches using the serum of acute DILD patients, DILD recovery patients, DILD-tolerant patients, patients with other related lung diseases, and healthy controls. RESULTS Serum levels of kynurenine and quinolinic acid (and kynurenine/tryptophan ratio) were elevated significantly and specifically in acute DILD patients. The diagnostic potentials of these biomarkers were superior to those of conventional lung injury biomarkers, Krebs von den Lungen-6 and surfactant protein-D, in discriminating between acute DILD patients and patients with other lung diseases, including idiopathic interstitial pneumonia and lung diseases associated with connective tissue diseases. In addition to identifying and evaluating the biomarkers, our data showed that kynurenine/tryptophan ratios (an indicator of kynurenine pathway activation) were positively correlated with serum C-reactive protein concentrations in patients with DILD, suggesting the potential association between the generation of these biomarkers and inflammation. Our in vitro experiments demonstrated that macrophage differentiation and inflammatory stimulations typified by interferon gamma could activate the kynurenine pathway, resulting in enhanced kynurenine levels in the extracellular space in macrophage-like cell lines or lung endothelial cells. Extracellular quinolinic acid levels were elevated only in macrophage-like cells but not endothelial cells owing to the lower expression levels of metabolic enzymes converting kynurenine to quinolinic acid. These findings provide clues about the molecular mechanisms behind their specific elevation in the serum of acute DILD patients. CONCLUSIONS The serum concentrations of kynurenine and quinolinic acid as well as kynurenine/tryptophan ratios are promising and specific biomarkers for detecting and monitoring DILD and its recovery, which could facilitate accurate decisions for appropriate clinical management of patients with DILD.
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Affiliation(s)
- Yuchen Sun
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kosuke Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Atsuhito Ushiki
- First Department of Internal Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Mitsuhiro Abe
- Department of Respirology (B2), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba, 260-8677, Japan
| | - Yoshinobu Saito
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Takeru Kashiwada
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Yasushi Horimasu
- Department of Respiratory Medicine, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, Hiroshima, 734-8551, Japan
| | - Akihiko Gemma
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo, 113-8602, Japan
| | - Koichiro Tatsumi
- Department of Respirology (B2), Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba-shi, Chiba, 260-8677, Japan
| | - Noboru Hattori
- Department of Respiratory Medicine, Hiroshima University Hospital, 1-2-3 Kasumi, Minami-ku, Hiroshima, Hiroshima, 734-8551, Japan
| | - Kenji Tsushima
- Division of General Internal Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa, 216-8511, Japan
| | - Kazuhisa Takemoto
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Rika Ishikawa
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Toshiko Momiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Shin-Ichiro Matsuyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Noriaki Arakawa
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Hirotoshi Akane
- Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Takeshi Toyoda
- Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Kumiko Ogawa
- Division of Pathology, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Motonobu Sato
- Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kazuhiko Takamatsu
- Astellas Pharma Inc., 21, Miyukigaoka, Tsukuba, Ibaraki, 305-8585, Japan
| | - Kazuhiko Mori
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Takayoshi Nishiya
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo, 134-8630, Japan
| | - Takashi Izumi
- Kihara Memorial Yokohama Foundation, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yasuo Ohno
- Kihara Memorial Yokohama Foundation, 1-6 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-9501, Japan.
| | - Masayuki Hanaoka
- First Department of Internal Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
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10
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Tadaka S, Kawashima J, Hishinuma E, Saito S, Okamura Y, Otsuki A, Kojima K, Komaki S, Aoki Y, Kanno T, Saigusa D, Inoue J, Shirota M, Takayama J, Katsuoka F, Shimizu A, Tamiya G, Shimizu R, Hiratsuka M, Motoike I, Koshiba S, Sasaki M, Yamamoto M, Kinoshita K. jMorp: Japanese Multi-Omics Reference Panel update report 2023. Nucleic Acids Res 2024; 52:D622-D632. [PMID: 37930845 PMCID: PMC10767895 DOI: 10.1093/nar/gkad978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/06/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
Modern medicine is increasingly focused on personalized medicine, and multi-omics data is crucial in understanding biological phenomena and disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing disease risk and drug response. Therefore, multi-omics data from specific ethnic populations are essential for the effective implementation of personalized medicine. Various prospective cohort studies, such as the UK Biobank, All of Us and Lifelines, have been conducted worldwide. The Tohoku Medical Megabank project was initiated after the Great East Japan Earthquake in 2011. It collects biological specimens and conducts genome and omics analyses to build a basis for personalized medicine. Summary statistical data from these analyses are available in the jMorp web database (https://jmorp.megabank.tohoku.ac.jp), which provides a multidimensional approach to the diversity of the Japanese population. jMorp was launched in 2015 as a public database for plasma metabolome and proteome analyses and has been continuously updated. The current update will significantly expand the scale of the data (metabolome, genome, transcriptome, and metagenome). In addition, the user interface and backend server implementations were rewritten to improve the connectivity between the items stored in jMorp. This paper provides an overview of the new version of the jMorp.
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Affiliation(s)
- Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Yasunobu Okamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Shohei Komaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa-gun, Iwate 028-3609, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Takanari Kanno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Faculty of Pharma-Science, Teikyo University, Tokyo 173-8605, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Jun Takayama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Atsushi Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa-gun, Iwate 028-3609, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo 103-0027, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Masahiro Hiratsuka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi 980-8578, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Shiwa-gun, Iwate 028-3609, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi 980-8579, Japan
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11
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Maekawa M. Analysis of Metabolic Changes in Endogenous Metabolites and Diagnostic Biomarkers for Various Diseases Using Liquid Chromatography and Mass Spectrometry. Biol Pharm Bull 2024; 47:1087-1105. [PMID: 38825462 DOI: 10.1248/bpb.b24-00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Analysis of endogenous metabolites in various diseases is useful for searching diagnostic biomarkers and elucidating the molecular mechanisms of pathophysiology. The author and collaborators have developed some LC/tandem mass spectrometry (LC/MS/MS) methods for metabolites and applied them to disease-related samples. First, we identified urinary conjugated cholesterol metabolites and serum N-palmitoyl-O-phosphocholine serine as useful biomarkers for Niemann-Pick disease type C (NPC). For the purpose of intraoperative diagnosis of glioma patients, we developed the LC/MS/MS analysis methods for 2-hydroxyglutaric acid or cystine and found that they could be good differential biomarkers. For renal cell carcinoma, we searched for various biomarkers for early diagnosis, malignancy evaluation and recurrence prediction by global metabolome analysis and targeted LC/MS/MS analysis. In pathological analysis, we developed a simultaneous LC/MS/MS analysis method for 13 steroid hormones and applied it to NPC cells, we found 6 types of reductions in NPC model cells. For non-alcoholic steatohepatitis (NASH), model mice were prepared with special diet and plasma bile acids were measured, and as a result, hydrophilic bile acids were significantly increased. In addition, we developed an LC/MS/MS method for 17 sterols and analyzed liver cholesterol metabolites and found a decrease in phytosterols and cholesterol synthetic markers and an increase in non-enzymatic oxidative sterols in the pre-onset stage of NASH. We will continue to challenge themselves to add value to clinical practice based on cutting-edge analytical chemistry methodology.
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12
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Suzuki J, Hemmi T, Maekawa M, Watanabe M, Inada H, Ikushima H, Oishi T, Ikeda R, Honkura Y, Kagawa Y, Kawase T, Mano N, Owada Y, Osumi N, Katori Y. Fatty acid binding protein type 7 deficiency preserves auditory function in noise-exposed mice. Sci Rep 2023; 13:21494. [PMID: 38057582 PMCID: PMC10700610 DOI: 10.1038/s41598-023-48702-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023] Open
Abstract
Fatty acid-binding protein 7 (FABP7) is vital for uptake and trafficking of fatty acids in the nervous system. To investigate the involvement of FABP7 in noise-induced hearing loss (NIHL) pathogenesis, we used Fabp7 knockout (KO) mice generated via CRISPR/Cas9 in the C57BL/6 background. Initial auditory brainstem response (ABR) measurements were conducted at 9 weeks, followed by noise exposure at 10 weeks. Subsequent ABRs were performed 24 h later, with final measurements at 12 weeks. Inner ears were harvested 24 h after noise exposure for RNA sequencing and metabolic analyses. We found no significant differences in initial ABR measurements, but Fabp7 KO mice showed significantly lower thresholds in the final ABR measurements. Hair cell survival was also enhanced in Fabp7 KO mice. RNA sequencing revealed that genes associated with the electron transport chain were upregulated or less impaired in Fabp7 KO mice. Metabolomic analysis revealed various alterations, including decreased glutamate and aspartate in Fabp7 KO mice. In conclusion, FABP7 deficiency mitigates cochlear damage following noise exposure. This protective effect was supported by the changes in gene expression of the electron transport chain, and in several metabolites, including excitotoxic neurotransmitters. Our study highlights the potential therapeutic significance of targeting FABP7 in NIHL.
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Affiliation(s)
- Jun Suzuki
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan.
| | - Tomotaka Hemmi
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Masahiro Watanabe
- Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Hitoshi Inada
- Department of Developmental Neuroscience, Centers for Neuroscience, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Hiroyuki Ikushima
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Tetsuya Oishi
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Ryoukichi Ikeda
- Department of Otolaryngology, Head and Neck Surgery, Iwate Medical University School of Medicine, 19-1 Odori, Yahaba, Shiwa, 020-8505, Japan
| | - Yohei Honkura
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Yoshiteru Kagawa
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Tetsuaki Kawase
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
- Graduate School of Pharmaceutical Sciences, Tohoku University, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
| | - Yuji Owada
- Department of Organ Anatomy, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Centers for Neuroscience, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Yukio Katori
- Department of Otolaryngology-Head and Neck Surgery, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8574, Japan
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13
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Sato K, Saigusa D, Kokubun T, Fujioka A, Feng Q, Saito R, Uruno A, Matsukawa N, Ohno-Oishi M, Kunikata H, Yokoyama Y, Yasuda M, Himori N, Omodaka K, Tsuda S, Maekawa S, Yamamoto M, Nakazawa T. Reduced glutathione level in the aqueous humor of patients with primary open-angle glaucoma and normal-tension glaucoma. NPJ AGING 2023; 9:28. [PMID: 37990002 PMCID: PMC10663551 DOI: 10.1038/s41514-023-00124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 09/22/2023] [Indexed: 11/23/2023]
Abstract
Glaucoma is a leading cause of blindness worldwide in older people. Profiling the aqueous humor, including the metabolites it contains, is useful to understand physiological and pathological conditions in the eye. In the current study, we used mass spectrometry (MS) to characterize the aqueous humor metabolomic profile and biological features of patients with glaucoma. Aqueous humor samples were collected during trabeculectomy surgery or cataract surgery and analyzed with global metabolomics. We included 40 patients with glaucoma (32 with POAG, 8 with NTG) and 37 control subjects in a discovery study. VIP analysis revealed five metabolites that were elevated and three metabolites that were reduced in the glaucoma patients. The identified metabolomic profile had an area under the receiver operating characteristic curve of 0.953. Among eight selected metabolites, the glutathione level was significantly decreased in association with visual field defects. Moreover, in a validation study to confirm the reproducibility of our findings, the glutathione level was reduced in NTG and POAG patients compared with a cataract control group. Our findings demonstrate that aqueous humor profiling can help to diagnose glaucoma and that various aqueous humor metabolites are correlated with clinical parameters in glaucoma patients. In addition, glutathione is clearly reduced in the aqueous humor of glaucoma patients with both IOP-dependent and IOP-independent disease subtypes. These findings indicate that antioxidant agents in the aqueous humor reflect glaucomatous optic nerve damage and that excessive oxidative stress may be involved in the pathogenesis of glaucoma.
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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
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- Medical Biochemistry, Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Taiki Kokubun
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Amane Fujioka
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Qiwei Feng
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 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
| | - 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
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Michiko Ohno-Oishi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiroshi Kunikata
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yu Yokoyama
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Masayuki Yasuda
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Noriko Himori
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Department of Aging Vision Healthcare, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kazuko Omodaka
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Satoru Tsuda
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Shigeto Maekawa
- Department of Ophthalmology, Tohoku University Graduate 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 Retinal Disease Control, 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 Collaborative Program for Ophthalmic Drug Discovery, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
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14
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Okami Y, Chan Q, Miura K, Kadota A, Elliott P, Masaki K, Okayama A, Okuda N, Yoshita K, Miyagawa N, Okamura T, Sakata K, Saitoh S, Sakurai M, Nakagawa H, Stamler (deceased) J, Ueshima H. Small High-Density Lipoprotein and Omega-3 Fatty Acid Intake Differentiates Japanese and Japanese-Americans: The INTERLIPID Study. J Atheroscler Thromb 2023; 30:884-906. [PMID: 36328528 PMCID: PMC10406687 DOI: 10.5551/jat.63762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/19/2022] [Indexed: 08/04/2023] Open
Abstract
AIM To identify the most differentiated serum lipids, especially concerning particle size and fractions, between Japanese living in Japan and Japanese-Americans in Hawaii, in the absence of possible genetic confounders, and cross-sectionally examine the associated modifiable lifestyle factors. METHODS Overall, 1,241 (aged 40-59 years) Japanese living in Japan and Japanese-Americans in Hawaii were included. We quantified 130 serum lipid profiles (VLDL 1-5, IDL, LDL 1-6, high-density lipoprotein [HDL] 1-4, and their subfractions) using Bruker's 1H-nuclear magnetic resonance spectrometer for the primary outcome. Modifiable lifestyle factors included body mass index (BMI), physical activity, alcohol and smoking habits, and 70 nutrient parameters. We evaluated the different lipids between the groups using partial least squares-discriminant analysis and association between extracted lipids and lifestyle factors using multivariable linear regression analysis. RESULTS Concentrations of HDL4, HDL with the smallest particle size, were lower in Japanese than in Japanese-Americans of both sexes. Higher fish-derived omega-3 fatty acid intake and lower alcohol intake were associated with lower HDL4 concentrations. A 1% higher kcal intake of total omega-3 fatty acids was associated with a 9.8-mg/dL lower HDL4. Fish-derived docosapentaenoic acid, eicosapentaenoic acid, and docosahexaenoic acid intake were inversely associated with HDL4 concentration. There was no relationship between country, sex, age, or BMI. CONCLUSIONS Japanese and Japanese-Americans can be differentiated based on HDL4 concentration. High fish intake among the Japanese may contribute to their lower HDL4 concentration. Thus, HDL particle size may be an important clinical marker for coronary artery diseases or a fish consumption biomarker.
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Affiliation(s)
- Yukiko Okami
- NCD Epidemiology Research Center, Shiga University of Medical Science, Shiga, Japan
| | - Queenie Chan
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Katsuyuki Miura
- NCD Epidemiology Research Center, Shiga University of Medical Science, Shiga, Japan
| | - Aya Kadota
- NCD Epidemiology Research Center, Shiga University of Medical Science, Shiga, Japan
| | - Paul Elliott
- MRC-PHE Centre for Environment and Health, Department of Epidemiology and Biostatistics, Faculty of Medicine, School of Public Health, Imperial College London, London, UK
| | - Kamal Masaki
- Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, USA
| | - Akira Okayama
- Research Institute of Strategy for Prevention, Tokyo, Japan
| | - Nagako Okuda
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto, Japan
| | - Katsushi Yoshita
- Graduate School of Human Life and Ecology Division of Human Life and Ecology, Osaka Metropolitan University, Osaka, Japan
| | - Naoko Miyagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Kiyomi Sakata
- Department of Hygiene and Preventive Medicine, Iwate Medical University, Iwate, Japan
| | - Shigeyuki Saitoh
- School of Health Sciences, School of Medicine, Sapporo Medical University, Sapporo, Japan
| | - Masaru Sakurai
- Department of Social and Environmental Medicine, Kanazawa Medical University, Ishikawa, Japan
| | - Hideaki Nakagawa
- Department of Social and Environmental Medicine, Kanazawa Medical University, Ishikawa, Japan
| | | | - Hirotsugu Ueshima
- NCD Epidemiology Research Center, Shiga University of Medical Science, Shiga, Japan
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15
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Sugimoto M, Aizawa Y, Tomita A. Data Processing and Analysis in Liquid Chromatography-Mass Spectrometry-Based Targeted Metabolomics. Methods Mol Biol 2023; 2571:241-255. [PMID: 36152165 DOI: 10.1007/978-1-0716-2699-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry (MS)-based metabolomics provides high-dimensional datasets; that is, the data include various metabolite features. Data analysis begins by converting the raw data obtained from the MS to produce a data matrix (metabolite × concentrations). This is followed by several steps, such as peak integration, alignment of multiple data, metabolite identification, and calculation of metabolite concentrations. Each step yields the analytical results and the accompanying information used for the quality assessment of the anterior steps. Thus, the measurement quality can be analyzed through data processing. Here, we introduce a typical data processing procedure and describe a method to utilize the intermediate data as quality control. Subsequently, commonly used data analysis methods for metabolomics data, such as statistical analyses, are also introduced.
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Affiliation(s)
- Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
- Institute for Advanced Biosciences, Yamagata, Japan.
| | - Yumi Aizawa
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Atsumi Tomita
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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16
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dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project. Hum Genome Var 2021; 8:44. [PMID: 34887386 PMCID: PMC8660797 DOI: 10.1038/s41439-021-00175-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/08/2022] Open
Abstract
To reveal gene-environment interactions underlying common diseases and estimate the risk for common diseases, the Tohoku Medical Megabank (TMM) project has conducted prospective cohort studies and genomic and multiomics analyses. To establish an integrated biobank, we developed an integrated database called “dbTMM” that incorporates both the individual cohort/clinical data and the genome/multiomics data of 157,191 participants in the Tohoku Medical Megabank project. To our knowledge, dbTMM is the first database to store individual whole-genome data on a variant-by-variant basis as well as cohort/clinical data for over one hundred thousand participants in a prospective cohort study. dbTMM enables us to stratify our cohort by both genome-wide genetic factors and environmental factors, and it provides a research and development platform that enables prospective analysis of large-scale data from genome cohorts. A database integrating 1.3 trillion genome cohort data entries from 157,191 individuals in Japan will facilitate research into the gene-environment interactions underlying common diseases. The Tohoku Medical Megabank integrated database called dbTMM was developed by Soichi Ogishima, Masayuki Yamamoto and colleagues at Tohoku University in Japan. It incorporates the genome, metabolome, proteome, clinical, sociodemographic, lifestyle and environmental data from 84,073 adults, and 73,529 pregnant women and their families, including children. Blood and urine samples were collected from participants and analysed, then obtained genome/multiomics data were stored in dbTMM. Users can stratify the entire population into smaller populations based on multiple data variables, including whole genome variants, to search for statistically significant differences that might warrant further research. The dbTMM is expected to help clarify the genes and gene-environment interactions underlying common diseases and improve disease risk prediction.
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17
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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] [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.
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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
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18
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Yamauchi T, Ochi D, Matsukawa N, Saigusa D, Ishikuro M, Obara T, Tsunemoto Y, Kumatani S, Yamashita R, Tanabe O, Minegishi N, Koshiba S, Metoki H, Kuriyama S, Yaegashi N, Yamamoto M, Nagasaki M, Hiyama S, Sugawara J. Machine learning approaches to predict gestational age in normal and complicated pregnancies via urinary metabolomics analysis. Sci Rep 2021; 11:17777. [PMID: 34493809 PMCID: PMC8423760 DOI: 10.1038/s41598-021-97342-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/25/2021] [Indexed: 02/07/2023] Open
Abstract
The elucidation of dynamic metabolomic changes during gestation is particularly important for the development of methods to evaluate pregnancy status or achieve earlier detection of pregnancy-related complications. Some studies have constructed models to evaluate pregnancy status and predict gestational age using omics data from blood biospecimens; however, less invasive methods are desired. Here we propose a model to predict gestational age, using urinary metabolite information. In our prospective cohort study, we collected 2741 urine samples from 187 healthy pregnant women, 23 patients with hypertensive disorders of pregnancy, and 14 patients with spontaneous preterm birth. Using gas chromatography-tandem mass spectrometry, we identified 184 urinary metabolites that showed dynamic systematic changes in healthy pregnant women according to gestational age. A model to predict gestational age during normal pregnancy progression was constructed; the correlation coefficient between actual and predicted weeks of gestation was 0.86. The predicted gestational ages of cases with hypertensive disorders of pregnancy exhibited significant progression, compared with actual gestational ages. This is the first study to predict gestational age in normal and complicated pregnancies by using urinary metabolite information. Minimally invasive urinary metabolomics might facilitate changes in the prediction of gestational age in various clinical settings.
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Affiliation(s)
- Takafumi Yamauchi
- grid.419819.c0000 0001 2184 8682X-Tech Development Department, NTT DOCOMO, INC, 3-6 Hikarino-oka, Yokosuka, Kanagawa 239-8536 Japan
| | - Daisuke Ochi
- grid.419819.c0000 0001 2184 8682X-Tech Development Department, NTT DOCOMO, INC, 3-6 Hikarino-oka, Yokosuka, Kanagawa 239-8536 Japan
| | - Naomi Matsukawa
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Daisuke Saigusa
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Mami Ishikuro
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Tohoku University Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Taku Obara
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Tohoku University Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
| | - Yoshiki Tsunemoto
- grid.419819.c0000 0001 2184 8682X-Tech Development Department, NTT DOCOMO, INC, 3-6 Hikarino-oka, Yokosuka, Kanagawa 239-8536 Japan
| | - Satsuki Kumatani
- grid.419819.c0000 0001 2184 8682X-Tech Development Department, NTT DOCOMO, INC, 3-6 Hikarino-oka, Yokosuka, Kanagawa 239-8536 Japan
| | - Riu Yamashita
- grid.272242.30000 0001 2168 5385Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577 Japan
| | - Osamu Tanabe
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.418889.40000 0001 2198 115XRadiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815 Japan
| | - Naoko Minegishi
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Seizo Koshiba
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Hirohito Metoki
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.412755.00000 0001 2166 7427Faculty of Medicine, Tohoku Medical Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai, 981-0905 Japan
| | - Shinichi Kuriyama
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Tohoku University Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan ,grid.69566.3a0000 0001 2248 6943International Research Institute of Disaster Science, Tohoku University, Aramaki Aza-Aoba 468-1, Aoba-ku, Sendai, 980-8572 Japan
| | - Nobuo Yaegashi
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Tohoku University Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masayuki Yamamoto
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan
| | - Masao Nagasaki
- grid.258799.80000 0004 0372 2033Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, 53 Shogoinkawahara-cho, Sakyo-ku, Kyoto City, Kyoto 606-8507 Japan ,grid.258799.80000 0004 0372 2033Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, 606-8507 Japan
| | - Satoshi Hiyama
- grid.419819.c0000 0001 2184 8682X-Tech Development Department, NTT DOCOMO, INC, 3-6 Hikarino-oka, Yokosuka, Kanagawa 239-8536 Japan
| | - Junichi Sugawara
- grid.69566.3a0000 0001 2248 6943Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573 Japan ,grid.69566.3a0000 0001 2248 6943Tohoku University Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575 Japan
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19
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Li SN, Tang SH, Ren R, Gong JX, Chen YM. Metabolomic profile of milk fermented with Streptococcus thermophilus cocultured with Bifidobacterium animalis ssp. lactis, Lactiplantibacillus plantarum, or both during storage. J Dairy Sci 2021; 104:8493-8505. [PMID: 34024601 DOI: 10.3168/jds.2021-20270] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/05/2021] [Indexed: 01/27/2023]
Abstract
In this study, the microbial interactions among cocultures of Streptococcus thermophilus (St) with potential probiotics of Bifidobacterium animalis ssp. lactis (Ba) and Lactiplantibacillus plantarum (Lp) in fermented milk were investigated during a storage period of 21 d at 4°C, in terms of acidifying activity (pH and titratable acidity), viable counts, and metabolites. A nontargeted metabolomics approach based on ultra-high-performance liquid chromatography coupled with mass spectrometry was employed for mapping the global metabolite profiles of fermented milk. Probiotic strains cocultured with St accelerated milk acidification, and improved the microbial viability compared with the single culture of St. The St-Ba/Lp treatment manifested a higher bacteria viability and acidification ability in comparison with the St-Ba or the St-Lp treatment. Relative quantitation of 179 significant metabolites was identified, including nucleosides, AA, short peptides, organic acids, lipid derivatives, carbohydrates, carbonyl compounds, and compounds related to energy metabolism. The principal component analysis indicated that St treatment and coculture treatments displayed a complete distinction in metabolite profiles, and Lp had a larger effect than Ba on metabolic profiles of fermented milk produced by cofermentation with St during storage. The heat map in combination with hierarchical cluster analysis showed that the abundance of metabolites significantly varied with the starter cultures over the storage, and high abundance of metabolites was observed in either St or coculture samples. The St-Ba/Lp treatment showed relatively high abundance for the vast majority of metabolites. These findings suggest that the profile of the metabolites characterizing fermented milk samples may depend on the starter cultures, and incorporation of probiotics may considerably influence the metabolomic activities of fermented milks.
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Affiliation(s)
- S N Li
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, P. R. China
| | - S H Tang
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, P. R. China.
| | - R Ren
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, P. R. China
| | - J X Gong
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, P. R. China
| | - Y M Chen
- College of Food Science and Technology, Southwest Minzu University, Chengdu 610041, P. R. China
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20
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Quality Assessment of Untargeted Analytical Data in a Large-Scale Metabolomic Study. J Clin Med 2021; 10:jcm10091826. [PMID: 33922230 PMCID: PMC8122759 DOI: 10.3390/jcm10091826] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Large-scale metabolomic studies have become common, and the reliability of the peak data produced by the various instruments is an important issue. However, less attention has been paid to the large number of uncharacterized peaks in untargeted metabolomics data. In this study, we tested various criteria to assess the reliability of 276 and 202 uncharacterized peaks that were detected in a gathered set of 30 plasma and urine quality control samples, respectively, using capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS). The linear relationship between the amounts of pooled samples and the corresponding peak areas was one of the criteria used to select reliable peaks. We used samples from approximately 3000 participants in the Tsuruoka Metabolome Cohort Study to investigate patterns of the areas of these uncharacterized peaks among the samples and clustered the peaks by combining the patterns and differences in the migration times. Our assessment pipeline removed substantial numbers of unreliable or redundant peaks and detected 35 and 74 reliable uncharacterized peaks in plasma and urine, respectively, some of which may correspond to metabolites involved in important physiological processes such as disease progression. We propose that our assessment pipeline can be used to help establish large-scale untargeted clinical metabolomic studies.
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21
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Meister I, Zhang P, Sinha A, Sköld CM, Wheelock ÅM, Izumi T, Chaleckis R, Wheelock CE. High-Precision Automated Workflow for Urinary Untargeted Metabolomic Epidemiology. Anal Chem 2021; 93:5248-5258. [PMID: 33739820 PMCID: PMC8041248 DOI: 10.1021/acs.analchem.1c00203] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/26/2021] [Indexed: 12/15/2022]
Abstract
Urine is a noninvasive biofluid that is rich in polar metabolites and well suited for metabolomic epidemiology. However, because of individual variability in health and hydration status, the physiological concentration of urine can differ >15-fold, which can pose major challenges in untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics. Although numerous urine normalization methods have been implemented (e.g., creatinine, specific gravity-SG), most are manual and, therefore, not practical for population-based studies. To address this issue, we developed a method to measure SG in 96-well-plates using a refractive index detector (RID), which exhibited accuracy within 85-115% and <3.4% precision. Bland-Altman statistics showed a mean deviation of -0.0001 SG units (limits of agreement: -0.0014 to 0.0011) relative to a hand-held refractometer. Using this RID-based SG normalization, we developed an automated LC-MS workflow for untargeted urinary metabolomics in a 96-well-plate format. The workflow uses positive and negative ionization HILIC chromatography and acquires mass spectra in data-independent acquisition (DIA) mode at three collision energies. Five technical internal standards (tISs) were used to monitor data quality in each method, all of which demonstrated raw coefficients of variation (CVs) < 10% in the quality controls (QCs) and < 20% in the samples for a small cohort (n = 87 urine samples, n = 22 QCs). Application in a large cohort (n = 842 urine samples, n = 248 QCs) demonstrated CVQC < 5% and CVsamples < 16% for 4/5 tISs after signal drift correction by cubic spline regression. The workflow identified >540 urinary metabolites including endogenous and exogenous compounds. This platform is suitable for performing urinary untargeted metabolomic epidemiology and will be useful for applications in population-based molecular phenotyping.
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Affiliation(s)
- Isabel Meister
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
| | - Pei Zhang
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
| | - Anirban Sinha
- Department
of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
- Department
of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands
- Computational
Physiology and Biostatistics, University
Children’s Hospital, Spitalstrasse 33, Basel 4056, Switzerland
| | - C. Magnus Sköld
- Respiratory
Medicine Unit, K2 Department of Medicine Solna and Center for Molecular
Medicine, Karolinska Institutet, Stockholm 141-86, Sweden
- Department
of Respiratory Medicine and Allergy, Karolinska
University Hospital, Stockholm 141-86, Sweden
| | - Åsa M. Wheelock
- Respiratory
Medicine Unit, K2 Department of Medicine Solna and Center for Molecular
Medicine, Karolinska Institutet, Stockholm 141-86, Sweden
- Department
of Respiratory Medicine and Allergy, Karolinska
University Hospital, Stockholm 141-86, Sweden
| | - Takashi Izumi
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Department
of Biochemistry, Gunma University Graduate
School of Medicine, 3-39-22
Showa-machi, Maebashi, Gunma 371-8511, Japan
| | - Romanas Chaleckis
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
| | - Craig E. Wheelock
- Gunma
University Initiative for Advanced Research (GIAR), Gunma University, 3-39-22 Showa-machi, Maebashi, Gunma 371-8511, Japan
- Division
of Physiological Chemistry 2, Department of Medical Biochemistry and
Biophysics, Karolinska Institutet, Biomedicum Quartier 9A, Stockholm 171-77, Sweden
- Department
of Respiratory Medicine and Allergy, Karolinska
University Hospital, Stockholm 141-86, Sweden
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22
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Ikeda A, Nagayama S, Sumazaki M, Konishi M, Fujii R, Saichi N, Muraoka S, Saigusa D, Shimada H, Sakai Y, Ueda K. Colorectal Cancer-Derived CAT1-Positive Extracellular Vesicles Alter Nitric Oxide Metabolism in Endothelial Cells and Promote Angiogenesis. Mol Cancer Res 2021; 19:834-846. [PMID: 33579815 DOI: 10.1158/1541-7786.mcr-20-0827] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/11/2020] [Accepted: 02/08/2021] [Indexed: 12/24/2022]
Abstract
Accumulating scientific evidences strongly support the importance of cancer-derived extracellular vesicles (EV) in organization of tumor microenvironment and metastatic niches, which are also considered as ideal tools for cancer liquid biopsy. To uncover the full scope of proteomic information packaged within EVs secreted directly from human colorectal cancer, we cultured surgically resected viable tissues and obtained tissue-exudative EVs (Te-EV). Our quantitative profiling of 6,307 Te-EV proteins and 8,565 tissue proteins from primary colorectal cancer and adjacent normal mucosa (n = 17) allowed identification of a specific cargo in colorectal cancer-derived Te-EVs, high-affinity cationic amino acid transporter 1 (CAT1, P = 5.0 × 10-3, fold change = 6.2), in addition to discovery of a new class of EV markers, VPS family proteins. The EV sandwich ELISA confirmed escalation of the EV-CAT1 level in plasma from patients with colorectal cancer compared with healthy donors (n = 119, P = 3.8 × 10-7). Further metabolomic analysis revealed that CAT1-overexpressed EVs drastically enhanced vascular endothelial cell growth and tubule formation via upregulation of arginine transport and downstream NO metabolic pathway. These findings demonstrate the potency of CAT1 as an EV-based biomarker for colorectal cancer and its functional significance on tumor angiogenesis. IMPLICATIONS: This study provides a proteome-wide compositional dataset for viable colorectal cancer tissue-derived EVs and especially emphasizes importance of EV-CAT1 as a key regulator of angiogenesis.
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Affiliation(s)
- Atsushi Ikeda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Satoshi Nagayama
- Department of Gastroenterological Surgery, Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Makoto Sumazaki
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Surgery, School of Medicine, Toho University, Tokyo, Japan
| | - Makoto Konishi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Risa Fujii
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Naomi Saichi
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoshi Muraoka
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Hideaki Shimada
- Department of Surgery, School of Medicine, Toho University, Tokyo, Japan
| | - Yoshiharu Sakai
- Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan.
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23
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Sands CJ, Gómez-Romero M, Correia G, Chekmeneva E, Camuzeaux S, Izzi-Engbeaya C, Dhillo WS, Takats Z, Lewis MR. Representing the Metabolome with High Fidelity: Range and Response as Quality Control Factors in LC-MS-Based Global Profiling. Anal Chem 2021; 93:1924-1933. [PMID: 33448796 DOI: 10.1021/acs.analchem.0c03848] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) is a powerful and widely used technique for measuring the abundance of chemical species in living systems. Its sensitivity, analytical specificity, and direct applicability to biofluids and tissue extracts impart great promise for the discovery and mechanistic characterization of biomarker panels for disease detection, health monitoring, patient stratification, and treatment personalization. Global metabolic profiling applications yield complex data sets consisting of multiple feature measurements for each chemical species observed. While this multiplicity can be useful in deriving enhanced analytical specificity and chemical identities from LC-MS data, data set inflation and quantitative imprecision among related features is problematic for statistical analyses and interpretation. This Perspective provides a critical evaluation of global profiling data fidelity with respect to measurement linearity and the quantitative response variation observed among components of the spectra. These elements of data quality are widely overlooked in untargeted metabolomics yet essential for the generation of data that accurately reflect the metabolome. Advanced feature filtering informed by linear range estimation and analyte response factor assessment is advocated as an attainable means of controlling LC-MS data quality in global profiling studies and exemplified herein at both the feature and data set level.
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Affiliation(s)
- Caroline J Sands
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - María Gómez-Romero
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Gonçalo Correia
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Elena Chekmeneva
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Stephane Camuzeaux
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Chioma Izzi-Engbeaya
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0HS, United Kingdom
| | - Waljit S Dhillo
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0HS, United Kingdom
| | - Zoltan Takats
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Matthew R Lewis
- National Phenome Centre, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom.,Section of Bioanalytical Chemistry, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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24
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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: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [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.
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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
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25
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Asteggiano A, Franceschi P, Zorzi M, Aigotti R, Dal Bello F, Baldassarre F, Lops F, Carlucci A, Medana C, Ciccarella G. HPLC-HRMS Global Metabolomics Approach for the Diagnosis of "Olive Quick Decline Syndrome" Markers in Olive Trees Leaves. Metabolites 2021; 11:metabo11010040. [PMID: 33429872 PMCID: PMC7827768 DOI: 10.3390/metabo11010040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/25/2022] Open
Abstract
Olive quick decline syndrome (OQDS) is a multifactorial disease affecting olive plants. The onset of this economically devastating disease has been associated with a Gram-negative plant pathogen called Xylella fastidiosa (Xf). Liquid chromatography separation coupled to high-resolution mass spectrometry detection is one the most widely applied technologies in metabolomics, as it provides a blend of rapid, sensitive, and selective qualitative and quantitative analyses with the ability to identify metabolites. The purpose of this work is the development of a global metabolomics mass spectrometry assay able to identify OQDS molecular markers that could discriminate between healthy (HP) and infected (OP) olive tree leaves. Results obtained via multivariate analysis through an HPLC-ESI HRMS platform (LTQ-Orbitrap from Thermo Scientific) show a clear separation between HP and OP samples. Among the differentially expressed metabolites, 18 different organic compounds highly expressed in the OP group were annotated; results obtained by this metabolomic approach could be used as a fast and reliable method for the biochemical characterization of OQDS and to develop targeted MS approaches for OQDS detection by foliage analysis.
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Affiliation(s)
- Alberto Asteggiano
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Pietro Giuria 5, 10125 Torino, Italy; (A.A.); (M.Z.); (R.A.); (F.D.B.)
| | - Pietro Franceschi
- Unit of Computational Biology, IASMA Research and Innovation Centre, Fondazione Edmund Mach via E. Mach, 1, 38010 San Michele all’ Adige, Italy;
| | - Michael Zorzi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Pietro Giuria 5, 10125 Torino, Italy; (A.A.); (M.Z.); (R.A.); (F.D.B.)
| | - Riccardo Aigotti
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Pietro Giuria 5, 10125 Torino, Italy; (A.A.); (M.Z.); (R.A.); (F.D.B.)
| | - Federica Dal Bello
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Pietro Giuria 5, 10125 Torino, Italy; (A.A.); (M.Z.); (R.A.); (F.D.B.)
| | - Francesca Baldassarre
- Biological and Environmental Sciences Department, UdR INSTM of Lecce University of Salento, Via Monteroni, 73100 Lecce, Italy;
- Institute of Nanotechnology, CNR NANOTEC, Consiglio Nazionale delle Ricerche, Via Monteroni, 73100 Lecce, Italy
| | - Francesco Lops
- Department of Science of Agriculture, Food and Environment, University of Foggia, Via Napoli, 25, 71122 Foggia, Italy; (F.L.); (A.C.)
| | - Antonia Carlucci
- Department of Science of Agriculture, Food and Environment, University of Foggia, Via Napoli, 25, 71122 Foggia, Italy; (F.L.); (A.C.)
| | - Claudio Medana
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Via Pietro Giuria 5, 10125 Torino, Italy; (A.A.); (M.Z.); (R.A.); (F.D.B.)
- Correspondence: (C.M.); (G.C.); Tel.: +39-011-670-5240 (C.M.); +39-083-231-9810 (G.C.)
| | - Giuseppe Ciccarella
- Biological and Environmental Sciences Department, UdR INSTM of Lecce University of Salento, Via Monteroni, 73100 Lecce, Italy;
- Institute of Nanotechnology, CNR NANOTEC, Consiglio Nazionale delle Ricerche, Via Monteroni, 73100 Lecce, Italy
- Correspondence: (C.M.); (G.C.); Tel.: +39-011-670-5240 (C.M.); +39-083-231-9810 (G.C.)
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26
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A Protocol for Untargeted Metabolomic Analysis: From Sample Preparation to Data Processing. Methods Mol Biol 2021; 2276:357-382. [PMID: 34060055 PMCID: PMC9284939 DOI: 10.1007/978-1-0716-1266-8_27] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Untargeted metabolomics has rapidly become a profiling method of choice in many areas of research, including mitochondrial biology. Most commonly, untargeted metabolomics is performed with liquid chromatography/mass spectrometry because it enables measurement of a relatively wide range of physiochemically diverse molecules. Specifically, to assess energy pathways that are associated with mitochondrial metabolism, hydrophilic interaction liquid chromatography (HILIC) is often applied before analysis with a high-resolution accurate mass instrument. The workflow produces large, complex data files that are impractical to analyze manually. Here, we present a protocol to perform untargeted metabolomics on biofluids such as plasma, urine, and cerebral spinal fluid with a HILIC separation and an Orbitrap mass spectrometer. Our protocol describes each step of the analysis in detail, from preparation of solvents for chromatography to selecting parameters during data processing.
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27
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Saigusa D, Matsukawa N, Hishinuma E, Koshiba S. Identification of biomarkers to diagnose diseases and find adverse drug reactions by metabolomics. Drug Metab Pharmacokinet 2020; 37:100373. [PMID: 33631535 DOI: 10.1016/j.dmpk.2020.11.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 12/12/2022]
Abstract
Metabolomics has been widely used for investigating the biological functions of disease expression and has the potential to discover biomarkers in circulating biofluids or tissue extracts that reflect in phenotypic changes. Metabolic profiling has advantages because of the use of unbiased techniques, including multivariate analysis, and has been applied in pharmacological studies to predict therapeutic and adverse reactions of drugs, which is called pharmacometabolomics (PMx). Nuclear magnetic resonance (NMR)- and mass spectrometry (MS)-based metabolomics has contributed to the discovery of recent disease biomarkers; however, the optimal strategy for the study purpose must be selected from many established protocols, methodologies and analytical platforms. Additionally, information on molecular localization in tissue is essential for further functional analyses related to therapeutic and adverse effects of drugs in the process of drug development. MS imaging (MSI) is a promising technology that can visualize molecules on tissue surfaces without labeling and thus provide localized information. This review summarizes recent uses of MS-based global and wide-targeted metabolomics technologies and the advantages of the MSI approach for PMx and highlights the PMx technique for the biomarker discovery of adverse drug effects.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; 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; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan; 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.
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Metabolomic Analysis to Elucidate Mechanisms of Sunitinib Resistance in Renal Cell Carcinoma. Metabolites 2020; 11:metabo11010001. [PMID: 33374949 PMCID: PMC7821950 DOI: 10.3390/metabo11010001] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
Metabolomics analysis possibly identifies new therapeutic targets in treatment resistance by measuring changes in metabolites accompanying cancer progression. We previously conducted a global metabolomics (G-Met) study of renal cell carcinoma (RCC) and identified metabolites that may be involved in sunitinib resistance in RCC. Here, we aimed to elucidate possible mechanisms of sunitinib resistance in RCC through intracellular metabolites. We established sunitinib-resistant and control RCC cell lines from tumor tissues of RCC cell (786-O)-injected mice. We also quantified characteristic metabolites identified in our G-Met study to compare intracellular metabolism between the two cell lines using liquid chromatography-mass spectrometry. The established sunitinib-resistant RCC cell line demonstrated significantly desuppressed protein kinase B (Akt) and mesenchymal-to-epithelial transition (MET) phosphorylation compared with the control RCC cell line under sunitinib exposure. Among identified metabolites, glutamine, glutamic acid, and α-KG (involved in glutamine uptake into the tricarboxylic acid (TCA) cycle for energy metabolism); fructose 6-phosphate, D-sedoheptulose 7-phosphate, and glucose 1-phosphate (involved in increased glycolysis and its intermediate metabolites); and glutathione and myoinositol (antioxidant effects) were significantly increased in the sunitinib-resistant RCC cell line. Particularly, glutamine transporter (SLC1A5) expression was significantly increased in sunitinib-resistant RCC cells compared with control cells. In this study, we demonstrated energy metabolism with glutamine uptake and glycolysis upregulation, as well as antioxidant activity, was also associated with sunitinib resistance in RCC cells.
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A Customizable Analysis Flow in Integrative Multi-Omics. Biomolecules 2020; 10:biom10121606. [PMID: 33260881 PMCID: PMC7760368 DOI: 10.3390/biom10121606] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/21/2022] Open
Abstract
The number of researchers using multi-omics is growing. Though still expensive, every year it is cheaper to perform multi-omic studies, often exponentially so. In addition to its increasing accessibility, multi-omics reveals a view of systems biology to an unprecedented depth. Thus, multi-omics can be used to answer a broad range of biological questions in finer resolution than previous methods. We used six omic measurements—four nucleic acid (i.e., genomic, epigenomic, transcriptomics, and metagenomic) and two mass spectrometry (proteomics and metabolomics) based—to highlight an analysis workflow on this type of data, which is often vast. This workflow is not exhaustive of all the omic measurements or analysis methods, but it will provide an experienced or even a novice multi-omic researcher with the tools necessary to analyze their data. This review begins with analyzing a single ome and study design, and then synthesizes best practices in data integration techniques that include machine learning. Furthermore, we delineate methods to validate findings from multi-omic integration. Ultimately, multi-omic integration offers a window into the complexity of molecular interactions and a comprehensive view of systems biology.
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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] [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.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
- 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.
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Untargeted Metabolomic Profiling Using UHPLC-QTOF/MS Reveals Metabolic Alterations Associated with Autism. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6105608. [PMID: 32964039 PMCID: PMC7502129 DOI: 10.1155/2020/6105608] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/25/2020] [Indexed: 12/16/2022]
Abstract
Autism spectrum disorder (ASD) is a clinical spectrum of neurodevelopment disorder characterized by deficits in social communication and social interaction along with repetitive/stereotyped behaviors. The current diagnosis for autism relies entirely on clinical evaluation and has many limitations. In this study, we aim to elucidate the potential mechanism behind autism and establish a series of potential biomarkers for diagnosis. Here, we established an ultra-high-performance liquid chromatography-quadrupole time-of-flight mass spectrometry- (UHPLC-QTOF/MS-) based metabonomic approach to discriminate the metabolic modifications between the cohort of autism patients and the healthy subjects. UHPLC-QTOF/MS analysis revealed that 24 of the identified potential biomarkers were primarily involved in amino acid or lipid metabolism and the tryptophan kynurenine pathway. The combination of nicotinamide, anthranilic acid, D-neopterin, and 7,8-dihydroneopterin allows for discrimination between ASD patients and controls, which were validated in an independent autism case-control cohort. The results indicated that UHPLC-QTOF/MS-based metabolomics is capable of rapidly profiling autism metabolites and is a promising technique for the discovery of potential biomarkers related to autism.
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Nrf2 contributes to the weight gain of mice during space travel. Commun Biol 2020; 3:496. [PMID: 32901092 PMCID: PMC7479603 DOI: 10.1038/s42003-020-01227-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/13/2020] [Indexed: 12/27/2022] Open
Abstract
Space flight produces an extreme environment with unique stressors, but little is known about how our body responds to these stresses. While there are many intractable limitations for in-flight space research, some can be overcome by utilizing gene knockout-disease model mice. Here, we report how deletion of Nrf2, a master regulator of stress defense pathways, affects the health of mice transported for a stay in the International Space Station (ISS). After 31 days in the ISS, all flight mice returned safely to Earth. Transcriptome and metabolome analyses revealed that the stresses of space travel evoked ageing-like changes of plasma metabolites and activated the Nrf2 signaling pathway. Especially, Nrf2 was found to be important for maintaining homeostasis of white adipose tissues. This study opens approaches for future space research utilizing murine gene knockout-disease models, and provides insights into mitigating space-induced stresses that limit the further exploration of space by humans. Using Nrf2 knockout mice, Suzuki, Uruno, Yumoto et al. show that space travel activates Nrf2 signaling, which contributes to the weight gain of mice by regulating fat metabolism of white adipose tissues. This study provides insights into potential interventions to mitigate stresses that accompany space travels.
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Kimble LP, Leslie S, Carlson N. Metabolomics Research Conducted by Nurse Scientists: A Systematic Scoping Review. Biol Res Nurs 2020; 22:436-448. [PMID: 32648468 DOI: 10.1177/1099800420940041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolomics, one of the newest omics, allows for investigation of holistic responses of living systems to myriad biological, behavioral, and environmental factors. Researcher use metabolomics to examine the underlying mechanisms of clinically observed phenotypes. However, these methods are complex, potentially impeding their uptake by scientists. In this scoping review, we summarize literature illustrating nurse scientists' use of metabolomics. Using electronic search methods, we identified metabolomics investigations conducted by nurse scientists and published in English-language journals between 1990 and November 2019. Of the studies included in the review (N = 30), 9 (30%) listed first and/or senior authors that were nurses. Studies were conducted predominantly in the United States and focused on a wide array of clinical conditions across the life span. The upward trend we note in the use of these methods by nurse scientists over the past 2 decades mirrors a similar trend across scientists of all backgrounds. A broad range of study designs were represented in the literature we reviewed, with the majority involving untargeted metabolomics (n = 16, 53.3%) used to generate hypotheses (n = 13, 76.7%) of potential metabolites and/or metabolic pathways as mechanisms of clinical conditions. Metabolomics methods match well with the unique perspective of nurse researchers, who seek to integrate the experiences of individuals to develop a scientific basis for clinical practice that emphasizes personalized approaches. Although small in number, metabolomics investigations by nurse scientists can serve as the foundation for robust programs of research to answer essential questions for nursing.
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Affiliation(s)
- Laura P Kimble
- School of Nursing, 1371Emory University, Atlanta, GA, USA
| | - Sharon Leslie
- Woodruff Health Sciences Center Library, 1371Emory University, Atlanta, GA, USA
| | - Nicole Carlson
- School of Nursing, 1371Emory University, Atlanta, GA, USA
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Pereira JAM, Porto-Figueira P, Taware R, Sukul P, Rapole S, Câmara JS. Unravelling the Potential of Salivary Volatile Metabolites in Oral Diseases. A Review. Molecules 2020; 25:E3098. [PMID: 32646009 PMCID: PMC7412334 DOI: 10.3390/molecules25133098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/24/2022] Open
Abstract
Fostered by the advances in the instrumental and analytical fields, in recent years the analysis of volatile organic compounds (VOCs) has emerged as a new frontier in medical diagnostics. VOCs analysis is a non-invasive, rapid and inexpensive strategy with promising potential in clinical diagnostic procedures. Since cellular metabolism is altered by diseases, the resulting metabolic effects on VOCs may serve as biomarkers for any given pathophysiologic condition. Human VOCs are released from biomatrices such as saliva, urine, skin emanations and exhaled breath and are derived from many metabolic pathways. In this review, the potential of VOCs present in saliva will be explored as a monitoring tool for several oral diseases, including gingivitis and periodontal disease, dental caries, and oral cancer. Moreover, the analytical state-of-the-art for salivary volatomics, e.g., the most common extraction techniques along with the current challenges and future perspectives will be addressed unequivocally.
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Affiliation(s)
- Jorge A. M. Pereira
- CQM–Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal;
| | - Priscilla Porto-Figueira
- CQM–Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal;
| | - Ravindra Taware
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind Road, SPPU Campus, Pune 411007, India; (R.T.); (S.R.)
| | - Pritam Sukul
- Department of Anaesthesiology and Intensive Care Medicine, Rostock Medical Breath Research Analytics and Technologies (ROMBAT), Rostock University Medical Centre, 18057 Rostock, Germany;
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science (NCCS), Ganeshkhind Road, SPPU Campus, Pune 411007, India; (R.T.); (S.R.)
| | - José S. Câmara
- CQM–Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal;
- Faculdade de Ciências Exatas e da Engenharia, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
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Sato T, Kawasaki Y, Maekawa M, Takasaki S, Shimada S, Morozumi K, Sato M, Kawamorita N, Yamashita S, Mitsuzuka K, Mano N, Ito A. Accurate quantification of urinary metabolites for predictive models manifest clinicopathology of renal cell carcinoma. Cancer Sci 2020; 111:2570-2578. [PMID: 32350988 PMCID: PMC7385347 DOI: 10.1111/cas.14440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 12/20/2022] Open
Abstract
Using surgically resected tissue, we identified characteristic metabolites related to the diagnosis and malignant status of clear cell renal cell carcinoma (ccRCC). Specifically, we quantified these metabolites in urine samples to evaluate their potential as clinically useful noninvasive biomarkers of ccRCC. Between January 2016 and August 2018, we collected urine samples from 87 patients who had pathologically diagnosed ccRCC and from 60 controls who were patients with benign urological conditions. Metabolite concentrations in urine samples were investigated using liquid chromatography‐mass spectrometry with an internal standard and adjustment based on urinary creatinine levels. We analyzed the association between metabolite concentration and predictability of diagnosis and of malignant status by multiple logistic regression and receiver operating characteristic (ROC) curves to establish ccRCC predictive models. Of the 47 metabolites identified in our previous study, we quantified 33 metabolites in the urine samples. Multiple logistic regression analysis revealed 5 metabolites (l‐glutamic acid, lactate, d‐sedoheptulose 7‐phosphate, 2‐hydroxyglutarate, and myoinositol) for a diagnostic predictive model and 4 metabolites (l‐kynurenine, l‐glutamine, fructose 6‐phosphate, and butyrylcarnitine) for a predictive model for clinical stage III/IV. The sensitivity and specificity of the diagnostic predictive model were 93.1% and 95.0%, respectively, yielding an area under the ROC curve (AUC) of 0.966. The sensitivity and specificity of the predictive model for clinical stage were 88.5% and 75.4%, respectively, with an AUC of 0.837. In conclusion, quantitative analysis of urinary metabolites yielded predictive models for diagnosis and malignant status of ccRCC. Urinary metabolites have the potential to be clinically useful noninvasive biomarkers of ccRCC to improve patient outcomes.
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Affiliation(s)
- Tomonori Sato
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihide Kawasaki
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Shinya Takasaki
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Shuichi Shimada
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kento Morozumi
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masahiko Sato
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoki Kawamorita
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shinichi Yamashita
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Koji Mitsuzuka
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Akihiro Ito
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Japan
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Nagai K, Uranbileg B, Chen Z, Fujioka A, Yamazaki T, Matsumoto Y, Tsukamoto H, Ikeda H, Yatomi Y, Chiba H, Hui S, Nakazawa T, Saito R, Koshiba S, Aoki J, Saigusa D, Tomioka Y. Identification of novel biomarkers of hepatocellular carcinoma by high-definition mass spectrometry: Ultrahigh-performance liquid chromatography quadrupole time-of-flight mass spectrometry and desorption electrospray ionization mass spectrometry imaging. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34 Suppl 1:e8551. [PMID: 31412144 PMCID: PMC7154627 DOI: 10.1002/rcm.8551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/26/2019] [Accepted: 08/06/2019] [Indexed: 05/13/2023]
Abstract
RATIONALE Hepatocellular carcinoma (HCC) is a highly malignant disease for which the development of prospective or prognostic biomarkers is urgently required. Although metabolomics is widely used for biomarker discovery, there are some bottlenecks regarding the comprehensiveness of detected features, reproducibility of methods, and identification of metabolites. In addition, information on localization of metabolites in tumor tissue is needed for functional analysis. Here, we developed a wide-polarity global metabolomics (G-Met) method, identified HCC biomarkers in human liver samples by high-definition mass spectrometry (HDMS), and demonstrated localization in cryosections using desorption electrospray ionization MS imaging (DESI-MSI) analysis. METHODS Metabolic profiling of tumor (n = 38) and nontumor (n = 72) regions in human livers of HCC was performed by an ultrahigh-performance liquid chromatography quadrupole time-of-flight MS (UHPLC/QTOFMS) instrument equipped with a mixed-mode column. The HCC biomarker candidates were extracted by multivariate analyses and identified by matching values of the collision cross section and their fragment ions on the mass spectra obtained by HDMS. Cryosections of HCC livers, which included both tumor and nontumor regions, were analyzed by DESI-MSI. RESULTS From the multivariate analysis, m/z 904.83 and m/z 874.79 were significantly high and low, respectively, in tumor samples and were identified as triglyceride (TG) 16:0/18:1(9Z)/20:1(11Z) and TG 16:0/18:1(9Z)/18:2(9Z,12Z) using the synthetic compounds. The TGs were clearly localized in the tumor or nontumor areas of the cryosection. CONCLUSIONS Novel biomarkers for HCC were identified by a comprehensive and reproducible G-Met method with HDMS using a mixed-mode column. The combination analysis of UHPLC/QTOFMS and DESI-MSI revealed that the different molecular species of TGs were associated with tumor distribution and were useful for characterizing the progression of tumor cells and discovering prospective biomarkers.
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Affiliation(s)
- Koshi Nagai
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical SciencesTohoku UniversitySendaiJapan
| | | | - Zhen Chen
- Faculty of Health ScienceHokkaido UniversityJapan
| | - Amane Fujioka
- Department of OphthalmologyTohoku University Graduate School of MedicineSendaiMiyagiJapan
| | - Takahiro Yamazaki
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical SciencesTohoku UniversitySendaiJapan
| | - Yotaro Matsumoto
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical SciencesTohoku UniversitySendaiJapan
| | - Hiroki Tsukamoto
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical SciencesTohoku UniversitySendaiJapan
| | - Hitoshi Ikeda
- Department of Clinical Laboratory MedicineUniversity of TokyoJapan
| | - Yutaka Yatomi
- Department of Clinical Laboratory MedicineUniversity of TokyoJapan
| | | | - Shu‐Ping Hui
- Faculty of Health ScienceHokkaido UniversityJapan
| | - Toru Nakazawa
- Department of OphthalmologyTohoku University Graduate School of MedicineSendaiMiyagiJapan
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine
| | - Ritsumi Saito
- Department of Integrative GenomicsTohoku University Tohoku Medical Megabank OrganizationSendaiJapan
- Medical BiochemistryTohoku University Graduate School of MedicineSendaiJapan
| | - Seizo Koshiba
- Tohoku University Advanced Research Center for Innovations in Next-Generation Medicine
- Department of Integrative GenomicsTohoku University Tohoku Medical Megabank OrganizationSendaiJapan
- Medical BiochemistryTohoku University Graduate School of MedicineSendaiJapan
| | - Junken Aoki
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical SciencesTohoku UniversitySendaiJapan
| | - Daisuke Saigusa
- Department of Integrative GenomicsTohoku University Tohoku Medical Megabank OrganizationSendaiJapan
- Medical BiochemistryTohoku University Graduate School of MedicineSendaiJapan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical SciencesTohoku UniversitySendaiJapan
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Ishii H, Saitoh M, Sakamoto K, Sakamoto K, Saigusa D, Kasai H, Ashizawa K, Miyazawa K, Takeda S, Masuyama K, Yoshimura K. Lipidome-based rapid diagnosis with machine learning for detection of TGF-β signalling activated area in head and neck cancer. Br J Cancer 2020; 122:995-1004. [PMID: 32020064 PMCID: PMC7109155 DOI: 10.1038/s41416-020-0732-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 01/05/2023] Open
Abstract
Background Several pro-oncogenic signals, including transforming growth factor beta (TGF-β) signalling from tumour microenvironment, generate intratumoural phenotypic heterogeneity and result in tumour progression and treatment failure. However, the precise diagnosis for tumour areas containing subclones with cytokine-induced malignant properties remains clinically challenging. Methods We established a rapid diagnostic system based on the combination of probe electrospray ionisation-mass spectrometry (PESI-MS) and machine learning without the aid of immunohistological and biochemical procedures to identify tumour areas with heterogeneous TGF-β signalling status in head and neck squamous cell carcinoma (HNSCC). A total of 240 and 90 mass spectra were obtained from TGF-β-unstimulated and -stimulated HNSCC cells, respectively, by PESI-MS and were used for the construction of a diagnostic system based on lipidome. Results This discriminant algorithm achieved 98.79% accuracy in discrimination of TGF-β1-stimulated cells from untreated cells. In clinical human HNSCC tissues, this approach achieved determination of tumour areas with activated TGF-β signalling as efficiently as a conventional histopathological assessment using phosphorylated-SMAD2 staining. Furthermore, several altered peaks on mass spectra were identified as phosphatidylcholine species in TGF-β-stimulated HNSCC cells. Conclusions This diagnostic system combined with PESI-MS and machine learning encourages us to clinically diagnose intratumoural phenotypic heterogeneity induced by TGF-β.
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Affiliation(s)
- Hiroki Ishii
- Department of Otolaryngology, Head and Neck Surgery, Chuo-city, Japan.
| | - Masao Saitoh
- Center for Medical Education and Sciences, Chuo-city, Japan
| | - Kaname Sakamoto
- Department of Otolaryngology, Head and Neck Surgery, Chuo-city, Japan
| | - Kei Sakamoto
- Section of Oral Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo City, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | | | - Kei Ashizawa
- Department of Otolaryngology, Head and Neck Surgery, Chuo-city, Japan
| | - Keiji Miyazawa
- Department of Biochemistry, Faculty of Medicine, University of Yamanashi, Chuo-city, Japan
| | - Sen Takeda
- Department of Anatomy and Cell Biology, Faculty of Medicine, University of Yamanashi, Chuo-city, Japan
| | - Keisuke Masuyama
- Department of Otolaryngology, Head and Neck Surgery, Chuo-city, Japan
| | - Kentaro Yoshimura
- Department of Anatomy and Cell Biology, Faculty of Medicine, University of Yamanashi, Chuo-city, Japan.
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Lee N, Jae Y, Kim M, Cho T, Lee C, Hong YR, Hyeon DY, Ahn S, Kwon H, Kim K, Jung JH, Chae S, Shin JO, Bok J, Byun Y, Hwang D, Koo J. A pathogen-derived metabolite induces microglial activation via odorant receptors. FEBS J 2020; 287:3841-3870. [PMID: 32003140 DOI: 10.1111/febs.15234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/10/2019] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
Abstract
Microglia (MG), the principal neuroimmune sentinels in the brain, continuously sense changes in their environment and respond to invading pathogens, toxins, and cellular debris, thereby affecting neuroinflammation. Microbial pathogens produce small metabolites that influence neuroinflammation, but the molecular mechanisms that determine whether pathogen-derived small metabolites affect microglial activation of neuroinflammation remain to be elucidated. We hypothesized that odorant receptors (ORs), the largest subfamily of G protein-coupled receptors, are involved in microglial activation by pathogen-derived small metabolites. We found that MG express high levels of two mouse ORs, Olfr110 and Olfr111, which recognize a pathogenic metabolite, 2-pentylfuran, secreted by Streptococcus pneumoniae. These interactions activate MG to engage in chemotaxis, cytokine production, phagocytosis, and reactive oxygen species generation. These effects were mediated through the Gαs -cyclic adenosine monophosphate-protein kinase A-extracellular signal-regulated kinase and Gβγ -phospholipase C-Ca2+ pathways. Taken together, our results reveal a novel interplay between the pathogen-derived metabolite and ORs, which has major implications for our understanding of microglial activation by pathogen recognition. DATABASE: Model data are available in the PMDB database under the accession number PM0082389.
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Affiliation(s)
- NaHye Lee
- Department of New Biology, DGIST, Daegu, Korea.,Department of Brain and Cognitive Sciences, DGIST, Daegu, Korea
| | - YoonGyu Jae
- Department of New Biology, DGIST, Daegu, Korea.,Department of Brain and Cognitive Sciences, DGIST, Daegu, Korea
| | - Minhyung Kim
- Center for Plant Aging Research, DGIST, Daegu, Korea
| | - TaeHo Cho
- Department of New Biology, DGIST, Daegu, Korea
| | - ChaeEun Lee
- Department of New Biology, DGIST, Daegu, Korea
| | - Yu Ri Hong
- Department of New Biology, DGIST, Daegu, Korea
| | | | - Sanghyun Ahn
- Center for Plant Aging Research, DGIST, Daegu, Korea
| | - Hongmok Kwon
- College of Pharmacy, Korea University, Sejong, Korea
| | - Kyul Kim
- College of Pharmacy, Korea University, Sejong, Korea
| | - Jae Hoon Jung
- Center for Plant Aging Research, DGIST, Daegu, Korea
| | - Sehyun Chae
- Center for Plant Aging Research, DGIST, Daegu, Korea
| | - Jeong-Oh Shin
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Korea
| | - Youngjoo Byun
- College of Pharmacy, Korea University, Sejong, Korea
| | - Daehee Hwang
- Center for Plant Aging Research, DGIST, Daegu, Korea.,Department of Biological Sciences, Seoul National University, Korea
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Nishizawa H, Matsumoto M, Shindo T, Saigusa D, Kato H, Suzuki K, Sato M, Ishii Y, Shimokawa H, Igarashi K. Ferroptosis is controlled by the coordinated transcriptional regulation of glutathione and labile iron metabolism by the transcription factor BACH1. J Biol Chem 2020; 295:69-82. [PMID: 31740582 PMCID: PMC6952604 DOI: 10.1074/jbc.ra119.009548] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/12/2019] [Indexed: 01/10/2023] Open
Abstract
Ferroptosis is an iron-dependent programmed cell death event, whose regulation and physiological significance remain to be elucidated. Analyzing transcriptional responses of mouse embryonic fibroblasts exposed to the ferroptosis inducer erastin, here we found that a set of genes related to oxidative stress protection is induced upon ferroptosis. We considered that up-regulation of these genes attenuates ferroptosis induction and found that the transcription factor BTB domain and CNC homolog 1 (BACH1), a regulator in heme and iron metabolism, promotes ferroptosis by repressing the transcription of a subset of the erastin-induced protective genes. We noted that these genes are involved in the synthesis of GSH or metabolism of intracellular labile iron and include glutamate-cysteine ligase modifier subunit (Gclm), solute carrier family 7 member 11 (Slc7a11), ferritin heavy chain 1 (Fth1), ferritin light chain 1 (Ftl1), and solute carrier family 40 member 1 (Slc40a1). Ferroptosis has also been previously shown to induce cardiomyopathy, and here we observed that Bach1-/- mice are more resistant to myocardial infarction than WT mice and that the severity of ischemic injury is decreased by the iron-chelator deferasirox, which suppressed ferroptosis. Our findings suggest that BACH1 represses genes that combat labile iron-induced oxidative stress, and ferroptosis is stimulated at the transcriptional level by BACH1 upon disruption of the balance between the transcriptional induction of protective genes and accumulation of iron-mediated damage. We propose that BACH1 controls the threshold of ferroptosis induction and may represent a therapeutic target for alleviating ferroptosis-related diseases, including myocardial infarction.
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Affiliation(s)
- Hironari Nishizawa
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Tomohiko Shindo
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Seiryo-machi 2-1, Sendai 980-8573, Japan
| | - Hiroki Kato
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Katsushi Suzuki
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Masaki Sato
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Yusho Ishii
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Hiroaki Shimokawa
- Department of Cardiovascular Medicine, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan; Center for Regulatory Epigenome and Diseases, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Sendai 980-8575, Japan.
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40
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Takanami Y, Kitamura N, Ito S. LC/MS analysis of three-dimensional model cells exposed to cigarette smoke or aerosol from a novel tobacco vapor product. J Toxicol Sci 2020; 45:769-782. [PMID: 33268677 DOI: 10.2131/jts.45.769] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
A novel tobacco vapor product (NTV) contains tobacco leaves and generates nicotine-containing aerosols using heating elements. Subchronic biological effects have been evaluated previously using three-dimensional bronchial epithelial model cells by repeated exposure to cigarette smoke (CS) and the NTV aerosols; however, the intracellular exposure characteristics have not been studied in detail. In this study, cells were initially exposed to an aqueous extract (AqE) of cigarette smoke (CS) at two concentration levels, and the cell lysate underwent untargeted analysis by LC-high resolution mass spectrometry to determine the exogenous compounds present in the cells. Among the thousands of peaks detected, four peaks showed a CS-dependency, which were reproducibly detected. Two of the peaks were nicotine and nicotine N-oxide, and the other two putative compounds were myosmine and norharman. The cells were then exposed to an AqE of CS in various combinations of exposure and post-exposure culture durations. Post-exposure culturing of cells with fresh medium markedly decreased the peak areas of the four compounds. The in-vitro switching study of CS to NTV aerosols was investigated by intermittently exposing cells to an AqE of CS four times, followed by exposure to either an AqE of CS, NTV aerosol or medium another four times. Switching to NTV reduced myosmine and norharman levels, which are known CS constituents. The results indicate that extracellular compounds inside cells reflect the exposure state outside cells. Thus, monitoring functional changes to cells in these exposure experiments is feasible.
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Affiliation(s)
| | | | - Shigeaki Ito
- Scientific Product Assessment Center, R&D Group, Japan Tobacco Inc
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41
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Kanemitsu Y, Mishima E, Maekawa M, Matsumoto Y, Saigusa D, Yamaguchi H, Ogura J, Tsukamoto H, Tomioka Y, Abe T, Mano N. Comprehensive and semi-quantitative analysis of carboxyl-containing metabolites related to gut microbiota on chronic kidney disease using 2-picolylamine isotopic labeling LC-MS/MS. Sci Rep 2019; 9:19075. [PMID: 31836785 PMCID: PMC6910927 DOI: 10.1038/s41598-019-55600-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 12/02/2019] [Indexed: 01/07/2023] Open
Abstract
Carboxyl-containing metabolites, such as bile acids and fatty acids, have many important functions and microbiota is involved in the production of them. In the previous study, we found that the chronic kidney disease (CKD) model mice raised under germ-free conditions provided more severe renal damage than the mice with commensal microbiota. However, the precise influence by the microbiome and carboxyl-containing metabolites to the renal functions is unknown. In this study, we aimed to develop a novel chemical isotope labeling-LC-MS/MS method using the 2-picolylamine and its isotopologue and applied the analysis of effects of microbiome and CKD pathophysiology. The developed semi-quantitative method provided the high accuracy not inferior to the absolute quantification. By comparing of four groups of mice, we found that both microbiota and renal function can alter the composition and level of these metabolites in both plasma and intestine. In particular, the intestinal level of indole-3-acetic acid, short-chain fatty acids and n-3 type of polyunsaturated fatty acid, which play important roles in the endothelial barrier function, were significantly lower in germ-free conditions mice with renal failure. Accordingly, it is suggested these metabolites might have a renoprotective effect on CKD by suppressing epithelial barrier disruption.
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Affiliation(s)
- Yoshitomi Kanemitsu
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Eikan Mishima
- Department of Clinical Biology and Hormonal Regulation and Division of Nephrology, Endocrinology, and Vascular Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan.
| | - Yotaro Matsumoto
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Yamaguchi
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Jiro Ogura
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Hiroki Tsukamoto
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Takaaki Abe
- Department of Clinical Biology and Hormonal Regulation and Division of Nephrology, Endocrinology, and Vascular Medicine, Graduate School of Medicine, Tohoku University, Sendai, Japan
- Department of Medical Science, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
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Minegishi N, Nishijima I, Nobukuni T, Kudo H, Ishida N, Terakawa T, Kumada K, Yamashita R, Katsuoka F, Ogishima S, Suzuki K, Sasaki M, Satoh M, Tohoku Medical Megabank Project Study Group, Yamamoto M. Biobank Establishment and Sample Management in the Tohoku Medical Megabank Project. TOHOKU J EXP MED 2019; 248:45-55. [PMID: 31130587 DOI: 10.1620/tjem.248.45] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Tohoku Medical Megabank biobank (TMM biobank) is the first major population-based biobank established in Japan. The TMM biobank was established based on two population cohorts and is a reconstruction program from the Great East Japan Earthquake and Tsunami of 2011. The biobank stores more than 3.4 million tubes of biospecimens and associated health and analytic data obtained from approximately 150,000 TMM cohort participants between May 2013 and December 2018, and the TMM biobank currently shares high-quality specimens and data. Various biospecimens, including peripheral and cord blood mononuclear cells, buffy coat, plasma, serum, urine, breast milk and saliva have been collected in the TMM biobank. To minimize human error and maintain the quality of data and specimens, we have been utilizing laboratory information management system into various biobank procedures from registration to storage with various automation systems, such as liquid dispensing, DNA extraction and their storage. The biobank procedures for the quality management system (ISO 9001:2015) and information security management system (ISO 27001:2013) are certified by the International Organization for Standardization. The quality of our biobank samples fulfills the pre-analytical requirements for researchers conducting next-generation whole genome sequencing, DNA array analyses, proteomics, metabolomics, etc. We established analytical centers to conduct standard genomic and multiomic analyses in-house and share the generated data. Additionally, we generate thousands of Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines and proliferating T cells for functional studies. The TMM biobank serves as an indispensable infrastructure for academic, clinical and industrial research to actualize next-generation medicine in Japan.
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Affiliation(s)
- Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Ichiko Nishijima
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Takahiro Nobukuni
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Noriko Ishida
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Takahiro Terakawa
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | - Mamoru Satoh
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University.,School of Medicine, Iwate Medical University
| | | | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
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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] [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.
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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
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Rombouts C, De Spiegeleer M, Van Meulebroek L, De Vos WH, Vanhaecke L. Validated comprehensive metabolomics and lipidomics analysis of colon tissue and cell lines. Anal Chim Acta 2019; 1066:79-92. [PMID: 31027537 DOI: 10.1016/j.aca.2019.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
Current untargeted approaches for metabolic fingerprinting of colon tissue and cell lines lack validation of reproducibility and/or focus on a selection of metabolites as opposed to the entire metabolome. Yet, both are critical to ensure reliable results and pursue a fully holistic analysis. Therefore, we have optimized and validated a platform for analyzing the polar metabolome and lipidome of colon-derived cell and tissue samples based on a consecutive extraction of polar and apolar components. Peak areas of selected targeted analytes and the number of untargeted components were assessed. Analysis was performed using ultra-high performance liquid-chromatography (UHPLC) coupled to hybrid quadrupole-Orbitrap high-resolution mass spectrometry (HRMS). This resulted in an optimized extraction protocol using 50% methanol/ultrapure water to obtain the polar fraction followed by a dichloromethane-based lipid extraction. Using this comprehensive approach, we have detected more than 15,000 components with CV < 30% in internal quality control (IQC) samples and were able to discriminate the non-transformed (NT) and transformed (T) state in human colon tissue and cell lines based on validated OPLS-DA models (R2Y > 0.719 and Q2 > 0.674). To conclude, our validated polar metabolomics and lipidomics fingerprinting approach could be of great value to reveal gastrointestinal disease-associated biomarkers and mechanisms.
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Affiliation(s)
- Caroline Rombouts
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium; Ghent University, Faculty of Bioscience Engineering, Department of Molecular Biotechnology, Cell Systems & Imaging, Coupure Links 653, 9000, Ghent, Belgium; Antwerp University, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Laboratory of Cell Biology & Histology, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Margot De Spiegeleer
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Winnok H De Vos
- Ghent University, Faculty of Bioscience Engineering, Department of Molecular Biotechnology, Cell Systems & Imaging, Coupure Links 653, 9000, Ghent, Belgium; Antwerp University, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Laboratory of Cell Biology & Histology, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Lynn Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium; Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom.
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45
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Sugawara J, Ochi D, Yamashita R, Yamauchi T, Saigusa D, Wagata M, Obara T, Ishikuro M, Tsunemoto Y, Harada Y, Shibata T, Mimori T, Kawashima J, Katsuoka F, Igarashi-Takai T, Ogishima S, Metoki H, Hashizume H, Fuse N, Minegishi N, Koshiba S, Tanabe O, Kuriyama S, Kinoshita K, Kure S, Yaegashi N, Yamamoto M, Hiyama S, Nagasaki M. Maternity Log study: a longitudinal lifelog monitoring and multiomics analysis for the early prediction of complicated pregnancy. BMJ Open 2019; 9:e025939. [PMID: 30782942 PMCID: PMC6398744 DOI: 10.1136/bmjopen-2018-025939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
PURPOSE A prospective cohort study for pregnant women, the Maternity Log study, was designed to construct a time-course high-resolution reference catalogue of bioinformatic data in pregnancy and explore the associations between genomic and environmental factors and the onset of pregnancy complications, such as hypertensive disorders of pregnancy, gestational diabetes mellitus and preterm labour, using continuous lifestyle monitoring combined with multiomics data on the genome, transcriptome, proteome, metabolome and microbiome. PARTICIPANTS Pregnant women were recruited at the timing of first routine antenatal visits at Tohoku University Hospital, Sendai, Japan, between September 2015 and November 2016. Of the eligible women who were invited, 65.4% agreed to participate, and a total of 302 women were enrolled. The inclusion criteria were age ≥20 years and the ability to access the internet using a smartphone in the Japanese language. FINDINGS TO DATE Study participants uploaded daily general health information including quality of sleep, condition of bowel movements and the presence of nausea, pain and uterine contractions. Participants also collected physiological data, such as body weight, blood pressure, heart rate and body temperature, using multiple home healthcare devices. The mean upload rate for each lifelog item was ranging from 67.4% (fetal movement) to 85.3% (physical activity), and the total number of data points was over 6 million. Biospecimens, including maternal plasma, serum, urine, saliva, dental plaque and cord blood, were collected for multiomics analysis. FUTURE PLANS Lifelog and multiomics data will be used to construct a time-course high-resolution reference catalogue of pregnancy. The reference catalogue will allow us to discover relationships among multidimensional phenotypes and novel risk markers in pregnancy for the future personalised early prediction of pregnancy complications.
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Affiliation(s)
- Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daisuke Ochi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Research Laboratories, NTT DoCoMo, Inc, Yokosuka, Japan
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takafumi Yamauchi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Research Laboratories, NTT DoCoMo, Inc, Yokosuka, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Maiko Wagata
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Yuki Harada
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomoko Shibata
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takahiro Mimori
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | | | - Hiroaki Hashizume
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Radiation Effects Research Foundation, Hiroshima, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Hospital, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Satoshi Hiyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Research Laboratories, NTT DoCoMo, Inc, Yokosuka, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Tohoku University Graduate School of Medicine, Sendai, Japan
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46
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Sato T, Kawasaki Y, Maekawa M, Takasaki S, Saigusa D, Ota H, Shimada S, Yamashita S, Mitsuzuka K, Yamaguchi H, Ito A, Kinoshita K, Koshiba S, Mano N, Arai Y. Value of global metabolomics in association with diagnosis and clinicopathological factors of renal cell carcinoma. Int J Cancer 2019; 145:484-493. [PMID: 30628065 DOI: 10.1002/ijc.32115] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/26/2018] [Accepted: 01/03/2019] [Indexed: 01/28/2023]
Abstract
Renal cell carcinoma (RCC) is a malignant tumor that currently lacks clinically useful biomarkers indicative of early diagnosis or disease status. RCC has commonly been diagnosed based on imaging results. Metabolomics offers a potential technology for discovering biomarkers and therapeutic targets by comprehensive screening of metabolites from patients with various cancers. We aimed to identify metabolites associated with early diagnosis and clinicopathological factors in RCC using global metabolomics (G-Met). Tumor and nontumor tissues were sampled from 20 cases of surgically resected clear cell RCC. G-Met was performed by liquid chromatography mass spectrometry and important metabolites specific to RCC were analyzed by multivariate statistical analysis for cancer diagnostic ability based on area under the curve (AUC) and clinicopathological factors (tumor volume, pathological T stage, Fuhrman grade, presence of coagulation necrosis and distant metastasis). We identified 58 metabolites showing significantly increased levels in tumor tissues, 34 of which showed potential early diagnostic ability (AUC >0.8), but 24 did not discriminate between tumor and nontumor tissues (AUC ≤0.8). We recognized 6 pathways from 9 metabolites with AUC >0.8 and 7 pathways from 10 metabolites with AUC ≤0.8 about malignant status. Clinicopathological factors involving malignant status correlated significantly with metabolites showing AUC ≤0.8 (p = 0.0279). The tricarboxylic acid cycle (TCA) cycle, TCA cycle intermediates, nucleotide sugar pathway and inositol pathway were characteristic pathways for the malignant status of RCC. In conclusion, our study found that metabolites and their pathways allowed discrimination between early diagnosis and malignant status in RCC according to our G-Met protocol.
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Affiliation(s)
- Tomonori Sato
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yoshihide Kawasaki
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Masamitsu Maekawa
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Shinya Takasaki
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Daisuke Saigusa
- Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan.,LEAP, Japan Agency for Medical Research and Development (AMED), Chiyoda, Tokyo, Japan
| | - Hideki Ota
- Diagnostic Radiology, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Shuichi Shimada
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Shinichi Yamashita
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Koji Mitsuzuka
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiroaki Yamaguchi
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Akihiro Ito
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Seizo Koshiba
- Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Miyagi, Japan
| | - Yoichi Arai
- Department of Urology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
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47
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La Frano MR, Carmichael SL, Ma C, Hardley M, Shen T, Wong R, Rosales L, Borkowski K, Pedersen TL, Shaw GM, Stevenson DK, Fiehn O, Newman JW. Impact of post-collection freezing delay on the reliability of serum metabolomics in samples reflecting the California mid-term pregnancy biobank. Metabolomics 2018; 14:151. [PMID: 30830400 DOI: 10.1007/s11306-018-1450-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/08/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND Population-based biorepositories are important resources, but sample handling can affect data quality. OBJECTIVE Identify metabolites of value for clinical investigations despite extended postcollection freezing delays, using protocols representing a California mid-term pregnancy biobank. METHODS Blood collected from non-pregnant healthy female volunteers (n = 20) underwent three handling protocols after 30 min clotting at room temperature: (1) ideal-samples frozen (- 80 °C) within 2 h of collection; (2) delayed freezing-samples held at room temperature for 3 days, then 4 °C for 9 days, the median times for biobank samples, and then frozen; (3) delayed freezing with freeze-thaw-the delayed freezing protocol with a freeze-thaw cycle simulating retrieved sample sub-aliquoting. Mass spectrometry-based untargeted metabolomic analyses of primary metabolism and complex lipids and targeted profiling of oxylipins, endocannabinoids, ceramides/sphingoid-bases, and bile acids were performed. Metabolite concentrations and intraclass correlation coefficients (ICC) were compared, with the ideal protocol as the reference. RESULTS Sixty-two percent of 428 identified compounds had good to excellent ICCs, a metric of concordance between measurements of samples handled with the different protocols. Sphingomyelins, phosphatidylcholines, cholesteryl esters, triacylglycerols, bile acids and fatty acid diols were the least affected by non-ideal handling, while sugars, organic acids, amino acids, monoacylglycerols, lysophospholipids, N-acylethanolamides, polyunsaturated fatty acids, and numerous oxylipins were altered by delayed freezing. Freeze-thaw effects were assay-specific with lipids being most stable. CONCLUSIONS Despite extended post-collection freezing delays characteristic of some biobanks of opportunistically collected clinical samples, numerous metabolomic compounds had both stable levels and good concordance.
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Affiliation(s)
- Michael R La Frano
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
- Department of Nutrition, University of California Davis, Davis, CA, USA
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | | | - Chen Ma
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Macy Hardley
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Tong Shen
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
| | - Ron Wong
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Lorenzo Rosales
- Department of Food Science and Nutrition, California Polytechnic State University, San Luis Obispo, CA, USA
| | - Kamil Borkowski
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA
| | | | - Gary M Shaw
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John W Newman
- West Coast Metabolomics Center, Genome Center, University of California Davis, Davis, CA, USA.
- Department of Nutrition, University of California Davis, Davis, CA, USA.
- USDA-ARS Western Human Nutrition Research Center, Davis, CA, USA.
- Obesity and Metabolism Research Unit, USDA-ARS-WHNRC, 430 West Health Sciences Drive, Davis, CA, 95616, USA.
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48
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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] [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.
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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.
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49
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Dong S, Zhang S, Chen Z, Zhang R, Tian L, Cheng L, Shang F, Sun J. Berberine Could Ameliorate Cardiac Dysfunction via Interfering Myocardial Lipidomic Profiles in the Rat Model of Diabetic Cardiomyopathy. Front Physiol 2018; 9:1042. [PMID: 30131709 PMCID: PMC6090155 DOI: 10.3389/fphys.2018.01042] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/12/2018] [Indexed: 12/11/2022] Open
Abstract
Background: Diabetic cardiomyopathy (DCM) is considered to be a distinct clinical entity independent of concomitant macro- and microvascular disorders, which is initiated partly by disturbances in energy substrates. This study was to observe the dynamic modulations of berberine in DCM rats and explore the changes of lipidomic profiles of myocardial tissue. Methods: Sprague-Dawley (SD) rats were fed high-sucrose and high-fat diet (HSHFD) for totally 22 weeks and intraperitoneally (i.p.) injected with 30 mg/kg of streptozotocin (STZ) at the fifth week to induce DCM. Seventy-two hours after STZ injection, the rats were orally given with berberine at 10, 30 mg/kg and metformin at 200 mg/kg, respectively. Dynamic changes of cardiac function, heart mass ratios and blood lipids were observed at f 4, 10, 16, and 22, respectively. Furthermore, lipid metabolites in myocardial tissue at week 16 were profiled by the ultra-high-performance liquid chromatography coupled to a quadruple time of flight mass spectrometer (UPLC/Q-TOF/MS) approach. Results: Berberine could protect against cardiac diastolic and systolic dysfunctions, as well as cardiac hypertrophy, and the most effective duration is with 16-week of administration. Meanwhile, 17 potential biomarkers of phosphatidylcholines (PCs), phosphatidylethanolamines (PEs) and sphingolipids (SMs) of DCM induced by HSFD/STZ were identified. The perturbations of lipidomic profiles could be partly reversed with berberine intervention, i.e., PC (16:0/20:4), PC (18:2/0:0), PC (18:0/18:2), PC (18:0/22:5), PC (20:4/0:0), PC (20:4/18:0), PC (20:4/18:1), PC (20:4/20:2), PE (18:2/0:0), and SM (d18:0/16:0). Conclusions: These results indicated a close relationship between PCs, PEs and SMs and cardiac damage mechanisms during development of DCM. The therapeutic effects of berberine on DCM are partly caused by interferences with PCs, PEs, and SMs metabolisms.
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Affiliation(s)
- Shifen Dong
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shuofeng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhirong Chen
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Rong Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Linyue Tian
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Long Cheng
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Fei Shang
- Department of Pharmacology, Analysis and Testing Center, Beijing University of Chemical Technology, Beijing, China
| | - Jianning Sun
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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50
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Koshiba S, Motoike I, Saigusa D, Inoue J, Shirota M, Katoh Y, Katsuoka F, Danjoh I, Hozawa A, Kuriyama S, Minegishi N, Nagasaki M, Takai-Igarashi T, Ogishima S, Fuse N, Kure S, Tamiya G, Tanabe O, Yasuda J, Kinoshita K, Yamamoto M. Omics research project on prospective cohort studies from the Tohoku Medical Megabank Project. Genes Cells 2018; 23:406-417. [PMID: 29701317 DOI: 10.1111/gtc.12588] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 03/22/2018] [Indexed: 01/05/2023]
Abstract
Population-based prospective cohort studies are indispensable for modern medical research as they provide important knowledge on the influences of many kinds of genetic and environmental factors on the cause of disease. Although traditional cohort studies are mainly conducted using questionnaires and physical examinations, modern cohort studies incorporate omics and genomic approaches to obtain comprehensive physical information, including genetic information. Here, we report the design and midterm results of multi-omics analysis on population-based prospective cohort studies from the Tohoku Medical Megabank (TMM) Project. We have incorporated genomic and metabolomic studies in the TMM cohort study as both metabolome and genome analyses are suitable for high-throughput analysis of large-scale cohort samples. Moreover, an association study between the metabolome and genome show that metabolites are an important intermediate phenotype connecting genetic and lifestyle factors to physical and pathologic phenotypes. We apply our metabolome and genome analyses to large-scale cohort samples in the following studies.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ikuko Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasutake Katoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masao Nagasaki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Takako Takai-Igarashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
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