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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Akiyama T, Saigusa D, Inoue T, Tokorodani C, Akiyama M, Michiue R, Mori A, Hishinuma E, Matsukawa N, Shibata T, Tsuchiya H, Kobayashi K. Exploration of urine metabolic biomarkers for new-onset, untreated pediatric epilepsy: A gas and liquid chromatography mass spectrometry-based metabolomics study. Brain Dev 2024; 46:180-186. [PMID: 38171994 DOI: 10.1016/j.braindev.2023.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/02/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
OBJECTIVE The discovery of objective indicators for recent epileptic seizures will help confirm the diagnosis of epilepsy and evaluate therapeutic effects. Past studies had shortcomings such as the inclusion of patients under treatment and those with various etiologies that could confound the analysis results significantly. We aimed to minimize such confounding effects and to explore the small molecule biomarkers associated with the recent occurrence of epileptic seizures using urine metabolomics. METHODS This is a multicenter prospective study. Subjects included pediatric patients aged 2 to 12 years old with new-onset, untreated epilepsy, who had had the last seizure within 1 month before urine collection. Controls included healthy children aged 2 to 12 years old. Those with underlying or chronic diseases, acute illnesses, or recent administration of medications or supplements were excluded. Targeted metabolome analysis of spot urine samples was conducted using gas chromatography (GC)- and liquid chromatography (LC)-tandem mass spectrometry (MS/MS). RESULTS We enrolled 17 patients and 21 controls. Among 172 metabolites measured by GC/MS/MS and 41 metabolites measured by LC/MS/MS, only taurine was consistently reduced in the epilepsy group. This finding was subsequently confirmed by the absolute quantification of amino acids. No other metabolites were consistently altered between the two groups. CONCLUSIONS Urine metabolome analysis, which covers a larger number of metabolites than conventional biochemistry analyses, found no consistently altered small molecule metabolites except for reduced taurine in epilepsy patients compared to healthy controls. Further studies with larger samples, subjects with different ages, expanded target metabolites, and the investigation of plasma samples are required.
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Affiliation(s)
- Tomoyuki Akiyama
- Department of Pediatrics (Child Neurology), Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan.
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takushi Inoue
- Department of Pediatric Neurology, NHO Okayama Medical Center, Okayama, Japan
| | - Chiho Tokorodani
- Department of Pediatrics, Kochi Health Sciences Center, Kochi, Japan
| | - Mari Akiyama
- Department of Pediatrics (Child Neurology), Okayama University Hospital, Okayama, Japan
| | - Rie Michiue
- Department of Pediatrics (Child Neurology), Okayama University Hospital, Okayama, Japan
| | - Atsushi Mori
- Department of Neurology, Shiga Medical Center for Children, Moriyama, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Advanced Research Centre for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takashi Shibata
- Department of Pediatrics (Child Neurology), Okayama University Hospital, Okayama, Japan
| | - Hiroki Tsuchiya
- Department of Pediatrics (Child Neurology), Okayama University Hospital, Okayama, Japan
| | - Katsuhiro Kobayashi
- Department of Pediatrics (Child Neurology), Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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Sato M, Hishinuma E, Matsukawa N, Shima Y, Saigusa D, Motoike IN, Kogure M, Nakaya N, Hozawa A, Kuriyama S, Yamamoto M, Koshiba S, Kinoshita K. Dietary habits and plasma lipid concentrations in a general Japanese population. Metabolomics 2024; 20:34. [PMID: 38441752 PMCID: PMC10914877 DOI: 10.1007/s11306-024-02087-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/02/2024] [Indexed: 03/07/2024]
Abstract
INTRODUCTION Accumulating data on the associations between food consumption and lipid composition in the body is essential for understanding the effects of dietary habits on health. OBJECTIVES As part of omics research in the Tohoku Medical Megabank Community-Based Cohort Study, this study sought to reveal the dietary impact on plasma lipid concentration in a Japanese population. METHODS We conducted a correlation analysis of food consumption and plasma lipid concentrations measured using mass spectrometry, for 4032 participants in Miyagi Prefecture, Japan. RESULTS Our analysis revealed 83 marked correlations between six food categories and the concentrations of plasma lipids in nine subclasses. Previously reported associations, including those between seafood consumption and omega-3 fatty acids, were validated, while those between dairy product consumption and odd-carbon-number fatty acids (odd-FAs) were validated for the first time in an Asian population. Further analysis suggested that dairy product consumption is associated with odd-FAs via sphingomyelin (SM), which suggests that SM is a carrier of odd-FAs. These results are important for understanding odd-FA metabolism with regards to dairy product consumption. CONCLUSION This study provides insight into the dietary impact on plasma lipid concentration in a Japanese population.
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Affiliation(s)
- Mitsuharu Sato
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Yoshiko Shima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
- International Research Institute of Disaster Science, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Doshi M, Natori Y, Ishii A, Saigusa D, Watanabe S, Hosoyamada M, Hirashima-Akae Y. Hypothermia increases adenosine monophosphate and xanthosine monophosphate levels in the mouse hippocampus, preventing their reduction by global cerebral ischemia. Sci Rep 2024; 14:3187. [PMID: 38326353 PMCID: PMC10850059 DOI: 10.1038/s41598-024-53530-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 02/01/2024] [Indexed: 02/09/2024] Open
Abstract
Global cerebral ischemia (GCI) caused by clinical conditions such as cardiac arrest leads to delayed neuronal death in the hippocampus, resulting in physical and mental disability. However, the mechanism of delayed neuronal death following GCI remains unclear. To elucidate the mechanism, we performed a metabolome analysis using a mouse model in which hypothermia (HT) during GCI, which was induced by the transient occlusion of the bilateral common carotid arteries, markedly suppressed the development of delayed neuronal death in the hippocampus after reperfusion. Fifteen metabolites whose levels were significantly changed by GCI and 12 metabolites whose levels were significantly changed by HT were identified. Furthermore, the metabolites common for both changes were narrowed down to two, adenosine monophosphate (AMP) and xanthosine monophosphate (XMP). The levels of both AMP and XMP were found to be decreased by GCI, but increased by HT, thereby preventing their decrease. In contrast, the levels of adenosine, inosine, hypoxanthine, xanthine, and guanosine, the downstream metabolites of AMP and XMP, were increased by GCI, but were not affected by HT. Our results may provide a clue to understanding the mechanism by which HT during GCI suppresses the development of delayed neuronal death in the hippocampus.
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Affiliation(s)
- Masaru Doshi
- Department of Human Physiology and Pathology, Faculty of Pharma-Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
| | - Yujin Natori
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Akira Ishii
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, 466-8550, Japan
| | - Daisuke Saigusa
- Department of Biomedical and Analytical Sciences, Faculty of Pharma-Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Shiro Watanabe
- Division of Nutritional Biochemistry, Institute of Natural Medicine, University of Toyama, 2630 Sugitani, Toyama, 930-0194, Japan
| | - Makoto Hosoyamada
- Department of Human Physiology and Pathology, Faculty of Pharma-Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
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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. Author Correction: Reduced glutathione level in the aqueous humor of patients with primary open-angle glaucoma and normal-tension glaucoma. NPJ Aging 2024; 10:8. [PMID: 38245546 PMCID: PMC10799874 DOI: 10.1038/s41514-024-00137-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2024]
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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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Saigusa D, Saito R, Kawamoto K, Uruno A, Kano K, Shimma S, Aoki J, Yamamoto M, Kawamoto T. Improving the Signal Intensity of Cryosections Using a Conductive Adhesive Film in Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging. Mass Spectrom (Tokyo) 2023; 12:A0137. [PMID: 38107656 PMCID: PMC10721960 DOI: 10.5702/massspectrometry.a0137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/27/2023] [Indexed: 12/19/2023] Open
Abstract
The matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) technique was used to obtain the molecular images of cryosections without labeling. Although MALDI-MSI has been widely used to detect small molecules from biological tissues, issues remain due to the technical process of cryosectioning and limited mass spectrometry parameters. The use of a conductive adhesive film is a unique method to obtain high-quality sections from cutting tissue, such as bone, muscle, adipose tissue, and whole body of mice or fish, and we have reported the utilization of the film for MALDI-MSI in previous. However, some signal of the small molecules using the conductive adhesive films was still lower than on the indium tin oxide (ITO) glass slide. Here, the sample preparation and analytical conditions for MALDI-MSI using an advanced conductive adhesive film were optimized to obtain strong signals from whole mice heads. The effects of tissue thickness and laser ionization power on signal intensity were verified using MALDI-MSI. The phospholipid signal intensity was measured for samples with three tissue thicknesses (5, 10, and 20 μm); compared to the signals from the samples on the ITO glass slides, the signals with conductive adhesive films exhibited significantly higher intensities when a laser with a higher range of power was used to ionize the small molecules. Thus, the technique using the advanced conductive adhesive film showed an improvement in MALDI-MSI analysis.
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Affiliation(s)
- Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, 2–11–1 Kaga, Itabashi-ku, Tokyo 173–8605, Japan
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8573, Japan
| | - Ritsumi Saito
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Komei Kawamoto
- School of Dental Medicine, Tsurumi University, 2–1–3 Tsurumi, Tsurumi-ku, Yokohama, Kanagawa 230–8501, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8573, Japan
- Medical Biochemistry, Tohoku University School of Medicine, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8575, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113–0033, Japan
| | - Shuichi Shimma
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2–1 Yamada-oka, Suita, Osaka 565–0871, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113–0033, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8573, Japan
- Medical Biochemistry, Tohoku University School of Medicine, 2–1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980–8575, Japan
| | - Tadafumi Kawamoto
- School of Dental Medicine, Tsurumi University, 2–1–3 Tsurumi, Tsurumi-ku, Yokohama, Kanagawa 230–8501, Japan
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Shao X, Saito R, Sato A, Okuno S, Saigusa D, Saito R, Uruno A, Osada Y, Kanamori M, Tominaga T. Local Delivery of Nimustine Hydrochloride against Brain Tumors: Basic Characterization Study. TOHOKU J EXP MED 2023; 261:187-194. [PMID: 37635063 DOI: 10.1620/tjem.2023.j069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Convection-enhanced delivery (CED) delivers agents directly into tumors and the surrounding parenchyma. Although a promising concept, clinical applications are often hampered by insufficient treatment efficacy. Toward developing an effective CED-based strategy for delivering drugs with proven clinical efficacy, we performed a basic characterization study to explore the locally delivered characteristics of the water soluble nitrosourea nimustine hydrochloride (ACNU). First, ACNU distribution after CED in rodent brain was studied using mass spectrometry imaging. Clearance of 14C-labeled ACNU after CED in striatum was also studied. ACNU was robustly distributed in rodent brain similar to the distribution of the hydrophilic dye Evans blue after CED, and locally delivered ACNU was observed for over 24 h at the delivery site. Subsequently, to investigate the potential of ACNU to induce an immunostimulative microenvironment, Fas and transforming growth factor-β1 (TGF-β1) was assessed in vitro. We found that ACNU significantly inhibited TGF-β1 secretion and reduced Fas expression. Further, after CED of ACNU in 9L-derived intracranial tumors, the infiltration of CD4/CD8 lymphocytes in tumors was evaluated by immunofluorescence.CED of ACNU in xenografted intracranial tumors induced tumor infiltration of CD4/CD8 lymphocytes. ACNU has a robust distribution in rodent brain by CED, and delayed clearance of the drug was observed at the local infusion site. Further, local delivery of ACNU affects the tumor microenvironment and induces immune cell migration in tumor. These characteristics make ACNU a promising agent for CED.
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Affiliation(s)
- Xiaodong Shao
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
| | - Ryuta Saito
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
- Department of Neurosurgery, Nagoya University Graduate School of Medicine
| | - Aya Sato
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
| | - Saori Okuno
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
| | - Daisuke Saigusa
- Faculty of Pharma-Science, Teikyo University
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University
| | - Ritsumi Saito
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University
| | - Akira Uruno
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University
| | - Yoshinari Osada
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
| | - Masayuki Kanamori
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine
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11
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Hishinuma E, Shimada M, Matsukawa N, Shima Y, Li B, Motoike IN, Shibuya Y, Hagihara T, Shigeta S, Tokunaga H, Saigusa D, Kinoshita K, Koshiba S, Yaegashi N. Identification of predictive biomarkers for endometrial cancer diagnosis and treatment response monitoring using plasma metabolome profiling. Cancer Metab 2023; 11:16. [PMID: 37821929 PMCID: PMC10568780 DOI: 10.1186/s40170-023-00317-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Endometrial cancer (EMC) is the most common female genital tract malignancy with an increasing prevalence in many countries including Japan, a fact that renders early detection and treatment necessary to protect health and fertility. Although early detection and treatment are necessary to further improve the prognosis of women with endometrial cancer, biomarkers that accurately reflect the pathophysiology of EMC patients are still unclear. Therefore, it is clinically critical to identify biomarkers to assess diagnosis and treatment efficacy to facilitate appropriate treatment and development of new therapies for EMC. METHODS In this study, wide-targeted plasma metabolome analysis was performed to identify biomarkers for EMC diagnosis and the prediction of treatment responses. The absolute quantification of 628 metabolites in plasma samples from 142 patients with EMC was performed using ultra-high-performance liquid chromatography with tandem mass spectrometry. RESULTS The concentrations of 111 metabolites increased significantly, while the concentrations of 148 metabolites decreased significantly in patients with EMC compared to healthy controls. Specifically, LysoPC and TGs, including unsaturated fatty acids, were reduced in patients with stage IA EMC compared to healthy controls, indicating that these metabolic profiles could be used as early diagnostic markers of EMC. In contrast, blood levels of amino acids such as histidine and tryptophan decreased as the risk of recurrence increased and the stages of EMC advanced. Furthermore, a marked increase in total TG and a decrease in specific TGs and free fatty acids including polyunsaturated fatty acids levels were observed in patients with EMC. These results suggest that the polyunsaturated fatty acids in patients with EMC are crucial for disease progression. CONCLUSIONS Our data identified specific metabolite profiles that reflect the pathogenesis of EMC and showed that these metabolites correlate with the risk of recurrence and disease stage. Analysis of changes in plasma metabolite profiles could be applied for the early diagnosis and monitoring of the course of treatment of EMC patients.
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Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Muneaki Shimada
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan.
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan.
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Yoshiko Shima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Bin Li
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, 980-8579, Japan
| | - Yusuke Shibuya
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Tatsuya Hagihara
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Shogo Shigeta
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Hideki Tokunaga
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, 173-8605, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, 980-8579, Japan
| | - Seizo Koshiba
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Nobuo Yaegashi
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
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12
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Hishinuma E, Shimada M, Matsukawa N, Li B, Motoike IN, Hagihara T, Shigeta S, Tokunaga H, Saigusa D, Kinoshita K, Koshiba S, Yaegashi N. Identification of predictive biomarkers for diagnosis and radiation sensitivity of uterine cervical cancer using wide-targeted metabolomics. J Obstet Gynaecol Res 2023. [PMID: 37291943 DOI: 10.1111/jog.15709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 05/28/2023] [Indexed: 06/10/2023]
Abstract
AIM Uterine cervical cancer (UCC) is the fourth most common cancer in women, responsible for more than 300 000 deaths worldwide. Its early detection, by cervical cytology, and prevention, by vaccinating against human papilloma virus, greatly contribute to reducing cervical cancer mortality in women. However, penetration of the effective prevention of UCC in Japan remains low. Plasma metabolome analysis is widely used for biomarker discovery and the identification of cancer-specific metabolic pathways. Here, we aimed to identify predictive biomarkers for the diagnosis and radiation sensitivity of UCC using wide-targeted plasma metabolomics. METHODS We analyzed 628 metabolites in plasma samples obtained from 45 patients with UCC using ultra-high-performance liquid chromatography with tandem mass spectrometry. RESULTS The levels of 47 metabolites were significantly increased and those of 75 metabolites were significantly decreased in patients with UCC relative to healthy controls. Increased levels of arginine and ceramides, and decreased levels of tryptophan, ornithine, glycosylceramides, lysophosphatidylcholine, and phosphatidylcholine were characteristic of patients with UCC. Comparison of metabolite profiles in groups susceptible and non-susceptible to radiation therapy, a treatment for UCC, revealed marked variations in polyunsaturated fatty acid, nucleic acid, and arginine metabolism in the group not susceptible to treatment. CONCLUSIONS Our findings suggest that the metabolite profile of patients with UCC may be an important indicator for distinguishing these patients from healthy cohorts, and may also be useful for predicting sensitivity to radiotherapy.
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Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Muneaki Shimada
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Bin Li
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Tatsuya Hagihara
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shogo Shigeta
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hideki Tokunaga
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Yaegashi
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
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13
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Takata S, Morikawa K, Tanaka H, Itani H, Ishihara M, Horiuchi K, Kato Y, Ikemura S, Nakagawa H, Nakahara Y, Seki Y, Bessho A, Takahashi N, Hayashi K, Endo T, Takeyama K, Maekura T, Takigawa N, Kawase A, Endoh M, Nemoto K, Kishi K, Soejima K, Okuma Y, Yoshimura K, Saigusa D, Kanai Y, Ueda K, Togashi A, Matsutani N, Seki N. Prospective exosome-focused translational research for afatinib (EXTRA) study of patients with nonsmall cell lung cancer harboring EGFR mutation: an observational clinical study. Ther Adv Med Oncol 2023; 15:17588359231177021. [PMID: 37323187 PMCID: PMC10262622 DOI: 10.1177/17588359231177021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/02/2023] [Indexed: 06/17/2023] Open
Abstract
Background The exosome-focused translational research for afatinib (EXTRA) study is the first trial to identify novel predictive biomarkers for longer treatment efficacy of afatinib in patients with epidermal growth factor receptor (EGFR) mutation-positive nonsmall cell lung cancer (NSCLC) via a comprehensive association study using genomic, proteomic, epigenomic, and metabolomic analyses. Objectives We report details of the clinical portion prior to omics analyses. Design A prospective, single-arm, observational study was conducted using afatinib 40 mg/day as an initial dose in untreated patients with EGFR mutation-positive NSCLC. Dose reduction to 20 mg every other day was allowed. Methods Progression-free survival (PFS), overall survival (OS), and adverse events (AEs) were evaluated. Results A total of 103 patients (median age 70 years, range 42-88 years) were enrolled from 21 institutions in Japan between February 2017 and March 2018. After a median follow-up of 35.0 months, 21% remained on afatinib treatment, whereas 9% had discontinued treatment because of AEs. The median PFS was 18.4 months, with a 3-year PFS rate of 23.3%. The median afatinib treatment duration in patients with final doses of 40 (n = 27), 30 (n = 23), and 20 mg/day (n = 35), and 20 mg every other day (n = 18) were 13.4, 15.4, 18.8, and 18.3 months, respectively. The median OS was not reached, with a 3-year OS rate of 58.5%. The median OS in patients who did (n = 25) and did not (n = 78) receive osimertinib during the entire course of treatment were 42.4 months and not reached, respectively (p = 0.654). Conclusions As the largest prospective study in Japan, this study confirmed favorable OS following first-line afatinib in patients with EGFR mutation-positive NSCLC in a real-world setting. Further analysis of the EXTRA study is expected to identify novel predictive biomarkers for afatinib. Trial registration UMIN-CTR identifier (UMIN000024935, https://center6.umin.ac.jp/cgi-open-bin/ctr/ctr_his_list.cgi?recptno=R000028688.
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Affiliation(s)
- Saori Takata
- Department of Respiratory Medicine, Kyorin University School of Medicine, Tokyo, Japan
| | - Kei Morikawa
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kanagawa, Japan
| | - Hisashi Tanaka
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Hidetoshi Itani
- Department of Respiratory Medicine, Ise Red Cross Hospital, Mie, Japan
| | - Masashi Ishihara
- Division of Medical Oncology, Department of Internal Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Kazuya Horiuchi
- Respiratory Disease Center, Showa University Northern Yokohama Hospital, Kanagawa, Japan
| | - Yasuhiro Kato
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Shinnosuke Ikemura
- Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | - Hideyuki Nakagawa
- Department of Respiratory Medicine, National Hospital Organization Hirosaki Hospital, Aomori, Japan
| | - Yoshiro Nakahara
- Department of Respiratory Medicine, Kitasato University School of Medicine, Kanagawa, Japan
| | - Yoshitaka Seki
- Department of Internal Medicine, The Jikei University Daisan Hospital, Tokyo, Japan
| | - Akihiro Bessho
- Department of Respiratory Medicine, Japanese Red Cross Okayama Hospital, Okayama, Japan
| | - Nobumasa Takahashi
- Department of General Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Saitama, Japan
| | - Kentaro Hayashi
- Division of Respiratory Medicine, Department of Internal Medicine, Nihon University School of Medicine, Tokyo, Japan
| | - Takeo Endo
- Department of Respiratory Medicine, National Hospital Organization Mito Medical Center, Ibaraki, Japan
| | - Kiyoshi Takeyama
- Department of Respiratory Medicine, Tokyo Women’s Medical University School of Medicine, Tokyo, Japan
| | - Toshiya Maekura
- Department of Respiratory Medicine, Hoshigaoka Medical Center, Osaka, Japan
| | - Nagio Takigawa
- Department of General Internal Medicine 4, Kawasaki Medical School, Okayama, Japan
| | - Akikazu Kawase
- First Department of Surgery, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Makoto Endoh
- Department of Thoracic Surgery, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Kenji Nemoto
- Department of Respiratory Medicine, National Hospital Organization, Ibarakihigashi National Hospital, Ibaraki, Japan
| | - Kazuma Kishi
- Department of Respiratory Medicine, Respiratory Center, Toranomon Hospital, Tokyo, Japan
| | - Kenzo Soejima
- Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | - Yusuke Okuma
- Department of Thoracic Oncology and Respiratory Medicine, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Kenichi Yoshimura
- Department of Biostatistics, Medical Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Koji Ueda
- Project for Realization of Personalized Cancer Medicine, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | | | - Noriyuki Matsutani
- Department of Surgery, Teikyo University Hospital, Mizonokuchi, Kanagawa, Japan
| | - Nobuhiko Seki
- Division of Medical Oncology, Department of Internal Medicine, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan
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14
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Furukawa Y, Saigusa D, Kano K, Uruno A, Saito R, Ito M, Matsumoto M, Aoki J, Yamamoto M, Nakamura T. Distributions of CHN compounds in meteorites record organic syntheses in the early solar system. Sci Rep 2023; 13:6683. [PMID: 37095091 PMCID: PMC10125961 DOI: 10.1038/s41598-023-33595-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 04/15/2023] [Indexed: 04/26/2023] Open
Abstract
Carbonaceous meteorites contain diverse soluble organic compounds. These compounds formed in the early solar system from volatiles accreted on tiny dust particles. However, the difference in the organic synthesis on respective dust particles in the early solar system remains unclear. We found micrometer-scale heterogeneous distributions of diverse CHN1-2 and CHN1-2O compounds in two primitive meteorites: the Murchison and NWA 801, using a surface-assisted laser desorption/ionization system connected to a high mass resolution mass spectrometer. These compounds contained mutual relationships of ± H2, ± CH2, ± H2O, and ± CH2O and showed highly similar distributions, indicating that they are the products of series reactions. The heterogeneity was caused by the micro-scale difference in the abundance of these compounds and the extent of the series reactions, indicating that these compounds formed on respective dust particles before asteroid accretion. The results of the present study provide evidence of heterogeneous volatile compositions and the extent of organic reactions among the dust particles that formed carbonaceous asteroids. The compositions of diverse small organic compounds associated with respective dust particles in meteorites are useful to understand different histories of volatile evolution in the early solar system.
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Affiliation(s)
| | - 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, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ritsumi Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Motoo Ito
- Kochi Institute for Core Sample Research, X-star, Japan Agency for Marine-Earth Science and Technology, Nankoku, Japan
| | | | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Tomoki Nakamura
- Department of Earth Science, Tohoku University, Sendai, Japan
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15
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Akiyama M, Akiyama T, Saigusa D, Hishinuma E, Matsukawa N, Shibata T, Tsuchiya H, Mori A, Fujii Y, Mogami Y, Tokorodani C, Kuwahara K, Numata-Uematsu Y, Inoue K, Kobayashi K. Comprehensive study of metabolic changes induced by a ketogenic diet therapy using GC/MS- and LC/MS-based metabolomics. Seizure 2023; 107:52-59. [PMID: 36958064 DOI: 10.1016/j.seizure.2023.03.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/07/2023] [Accepted: 03/15/2023] [Indexed: 03/17/2023] Open
Abstract
OBJECTIVE The ketogenic diet (KD), a high-fat and low-carbohydrate diet, is effective for a subset of patients with drug-resistant epilepsy, although the mechanisms of the KD have not been fully elucidated. The aims of this observational study were to investigate comprehensive short-term metabolic changes induced by the KD and to explore candidate metabolites or pathways for potential new therapeutic targets. METHODS Subjects included patients with intractable epilepsy who had undergone the KD therapy (the medium-chain triglyceride [MCT] KD or the modified Atkins diet using MCT oil). Plasma and urine samples were obtained before and at 2-4 weeks after initiation of the KD. Targeted metabolome analyses of these samples were performed using gas chromatography-tandem mass spectrometry (GC/MS/MS) and liquid chromatography-tandem mass spectrometry (LC/MS/MS). RESULTS Samples from 10 and 11 patients were analysed using GC/MS/MS and LC/MS/MS, respectively. The KD increased ketone bodies, various fatty acids, lipids, and their conjugates. In addition, levels of metabolites located upstream of acetyl-CoA and propionyl-CoA, including catabolites of branched-chain amino acids and structural analogues of γ-aminobutyric acid and lactic acid, were elevated. CONCLUSIONS The metabolites that were significantly changed after the initiation of the KD and related metabolites may be candidates for further studies for neuronal actions to develop new anti-seizure medications.
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Affiliation(s)
- Mari Akiyama
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Tomoyuki Akiyama
- Department of Paediatrics (Child Neurology), Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiji Hishinuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Advanced Research Centre for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takashi Shibata
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Hiroki Tsuchiya
- Department of Child Neurology, Okayama University Hospital, Okayama, Japan
| | - Atsushi Mori
- Department of Neurology, Shiga Medical Centre for Children, Moriyama, Japan
| | - Yuji Fujii
- Department of Paediatrics, Hiroshima City Funairi Citizens Hospital, Hiroshima, Japan
| | - Yukiko Mogami
- Department of Paediatric Neurology, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Chiho Tokorodani
- Department of Paediatrics, Kochi Health Sciences Centre, Kochi, Japan
| | - Kozue Kuwahara
- Department of Paediatrics, Ehime Prefectural Central Hospital, Matsuyama, Japan
| | | | - Kenji Inoue
- Department of Neurology, Shiga Medical Centre for Children, Moriyama, Japan
| | - Katsuhiro Kobayashi
- Department of Paediatrics (Child Neurology), Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan
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16
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Sato S, Yu Z, Sakai M, Motoike IN, Saigusa D, Hirayama R, Kikuchi Y, Abe T, Kinoshita K, Koshiba S, Tomita H. Decreased β-hydroxybutyrate and ketogenic amino acid levels in depressed human adults. Eur J Neurosci 2023; 57:1018-1032. [PMID: 36750311 DOI: 10.1111/ejn.15931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 01/24/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023]
Abstract
β-hydroxybutyrate (BHB) is a major ketone body synthesized mainly in the liver mitochondria and is associated with stress and severity of depression in humans. It is known to alleviate depressive-like behaviors in mouse models of depression. In this study, plasma BHB, ketogenic and glucogenic amino acids selected from the Tohoku Medical Megabank Project Community-Based Cohort Study were analysed and measured using nuclear magnetic resonance spectroscopy. The Center for Epidemiologic Studies Depression Scale (CES-D) was utilized to select adult participants with depressive symptoms (CES-D ≥ 16; n = 5722) and control participants (CES-D < 16; n = 18,150). We observed significantly reduced plasma BHB, leucine, and tryptophan levels in participants with depressive symptoms. Using social defeat stress (SDS) mice models, we found that BHB levels in mice sera increased after acute SDS, but showed no change after chronic SDS, which differed from human plasma results. Furthermore, acute SDS increased mitochondrial BHB levels in the prefrontal cortex at 6 h. In contrast, chronic SDS significantly increased the amount of food intake but reduced hepatic mitochondrial BHB levels in mice. Moreover, gene transcriptions of voltage-dependent anion-selective channel 1 (Vdac1) and monocarboxylic acid transporter 1 (Mct1), major molecules relevant to mitochondrial biogenesis and BHB transporter, significantly decreased in the liver and PFC after chronic SDS exposure. These results provide evidence that hepatic and prefrontal mitochondrial biogenesis plays an important role in BHB synthesis under chronic stress and in humans with depressive symptoms.
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Affiliation(s)
- Shiho Sato
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Mai Sakai
- Department of Psychiatric Nursing, Graduate School of Health Science, Tohoku University, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ryo Hirayama
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Takaaki Abe
- Department of Biomedical Engineering Regenerative and Biomedical Engineering Medical Science, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Preventive Medicine and Epidemiology, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Psychiatry, Tohoku University Hospital, Sendai, Japan
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17
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Tatara Y, Yamazaki H, Katsuoka F, Chiba M, Saigusa D, Kasai S, Nakamura T, Inoue J, Aoki Y, Shoji M, Motoike IN, Tamada Y, Hashizume K, Shoji M, Kinoshita K, Murashita K, Nakaji S, Yamamoto M, Itoh K. Multiomics and artificial intelligence enabled peripheral blood-based prediction of amnestic mild cognitive impairment. Curr Res Transl Med 2023; 71:103367. [PMID: 36446162 DOI: 10.1016/j.retram.2022.103367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/03/2022] [Accepted: 10/20/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND Since dementia is preventable with early interventions, biomarkers that assist in diagnosing early stages of dementia, such as mild cognitive impairment (MCI), are urgently needed. METHODS Multiomics analysis of amnestic MCI (aMCI) peripheral blood (n = 25) was performed covering the transcriptome, microRNA, proteome, and metabolome. Validation analysis for microRNAs was conducted in an independent cohort (n = 12). Artificial intelligence was used to identify the most important features for predicting aMCI. FINDINGS We found that hsa-miR-4455 is the best biomarker in all omics analyses. The diagnostic index taking a ratio of hsa-miR-4455 to hsa-let-7b-3p predicted aMCI patients against healthy subjects with 97% overall accuracy. An integrated review of multiomics data suggested that a subset of T cells and the GCN (general control nonderepressible) pathway are associated with aMCI. INTERPRETATION The multiomics approach has enabled aMCI biomarkers with high specificity and illuminated the accompanying changes in peripheral blood. Future large-scale studies are necessary to validate candidate biomarkers for clinical use.
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Affiliation(s)
- Yota Tatara
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Hiromi Yamazaki
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Mitsuru Chiba
- Department of Bioscience and Laboratory Medicine, Hirosaki University Graduate School of Health Sciences, 66-1 Hon-cho, Hirosaki, Aomori 036-8564, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shuya Kasai
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Tomohiro Nakamura
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Division of Personalized Prevention and Epidemiology, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jin Inoue
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Miho Shoji
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yoshinori Tamada
- Innovation Center for Health Promotion, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan
| | - Katsuhito Hashizume
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Mikio Shoji
- Department of Neurology, Gunma University Hospital, 3-39-15 Showamachi, Maebashi, Gunma 371-8511, Japan; Department of Neurology, Dementia Research Center, Geriatrics Research Institute and Hospital, 3-26-8 Ootomo-machi, Maebashi, Gunma 371-0847 Japan; COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, 6-6-05 Aramaki Aza Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Koichi Murashita
- COI Research Initiatives Organization, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Shigeyuki Nakaji
- Department of Social Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori 036-8216, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Department of Medical Biochemistry, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Ken Itoh
- Department of Stress Response Science, Center for Advanced Medical Research, Graduate School of Medicine, Hirosaki University, 5 Zaifu-cho, Hirosaki, Aomori 036-8562, Japan.
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18
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Kurano M, Saito Y, Uranbileg B, Saigusa D, Kano K, Aoki J, Yatomi Y. Modulations of bioactive lipids and their receptors in postmortem Alzheimer's disease brains. Front Aging Neurosci 2022; 14:1066578. [PMID: 36570536 PMCID: PMC9780287 DOI: 10.3389/fnagi.2022.1066578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Background Analyses of brain samples from Alzheimer's disease (AD) patients may be expected to help us improve our understanding of the pathogenesis of AD. Bioactive lipids, including sphingolipids, glycerophospholipids, and eicosanoids/related mediators have been demonstrated to exert potent physiological actions and to be involved in the pathogenesis of various human diseases. In this cross-sectional study, we attempted to elucidate the associations of these bioactive lipids with the pathogenesis/pathology of AD through postmortem studies of human brains. Methods We measured the levels of glycerophospholipids, sphingolipids, and eicosanoids/related mediators in the brains of patients with AD (AD brains), patients with Cerad score B (Cerad-b brains), and control subjects (control brains), using a liquid chromatography-mass spectrometry method; we also measured the mRNA levels of specific receptors for these bioactive lipids in the same brain specimens. Results The levels of several species of sphingomyelins and ceramides were higher in the Cerad-b and AD brains. Levels of several species of lysophosphatidic acids (LPAs), lysophosphatidylcholine, lysophosphatidylserine, lysophosphatidylethanolamine (LPE), lysophosphatidylinositol, phosphatidylcholine, phosphatidylserine (PS), phosphatidylethanolamine (PE), phosphatidylinositol, and phosphatidylglycerol were especially high in the Cerad-b brains, while those of lysophosphatidylglycerol (LPG) were especially high in the AD brains. Several eicosanoids, including metabolites of prostaglandin E2, oxylipins, metabolites of epoxide, and metabolites of DHA and EPA, such as resolvins, were also modulated in the AD brains. Among the lipid mediators, the levels of S1P2, S1P5, LPA1, LPA2, LPA6, P2Y10, GPR174, EP1, DP1, DP2, IP, FP, and TXA2r were lower in the AD and/or Cerad-b brains. The brain levels of ceramides, LPC, LPI, PE, and PS showed strong positive correlations with the Aβ contents, while those of LPG showed rather strong positive correlations with the presence of senile plaques and neurofibrillary tangles. A discriminant analysis revealed that LPG is especially important for AD and the LPE/PE axis is important for Cerad-b. Conclusions Comprehensive lipidomics, together with the measurement of lipid receptor expression levels provided novel evidence for the associations of bioactive lipids with AD, which is expected to facilitate future translational research and reverse translational research.
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Affiliation(s)
- Makoto Kurano
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,*Correspondence: Makoto Kurano,
| | - Yuko Saito
- Tokyo Metropolitan Geriatric Hospital, Institute of Gerontology, Tokyo, Japan
| | - Baasanjav Uranbileg
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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19
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Yu Z, Matsukawa N, Saigusa D, Motoike IN, Ono C, Okamura Y, Onuma T, Takahashi Y, Sakai M, Kudo H, Obara T, Murakami K, Shirota M, Kikuchi S, Kobayashi N, Kikuchi Y, Sugawara J, Minegishi N, Ogishima S, Kinoshita K, Yamamoto M, Yaegashi N, Kuriyama S, Koshiba S, Tomita H. Plasma metabolic disturbances during pregnancy and postpartum in women with depression. iScience 2022; 25:105666. [PMID: 36505921 PMCID: PMC9732390 DOI: 10.1016/j.isci.2022.105666] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/17/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Examining plasma metabolic profiling during pregnancy and postpartum could help clinicians understand the risk factors for postpartum depression (PPD) development. This analysis targeted paired plasma metabolites in mid-late gestational and 1 month postpartum periods in women with (n = 209) or without (n = 222) PPD. Gas chromatogram-mass spectrometry was used to analyze plasma metabolites at these two time points. Among the 170 objected plasma metabolites, principal component analysis distinguished pregnancy and postpartum metabolites but failed to discriminate women with and without PPD. Compared to women without PPD, those with PPD exhibited 37 metabolites with disparate changes during pregnancy and the 1-month postpartum period and an enriched citrate cycle. Machine learning and multivariate statistical analysis identified two or three compounds that could be potential biomarkers for PPD prediction during pregnancy. Our findings suggest metabolic disturbances in women with depression and may help to elucidate metabolic processes associated with PPD development.
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Affiliation(s)
- Zhiqian Yu
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Corresponding author
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University
| | - Ikuko N. Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Chiaki Ono
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yasunobu Okamura
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Innovations in Next-Generation Medicine, Advanced Research Center, Tohoku University, Sendai, Japan
| | - Tomomi Onuma
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yuta Takahashi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Mai Sakai
- Department of Disaster Psychiatry, International Research Institute for Disaster Science, Tohoku University, Sendai, Japan
| | - Hisaaki Kudo
- Department of Biobank Life Science, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Keiko Murakami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matusyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Saya Kikuchi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Natsuko Kobayashi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yoshie Kikuchi
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Department of Biobank Life Science, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Division of Disaster Public Health, International Research Institute for Disaster Science, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Department of Psychiatry, Graduate School of Medicine, Tohoku University, Sendai, Japan,Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Department of Disaster Psychiatry, International Research Institute for Disaster Science, Tohoku University, Sendai, Japan
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20
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Kurano M, Jubishi D, Okamoto K, Hashimoto H, Sakai E, Morita Y, Saigusa D, Kano K, Aoki J, Harada S, Okugawa S, Doi K, Moriya K, Yatomi Y. Dynamic modulations of urinary sphingolipid and glycerophospholipid levels in COVID-19 and correlations with COVID-19-associated kidney injuries. J Biomed Sci 2022; 29:94. [PMCID: PMC9647768 DOI: 10.1186/s12929-022-00880-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Among various complications of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), renal complications, namely COVID-19-associated kidney injuries, are related to the mortality of COVID-19. Methods In this retrospective cross-sectional study, we measured the sphingolipids and glycerophospholipids, which have been shown to possess potent biological properties, using liquid chromatography-mass spectrometry in 272 urine samples collected longitudinally from 91 COVID-19 subjects and 95 control subjects without infectious diseases, to elucidate the pathogenesis of COVID-19-associated kidney injuries. Results The urinary levels of C18:0, C18:1, C22:0, and C24:0 ceramides, sphingosine, dihydrosphingosine, phosphatidylcholine, lysophosphatidylcholine, lysophosphatidic acid, and phosphatidylglycerol decreased, while those of phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, and lysophosphatidylethanolamine increased in patients with mild COVID-19, especially during the early phase (day 1–3), suggesting that these modulations might reflect the direct effects of infection with SARS-CoV-2. Generally, the urinary levels of sphingomyelin, ceramides, sphingosine, dihydrosphingosine, dihydrosphingosine l-phosphate, phosphatidylcholine, lysophosphatidic acid, phosphatidylserine, lysophosphatidylserine, phosphatidylethanolamine, lysophosphatidylethanolamine, phosphatidylglycerol, lysophosphatidylglycerol, phosphatidylinositol, and lysophosphatidylinositol increased, especially in patients with severe COVID-19 during the later phase, suggesting that their modulations might result from kidney injuries accompanying severe COVID-19. Conclusions Considering the biological properties of sphingolipids and glycerophospholipids, an understanding of their urinary modulations in COVID-19 will help us to understand the mechanisms causing COVID-19-associated kidney injuries as well as general acute kidney injuries and may prompt researchers to develop laboratory tests for predicting maximum severity and/or novel reagents to suppress the renal complications of COVID-19. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00880-5.
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Affiliation(s)
- Makoto Kurano
- grid.26999.3d0000 0001 2151 536XDepartment of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan ,grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Daisuke Jubishi
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koh Okamoto
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Hashimoto
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Sakai
- grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshifumi Morita
- grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
| | - Daisuke Saigusa
- grid.264706.10000 0000 9239 9995Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kuniyuki Kano
- grid.26999.3d0000 0001 2151 536XDepartment of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- grid.26999.3d0000 0001 2151 536XDepartment of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sohei Harada
- grid.26999.3d0000 0001 2151 536XDepartment of Infection Control and Prevention, The University of Tokyo, Tokyo, Japan
| | - Shu Okugawa
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kent Doi
- grid.412708.80000 0004 1764 7572Department of Emergency and Critical Care Medicine, The University of Tokyo Hospital, Tokyo, Japan
| | - Kyoji Moriya
- grid.26999.3d0000 0001 2151 536XDepartment of Infectious Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Infection Control and Prevention, The University of Tokyo, Tokyo, Japan
| | - Yutaka Yatomi
- grid.26999.3d0000 0001 2151 536XDepartment of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-8655 Japan ,grid.412708.80000 0004 1764 7572Department of Clinical Laboratory, The University of Tokyo Hospital, Tokyo, Japan
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21
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Liu Y, Uruno A, Saito R, Matsukawa N, Hishinuma E, Saigusa D, Liu H, Yamamoto M. Nrf2 deficiency deteriorates diabetic kidney disease in Akita model mice. Redox Biol 2022; 58:102525. [PMID: 36335764 PMCID: PMC9641024 DOI: 10.1016/j.redox.2022.102525] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/13/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress is an essential component in the progression of diabetic kidney disease (DKD), and the transcription factor NF-E2-related factor-2 (Nrf2) plays critical roles in protecting the body against oxidative stress. To clarify the roles of Nrf2 in protecting against DKD, in this study we prepared compound mutant mice with diabetes and loss of antioxidative defense. Specifically, we prepared compound Ins2Akita/+ (Akita) and Nrf2 knockout (Akita::Nrf2-/-) or Akita and Nrf2 induction (Akita::Keap1FA/FA) mutant mice. Eighteen-week-old Akita::Nrf2-/- mice showed more severe diabetic symptoms than Akita mice. In the Akita::Nrf2-/- mouse kidneys, the glomeruli showed distended capillary loops, suggesting enhanced mesangiolysis. Distal tubules showed dilation and an increase in 8-hydroxydeoxyguanosine-positive staining. In the Akita::Nrf2-/- mouse kidneys, the expression of glutathione (GSH) synthesis-related genes was decreased, and the actual GSH level was decreased in matrix-assisted laser desorption/ionization mass spectrometry imaging analysis. Akita::Nrf2-/- mice exhibited severe inflammation and enhancement of infiltrated macrophages in the kidney. To further examine the progression of DKD, we compared forty-week-old Akita mouse kidney compounds with Nrf2-knockout or Nrf2 mildly induced (Akita::Keap1FA/FA) mice. Nrf2-knockout Akita (Akita::Nrf2-/-) mice displayed severe medullary cast formation, but the formation was ameliorated in Akita::Keap1FA/FA mice. Moreover, in Akita::Keap1FA/FA mice, tubule injury and inflammation-related gene expression were significantly suppressed, which was evident in Akita::Nrf2-/- mouse kidneys. These results demonstrate that Nrf2 contributes to the protection of the kidneys against DKD by suppressing oxidative stress and inflammation.
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Affiliation(s)
- Yexin Liu
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Nephrology, Blood Purification Center of the Second Xiangya Hospital, Central South University, Changsha, China
| | - Akira Uruno
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Corresponding author. Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 9808575, Japan.
| | - Ritsumi Saito
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Advanced Research Center for Innovations in Next-Generation Medicine Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Hong Liu
- Department of Nephrology, Blood Purification Center of the Second Xiangya Hospital, Central South University, Changsha, China
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Corresponding author. Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 9808575, Japan.
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22
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Kurano M, Okamoto K, Jubishi D, Hashimoto H, Sakai E, Saigusa D, Kano K, Aoki J, Harada S, Okugawa S, Doi K, Moriya K, Yatomi Y. Dynamic modulations of sphingolipids and glycerophospholipids in COVID-19. Clin Transl Med 2022; 12:e1069. [PMID: 36214754 PMCID: PMC9549873 DOI: 10.1002/ctm2.1069] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND A heterogeneous clinical phenotype is a characteristic of coronavirus disease 2019 (COVID-19). Therefore, investigating biomarkers associated with disease severity is important for understanding the mechanisms responsible for this heterogeneity and for developing novel agents to prevent critical conditions. This study aimed to elucidate the modulations of sphingolipids and glycerophospholipids, which have been shown to possess potent biological properties. METHODS We measured the serum sphingolipid and glycerophospholipid levels in a total of 887 samples from 215 COVID-19 subjects, plus 115 control subjects without infectious diseases and 109 subjects with infectious diseases other than COVID-19. RESULTS We observed the dynamic modulations of sphingolipids and glycerophospholipids in the serum of COVID-19 subjects, depending on the time course and severity. The elevation of C16:0 ceramide and lysophosphatidylinositol and decreases in C18:1 ceramide, dihydrosphingosine, lysophosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol were specific to COVID-19. Regarding the association with maximum severity, phosphatidylinositol and phosphatidylcholine species with long unsaturated acyl chains were negatively associated, while lysophosphatidylethanolamine and phosphatidylethanolamine were positively associated with maximum severity during the early phase. Lysophosphatidylcholine and phosphatidylcholine had strong negative correlations with CRP, while phosphatidylethanolamine had strong positive ones. C16:0 ceramide, lysophosphatidylcholine, phosphatidylcholine and phosphatidylethanolamine species with long unsaturated acyl chains had negative correlations with D-dimer, while phosphatidylethanolamine species with short acyl chains and phosphatidylinositol had positive ones. Several species of phosphatidylcholine, phosphatidylethanolamine and sphingomyelin might serve as better biomarkers for predicting severe COVID-19 during the early phase than CRP and D-dimer. Compared with the lipid modulations seen in mice treated with lipopolysaccharide, tissue factor, or histone, the lipid modulations observed in severe COVID-19 were most akin to those in mice administered lipopolysaccharide. CONCLUSION A better understanding of the disturbances in sphingolipids and glycerophospholipids observed in this study will prompt further investigation to develop laboratory testing for predicting maximum severity and/or novel agents to suppress the aggravation of COVID-19.
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Affiliation(s)
- Makoto Kurano
- Department of Clinical Laboratory MedicineGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Koh Okamoto
- Department of Infectious DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Daisuke Jubishi
- Department of Infectious DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Hideki Hashimoto
- Department of Infectious DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Eri Sakai
- Department of Clinical Laboratory MedicineGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical SciencesFaculty of Pharma‐ScienceTeikyo UniversityTokyoJapan
| | - Kuniyuki Kano
- Department of Health ChemistryGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Junken Aoki
- Department of Health ChemistryGraduate School of Pharmaceutical SciencesThe University of TokyoTokyoJapan
| | - Sohei Harada
- Department of Infection Control and PreventionThe University of TokyoTokyoJapan
| | - Shu Okugawa
- Department of Infectious DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Kent Doi
- Department of Emergency and Critical Care MedicineThe University of Tokyo Hospital, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious DiseasesGraduate School of MedicineThe University of TokyoTokyoJapan,Department of Infection Control and PreventionThe University of TokyoTokyoJapan
| | - Yutaka Yatomi
- Department of Clinical Laboratory MedicineGraduate School of MedicineThe University of TokyoTokyoJapan
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23
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Rashad S, Byrne SR, Saigusa D, Xiang J, Zhou Y, Zhang L, Begley TJ, Tominaga T, Niizuma K. Codon Usage and mRNA Stability are Translational Determinants of Cellular Response to Canonical Ferroptosis Inducers. Neuroscience 2022; 501:103-130. [PMID: 35987429 PMCID: PMC10023133 DOI: 10.1016/j.neuroscience.2022.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/29/2022]
Abstract
Ferroptosis is a non-apoptotic cell death mechanism characterized by the generation of lipid peroxides. While many effectors in the ferroptosis pathway have been mapped, its epitranscriptional regulation is not yet fully understood. Ferroptosis can be induced via system xCT inhibition (Class I) or GPX4 inhibition (Class II). Previous works have revealed important differences in cellular response to different ferroptosis inducers. Importantly, blocking mRNA transcription or translation appears to protect cells against Class I ferroptosis inducing agents but not Class II. In this work, we examined the impact of blocking transcription (via Actinomycin D) or translation (via Cycloheximide) on Erastin (Class I) or RSL3 (Class II) induced ferroptosis. Blocking transcription or translation protected cells against Erastin but was detrimental against RSL3. Cycloheximide led to increased levels of GSH alone or when co-treated with Erastin via the activation of the reverse transsulfuration pathway. RNA sequencing analysis revealed early activation of a strong alternative splice program before observed changes in transcription. mRNA stability analysis revealed divergent mRNA stability changes in cellular response to Erastin or RSL3. Importantly, codon optimality biases were drastically different in either condition. Our data also implicated translation repression and rate as an important determinant of the cellular response to ferroptosis inducers. Given that mRNA stability and codon usage can be influenced via the tRNA epitranscriptome, we evaluated the role of a tRNA modifying enzyme in ferroptosis stress response. Alkbh1, a tRNA demethylase, led to translation repression and increased the resistance to Erastin but made cells more sensitive to RSL3.
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Affiliation(s)
- Sherif Rashad
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan; Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Shane R Byrne
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan; Department of Integrative Genomics, Tohoku University Medical Megabank Organization, Sendai, Japan
| | - Jingdong Xiang
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yuan Zhou
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Liyin Zhang
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Thomas J Begley
- The RNA Institute, University at Albany, Albany, NY, USA; Department of Biological Sciences, University at Albany, Albany, NY, USA; RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY, USA
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan; Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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24
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McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, Ekroos K. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab 2022; 4:1086-1088. [PMID: 35934691 DOI: 10.1038/s42255-022-00628-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey G McDonald
- Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Makoto Arita
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Justine Bertrand-Michel
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France
| | - John A Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Maria Fedorova
- Center for Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | | | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Todd W Mitchell
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Dominik Schwudke
- Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Candice Z Ulmer
- Office of Public Health Science, Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, USA
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Robert Ahrends
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland.
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25
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Ohkouchi S, Kanehira M, Saigusa D, Ono M, Tazawa R, Terunuma H, Hirano T, Numakura T, Notsuda H, Inoue C, Saito-Koyama R, Tabata M, Irokawa T, Ogawa H, Kurosawa H, Okada Y. Metabolic and Epigenetic Regulation of SMAD7 by Stanniocalcin-1 (STC1) Ameliorates Lung Fibrosis. Am J Respir Cell Mol Biol 2022; 67:320-333. [PMID: 35696344 DOI: 10.1165/rcmb.2021-0445oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
As shown in our previous studies, the intratracheal-administration of stanniocalcin-1 (STC1) ameliorates pulmonary fibrosis by reducing oxidative and endoplasmic reticulum stress through the uncoupling of respiration in a bleomycin (BLM)-treated mouse model. However, the overall effect of STC1 on metabolism was not examined. Therefore, we first conducted a comprehensive metabolomics analysis to screen the overall metabolic changes induced by STC1 in an alveolar epithelial cell line using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS). The results were subsequently validated in multiple alveolar epithelial and fibroblast cell lines by performing precise analyses of each substance. STC1 stimulated glycolysis, acetyl-CoA synthesis, and the methionine and cysteine-glutathione pathways, which are closely related to the uncoupling of respiration, modulation of epigenetics and reduction in oxidative stress. These results are consistent with our previous study. Subsequently, we focused on the inhibitory factor SMAD7, which exerts an antifibrotic effect and is susceptible to epigenetic regulation. STC1 upregulates SMAD7 in an uncoupling protein 2-dependent manner, induces demethylation of the SMAD7 promoter region and acetylation of the SMAD7 protein in human alveolar epithelial and fibroblast cell lines and a BLM-treated mouse model, and subsequently attenuates fibrosis. The antifibrotic effects of STC1 may partially depend on the regulation of SMAD7. In the evaluation using lung tissue from idiopathic pulmonary fibrosis patients, SMAD7 expression and acetylation were high in the alveolar structure-preserving region and low in the fibrotic region. The intratracheal-administration of STC1 may prevent the development of pulmonary fibrosis by regulating the metabolism-mediated epigenetic modification of SMAD7 in patients.
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Affiliation(s)
- Shinya Ohkouchi
- Tohoku University Graduate School of Medicine, Occupational Health, Sendai, Japan.,Institute of Devepolment, Aging and Cancer, Tohoku University, Department of Thoracic surgery, Sendai, Japan;
| | - Masahiko Kanehira
- University of Yamanashi, 38146, Center for Life Science Research, Kofu, Japan.,Institute of Devepolment, Aging and Cancer, Tohoku University, Department of Thoracic surgery, Sendai, Japan
| | - Daisuke Saigusa
- Teikyo University School of Medicine Graduate School of Medicine, 36906, Faculty of Pharma-Science, Itabashi-ku, Japan
| | - Manabu Ono
- Tohoku University Graduate School of Medicine, Department of Respiratory Medicine, Sendai, Japan
| | - Ryushi Tazawa
- Tokyo Medical and Dental University, 13100, Student Support and Health Administration Organization, Tokyo, Japan.,Niigata University, 12978, Medical and Dental Hospital, Niigata, Japan
| | | | - Taizou Hirano
- Tohoku University Graduate School of Medicine, Department of Respiratory Medicine, Sensai, Japan
| | - Tadahisa Numakura
- Tohoku University Graduate School of Medicine, Department of Respiratory Medicine, Sendai, Japan
| | - Hirotsugu Notsuda
- Institute of Devepolment, Aging and Cancer, Tohoku University, Department of Thoracic surgery, Sendai, Japan
| | - Chihiro Inoue
- Tohoku University Graduate School of Medicine, Department of Anatomic Pathology, Sendai, Japan
| | - Ryoko Saito-Koyama
- Tohoku University Graduate School of Medicine, Department of Anatomic Pathology, Sendai, Japan
| | - Masao Tabata
- Tohoku University Graduate School of Medicine, Occupational Health, Sendai, Japan
| | - Toshiya Irokawa
- Tohoku University Graduate School of Medicine, Occupational Health, Sendai, Japan
| | - Hiromasa Ogawa
- Tohoku University Graduate School of Medicine, Occupational Health, Sendai, Japan
| | - Hajime Kurosawa
- Tohoku University Graduate School of Medicine, Occupational Health, Sendai, Japan
| | - Yoshinori Okada
- Institute of Devepolment, Aging and Cancer, Tohoku University, Department of Thoracic surgery, Sendai, Japan
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26
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Murakami K, Tamada T, Saigusa D, Miyauchi E, Nara M, Ichinose M, Kurano M, Yatomi Y, Sugiura H. Urine autotaxin levels reflect the disease activity of sarcoidosis. Sci Rep 2022; 12:4372. [PMID: 35288647 PMCID: PMC8921313 DOI: 10.1038/s41598-022-08388-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 03/04/2022] [Indexed: 12/17/2022] Open
Abstract
Since the clinical outcome of patients with sarcoidosis is still unpredictable, a good prognostic biomarker is necessary. Autotaxin (ATX) and phosphatidylserine-specific phospholipase A1 (PS-PLA1) function as main enzymes to produce lysophospholipids (LPLs), and these enzymes are attracting attention as useful biomarkers for several chronic inflammatory diseases. Here, we investigated the relationships between LPLs-producing enzymes and the disease activity of sarcoidosis. In total, 157 patients with sarcoidosis (active state, 51%) were consecutively enrolled. Using plasma or urine specimens, we measured the values of LPLs-producing enzymes. Urine ATX (U-ATX) levels were significantly lower in the active state compared to those in the inactive state, while the plasma ATX (P-ATX) and PS-PLA1 levels showed no significant difference between these two states. Concerning the comparison with existing clinical biomarkers for sarcoidosis, U-ATX showed a weak negative correlation to ACE, P-ATX a weak positive correlation to both ACE and sIL-2R, and PS-PLA1 a weak positive one to sIL-2R. Notably, only the U-ATX levels inversely fluctuated depending on the status of disease activity whether OCS had been used or not. These findings suggest that U-ATX is likely to be a novel and useful molecule for assessing the disease activity of sarcoidosis.
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Hoshino Y, Okuno T, Saigusa D, Kano K, Yamamoto S, Shindou H, Aoki J, Uchida K, Yokomizo T, Ito N. Lysophosphatidic acid receptor 1/3 antagonist inhibits the activation of satellite glial cells and reduces acute nociceptive responses. FASEB J 2022; 36:e22236. [PMID: 35218596 DOI: 10.1096/fj.202101678r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/10/2022] [Accepted: 02/14/2022] [Indexed: 02/06/2023]
Abstract
Lysophosphatidic acid (LPA) exerts various biological activities through six characterized G protein-coupled receptors (LPA1-6 ). While LPA-LPA1 signaling contributes toward the demyelination and retraction of C-fiber and induces neuropathic pain, the effects of LPA-LPA1 signaling on acute nociceptive pain is uncertain. This study investigated the role of LPA-LPA1 signaling in acute nociceptive pain using the formalin test. The pharmacological inhibition of the LPA-LPA1 axis significantly attenuated formalin-induced nociceptive behavior. The LPA1 mRNA was expressed in satellite glial cells (SGCs) in dorsal root ganglion (DRG) and was particularly abundant in SGCs surrounding large DRG neurons, which express neurofilament 200. Treatment with LPA1/3 receptor (LPA1/3 ) antagonist inhibited the upregulation of glial markers and inflammatory cytokines in DRG following formalin injection. The LPA1/3 antagonist also attenuated phosphorylation of extracellular signal-regulated kinase, especially in SGCs and cyclic AMP response element-binding protein in the dorsal horn following formalin injection. LPA amounts after formalin injection to the footpad were quantified by liquid chromatography/tandem mass spectrometry, and LPA levels were found to be increased in the innervated DRGs. Our results indicate that LPA produced in the innervated DRGs promotes the activation of SGCs through LPA1 , increases the sensitivity of primary neurons, and modulates pain behavior. These results facilitate our understanding of the pathology of acute nociceptive pain and demonstrate the possibility of the LPA1 on SGCs as a novel target for acute pain control.
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Affiliation(s)
- Yoko Hoshino
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Tokyo, Japan.,Department of Anesthesiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiaki Okuno
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan.,Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Shota Yamamoto
- Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan
| | - Hideo Shindou
- Department of Lipid Signaling, National Center for Global Health and Medicine, Tokyo, Japan.,Department of Lipid Medical Science, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kanji Uchida
- Department of Anesthesiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takehiko Yokomizo
- Department of Biochemistry, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Nobuko Ito
- Department of Anesthesiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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28
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Nakai T, Saigusa D, Iwamura Y, Matsumoto Y, Umeda K, Kato K, Yamaki H, Tomioka Y, Hirano I, Koshiba S, Yamamoto M, Suzuki N. Esterification promotes the intracellular accumulation of roxadustat, an activator of hypoxia-inducible factors, to extend its effective duration. Biochem Pharmacol 2022; 197:114939. [PMID: 35114188 DOI: 10.1016/j.bcp.2022.114939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 11/02/2022]
Abstract
Kidney injury often causes anemia due to a lack of production of the erythroid growth factor erythropoietin (EPO) in the kidneys. Roxadustat is one of the first oral medicines inducing EPO production in patients with renal anemia by activating hypoxia-inducible factors (HIFs), which are activators of EPO gene expression. In this study, to develop prodrugs of roxadustat with improved permeability through cell membrane, we investigated the effects of 8 types of esterification on the pharmacokinetics and bioactivity of roxadustat using Hep3B hepatoma cells that HIF-dependently produce EPO. Mass spectrometry of cells incubated with the esterified roxadustat derivatives revealed that the designed compounds were deesterified after being taken up by cells and showed low cytotoxicity compared to the original compound. Esterification prolonged the effective duration of roxadustat with respect to EPO gene induction and HIF activation in cells transiently exposed to the compounds. In the kidneys and livers of mice, both of which are unique sites of EPO production, a majority of the methyl-esterified roxadustat was deesterified within 6 h after drug administration. The deesterified roxadustat derivative was continuously detectable in plasma and urine for at least 48 h after administration, while the administered compound became undetectable 24 h after administration. Additionally, we confirmed that methyl-esterified roxadustat activated erythropoiesis in mice by inducing Epo mRNA expression exclusively in renal interstitial cells, which have intrinsic EPO-producing potential. These data suggest that esterification could lead to the development of roxadustat prodrugs with improvements in cell membrane permeability, effective duration and cytotoxicity.
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Affiliation(s)
- Taku Nakai
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Kaga 2-11-1, Itabashi-ku, Tokyo 173-8605, Japan
| | - Yuma Iwamura
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Yotaro Matsumoto
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Keiko Umeda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Koichiro Kato
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Hayato Yamaki
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Ikuo Hirano
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Norio Suzuki
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Applied Oxygen Physiology Project, New Industry Creation Hatchery Center, Tohoku University, Seiryo-machi 2-1, Aoba-ku, Sendai, Miyagi 980-8575, Japan.
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29
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Uruno A, Saigusa D, Suzuki T, Yumoto A, Nakamura T, Matsukawa N, Yamazaki T, Saito R, Taguchi K, Suzuki M, Suzuki N, Otsuki A, Katsuoka F, Hishinuma E, Okada R, Koshiba S, Tomioka Y, Shimizu R, Shirakawa M, Kensler TW, Shiba D, Yamamoto M. Nrf2 plays a critical role in the metabolic response during and after spaceflight. Commun Biol 2021; 4:1381. [PMID: 34887485 PMCID: PMC8660801 DOI: 10.1038/s42003-021-02904-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/16/2021] [Indexed: 11/09/2022] Open
Abstract
Space travel induces stresses that contribute to health problems, as well as inducing the expression of Nrf2 (NF-E2-related factor-2) target genes that mediate adaptive responses to oxidative and other stress responses. The volume of epididymal white adipose tissue (eWAT) in mice increases during spaceflight, a change that is attenuated by Nrf2 knockout. We conducted metabolome analyses of plasma from wild-type and Nrf2 knockout mice collected at pre-flight, in-flight and post-flight time points, as well as tissues collected post-flight to clarify the metabolic responses during and after spaceflight and the contribution of Nrf2 to these responses. Plasma glycerophospholipid and sphingolipid levels were elevated during spaceflight, whereas triacylglycerol levels were lower after spaceflight. In wild-type mouse eWAT, triacylglycerol levels were increased, but phosphatidylcholine levels were decreased, and these changes were attenuated in Nrf2 knockout mice. Transcriptome analyses revealed marked changes in the expression of lipid-related genes in the liver and eWAT after spaceflight and the effects of Nrf2 knockout on these changes. Based on these results, we concluded that space stress provokes significant responses in lipid metabolism during and after spaceflight; Nrf2 plays critical roles in these responses.
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Affiliation(s)
- Akira Uruno
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Daisuke Saigusa
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takafumi Suzuki
- grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akane Yumoto
- JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Tsukuba, Japan
| | - Tomohiro Nakamura
- grid.69566.3a0000 0001 2248 6943Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naomi Matsukawa
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takahiro Yamazaki
- grid.69566.3a0000 0001 2248 6943Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ristumi Saito
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Keiko Taguchi
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-GEneration Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Mikiko Suzuki
- grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Norio Suzuki
- grid.69566.3a0000 0001 2248 6943Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akihito Otsuki
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiki Katsuoka
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-GEneration Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Eiji Hishinuma
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-GEneration Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Risa Okada
- JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Tsukuba, Japan
| | - Seizo Koshiba
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Advanced Research Center for Innovations in Next-GEneration Medicine (INGEM), Tohoku University, Sendai, Japan
| | - Yoshihisa Tomioka
- grid.69566.3a0000 0001 2248 6943Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- grid.69566.3a0000 0001 2248 6943Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan ,grid.69566.3a0000 0001 2248 6943Department of Molecular Hematology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masaki Shirakawa
- JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Tsukuba, Japan
| | - Thomas W. Kensler
- grid.270240.30000 0001 2180 1622Translational Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Dai Shiba
- JEM Utilization Center, Human Spaceflight Technology Directorate, JAXA, Tsukuba, Japan.
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan. .,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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Ho H, Kikuchi K, Oikawa D, Watanabe S, Kanemitsu Y, Saigusa D, Kujirai R, Ikeda‐Ohtsubo W, Ichijo M, Akiyama Y, Aoki Y, Mishima E, Ogata Y, Oikawa Y, Matsuhashi T, Toyohara T, Suzuki C, Suzuki T, Mano N, Kagawa Y, Owada Y, Katayama T, Nakayama T, Tomioka Y, Abe T. SGLT-1-specific inhibition ameliorates renal failure and alters the gut microbial community in mice with adenine-induced renal failure. Physiol Rep 2021; 9:e15092. [PMID: 34921520 PMCID: PMC8683788 DOI: 10.14814/phy2.15092] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/20/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022] Open
Abstract
Sodium-dependent glucose cotransporters (SGLTs) have attracted considerable attention as new targets for type 2 diabetes mellitus. In the kidney, SGLT2 is the major glucose uptake transporter in the proximal tubules, and inhibition of SGLT2 in the proximal tubules shows renoprotective effects. On the other hand, SGLT1 plays a role in glucose absorption from the gastrointestinal tract, and the relationship between SGLT1 inhibition in the gut and renal function remains unclear. Here, we examined the effect of SGL5213, a novel and potent intestinal SGLT1 inhibitor, in a renal failure (RF) model. SGL5213 improved renal function and reduced gut-derived uremic toxins (phenyl sulfate and trimethylamine-N-oxide) in an adenine-induced RF model. Histological analysis revealed that SGL5213 ameliorated renal fibrosis and inflammation. SGL5213 also reduced gut inflammation and fibrosis in the ileum, which is a primary target of SGL5213. Examination of the gut microbiota community revealed that the Firmicutes/Bacteroidetes ratio, which suggests gut dysbiosis, was increased in RF and SGL5213 rebalanced the ratio by increasing Bacteroidetes and reducing Firmicutes. At the genus level, Allobaculum (a major component of Erysipelotrichaceae) was significantly increased in the RF group, and this increase was canceled by SGL5213. We also measured the effect of SGL5213 on bacterial phenol-producing enzymes that catalyze tyrosine into phenol, following the reduction of phenyl sulfate, which is a novel marker and a therapeutic target for diabetic kidney disease DKD. We found that the enzyme inhibition was less potent, suggesting that the change in the microbial community and the reduction of uremic toxins may be related to the renoprotective effect of SGL5213. Because SGL5213 is a low-absorbable SGLT1 inhibitor, these data suggest that the gastrointestinal inhibition of SGLT1 is also a target for chronic kidney diseases.
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Affiliation(s)
- Hsin‐Jung Ho
- Department of Medical ScienceTohoku University Graduate School of Biomedical EngineeringSendaiJapan
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Koichi Kikuchi
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
- Department of Medical MegabankTohoku UniversitySendaiJapan
| | - Daiki Oikawa
- Department of Biomolecular Engineering Applied Life ChemistryTohoku University Graduate School of EngineeringSendaiJapan
| | - Shun Watanabe
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
- Department of Clinical Biology and Hormonal RegulationTohoku University Graduate School of MedicineSendaiJapan
| | | | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank OrganizationTohoku UniversitySendaiJapan
| | - Ryota Kujirai
- Laboratory of OncologyPharmacy Practice and SciencesTohoku University Graduate School of Pharmaceutical SciencesSendaiJapan
| | - Wakako Ikeda‐Ohtsubo
- Laboratory of Animal Products ChemistryGraduate School of Agricultural ScienceTohoku UniversitySendaiJapan
| | - Mariko Ichijo
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Yukako Akiyama
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank OrganizationTohoku UniversitySendaiJapan
| | - Eikan Mishima
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Yoshiaki Ogata
- Department of Clinical Biology and Hormonal RegulationTohoku University Graduate School of MedicineSendaiJapan
| | - Yoshitsugu Oikawa
- Department of PediatricsTohoku University Graduate School of MedicineSendaiJapan
| | - Tetsuro Matsuhashi
- Department of PediatricsTohoku University Graduate School of MedicineSendaiJapan
| | - Takafumi Toyohara
- Department of Medical ScienceTohoku University Graduate School of Biomedical EngineeringSendaiJapan
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Chitose Suzuki
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Takehiro Suzuki
- Department of Medical ScienceTohoku University Graduate School of Biomedical EngineeringSendaiJapan
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
| | - Nariyasu Mano
- Department of Pharmaceutical SciencesTohoku University HospitalSendaiJapan
| | - Yoshiteru Kagawa
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
| | - Yuji Owada
- Department of Organ AnatomyTohoku University Graduate School of MedicineSendaiJapan
| | - Takane Katayama
- Laboratory of Molecular Biology of BioresponseGraduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Toru Nakayama
- Department of Biomolecular Engineering Applied Life ChemistryTohoku University Graduate School of EngineeringSendaiJapan
| | - Yoshihisa Tomioka
- Laboratory of Molecular Biology of BioresponseGraduate School of BiostudiesKyoto UniversityKyotoJapan
| | - Takaaki Abe
- Department of Medical ScienceTohoku University Graduate School of Biomedical EngineeringSendaiJapan
- Division of Nephrology, Endocrinology and Vascular MedicineTohoku University Graduate School of MedicineSendaiJapan
- Department of Clinical Biology and Hormonal RegulationTohoku University Graduate School of MedicineSendaiJapan
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31
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Suzuki N, Iwamura Y, Nakai T, Kato K, Otsuki A, Uruno A, Saigusa D, Taguchi K, Suzuki M, Shimizu R, Yumoto A, Okada R, Shirakawa M, Shiba D, Takahashi S, Suzuki T, Yamamoto M. Gene expression changes related to bone mineralization, blood pressure and lipid metabolism in mouse kidneys after space travel. Kidney Int 2021; 101:92-105. [PMID: 34767829 DOI: 10.1016/j.kint.2021.09.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 12/14/2022]
Abstract
Space travel burdens health by imposing considerable environmental stress associated with radioactivity and microgravity. In particular, gravity change predominantly impacts blood pressure and bone homeostasis, both of which are controlled mainly by the kidneys. Nuclear factor erythroid-2-related transcription factor 2 (Nrf2) plays essential roles in protecting the kidneys from various environmental stresses and injuries. To elucidate the effects of space travel on mammals in preparation for the upcoming space era, our study investigated the contribution of Nrf2 to kidney function in mice two days after their return from a 31-day stay in the International Space Station using Nrf2 knockout mice. Meaningfully, expression levels of genes regulating bone mineralization, blood pressure and lipid metabolism were found to be significantly altered in the kidneys after space travel in an Nrf2-independent manner. In particular, uridine diphosphate-glucuronosyltransferase 1A (Ugt1a) isoform genes were found to be expressed in an Nrf2-dependent manner and induced exclusively in the kidneys after return to Earth. Since spaceflight elevated the concentrations of fatty acids in the mouse plasma, we suggest that Ugt1a isoform expression in the kidneys was induced to promote glucuronidation of excessively accumulated lipids and excrete them into urine after the return from space. Thus, the kidneys were proven to play central roles in adaptation to gravity changes caused by going to and returning from space by controlling blood pressure and bone mineralization. Additionally, kidney Ugt1a isoform induction after space travel implies a significant role of the kidneys for space travelers in the excretion of excessive lipids.
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Affiliation(s)
- Norio Suzuki
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan.
| | - Yuma Iwamura
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Taku Nakai
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Koichiro Kato
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akihito Otsuki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Keiko Taguchi
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Mikiko Suzuki
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan; Center for Radioisotope Sciences, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ritsuko Shimizu
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Department of Molecular Hematology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Akane Yumoto
- Japanese Experiment Module (JEM) Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Risa Okada
- Japanese Experiment Module (JEM) Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Masaki Shirakawa
- Japanese Experiment Module (JEM) Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Dai Shiba
- Japanese Experiment Module (JEM) Utilization Center, Human Spaceflight Technology Directorate, Japan Aerospace Exploration Agency (JAXA), Tsukuba, Japan
| | - Satoru Takahashi
- Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Takafumi Suzuki
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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32
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic profiling is an omics approach that can be used to observe phenotypic changes, making it particularly attractive for biomarker discovery. Although several candidate metabolites biomarkers for disease expression have been identified in recent clinical studies, the reference values of healthy subjects have not been established. In particular, the accuracy of concentrations measured by mass spectrometry (MS) is unclear. Therefore, comprehensive metabolic profiling in large-scale cohorts by MS to create a database with reference ranges is essential for evaluating the quality of the discovered biomarkers. In this study, we tested 8700 plasma samples by commercial kit-based metabolomics and separated them into two groups of 6159 and 2541 analyses based on the different ultra-high-performance tandem mass spectrometry (UHPLC-MS/MS) systems. We evaluated the quality of the quantified values of the detected metabolites from the reference materials in the group of 2541 compared with the quantified values from other platforms, such as nuclear magnetic resonance (NMR), supercritical fluid chromatography tandem mass spectrometry (SFC-MS/MS) and UHPLC-Fourier transform mass spectrometry (FTMS). The values of the amino acids were highly correlated with the NMR results, and lipid species such as phosphatidylcholines and ceramides showed good correlation, while the values of triglycerides and cholesterol esters correlated less to the lipidomics analyses performed using SFC-MS/MS and UHPLC-FTMS. The evaluation of the quantified values by MS-based techniques is essential for metabolic profiling in a large-scale cohort.
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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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33
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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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [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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Nishimura T, Oyama T, Hu HT, Fujioka T, Hanawa-Suetsugu K, Ikeda K, Yamada S, Kawana H, Saigusa D, Ikeda H, Kurata R, Oono-Yakura K, Kitamata M, Kida K, Hikita T, Mizutani K, Yasuhara K, Mimori-Kiyosue Y, Oneyama C, Kurimoto K, Hosokawa Y, Aoki J, Takai Y, Arita M, Suetsugu S. Filopodium-derived vesicles produced by MIM enhance the migration of recipient cells. Dev Cell 2021; 56:842-859.e8. [PMID: 33756122 DOI: 10.1016/j.devcel.2021.02.029] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 12/31/2020] [Accepted: 02/23/2021] [Indexed: 12/19/2022]
Abstract
Extracellular vesicles (EVs) are classified as large EVs (l-EVs, or microvesicles) and small EVs (s-EVs, or exosomes). S-EVs are thought to be generated from endosomes through a process that mainly depends on the ESCRT protein complex, including ALG-2 interacting protein X (ALIX). However, the mechanisms of l-EV generation from the plasma membrane have not been identified. Membrane curvatures are generated by the bin-amphiphysin-rvs (BAR) family proteins, among which the inverse BAR (I-BAR) proteins are involved in filopodial protrusions. Here, we show that the I-BAR proteins, including missing in metastasis (MIM), generate l-EVs by scission of filopodia. Interestingly, MIM-containing l-EV production was promoted by in vivo equivalent external forces and by the suppression of ALIX, suggesting an alternative mechanism of vesicle formation to s-EVs. The MIM-dependent l-EVs contained lysophospholipids and proteins, including IRS4 and Rac1, which stimulated the migration of recipient cells through lamellipodia formation. Thus, these filopodia-dependent l-EVs, which we named as filopodia-derived vesicles (FDVs), modify cellular behavior.
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Affiliation(s)
- Tamako Nishimura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Takuya Oyama
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Hooi Ting Hu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Toshifumi Fujioka
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kyoko Hanawa-Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; Kazusa DNA Research Institute, 2-6-7 Kazusa, kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sohei Yamada
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Hiroki Kawana
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Daisuke Saigusa
- Tohoku University Tohoku Medical Megabank Organization, 2-1, Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Hiroki Ikeda
- Department of Embryology, Nara Medical University, Kashihara 634-0813, Nara, Japan
| | - Rie Kurata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kayoko Oono-Yakura
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Manabu Kitamata
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Kazuki Kida
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Tomoya Hikita
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
| | - Kiyohito Mizutani
- Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Kazuma Yasuhara
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Yuko Mimori-Kiyosue
- Laboratory for Molecular and Cellular Dynamics, RIKEN Center for Biosystems Dynamics Research, Minatojima-minaminachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Chitose Oneyama
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, 1-1 Kanokoden, Chikusa-ku, Nagoya 464-8681, Japan
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Kashihara 634-0813, Nara, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan
| | - Junken Aoki
- Laboratory of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Yoshimi Takai
- Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo 105-0011, Japan
| | - Shiro Suetsugu
- Division of Biological Science, Nara Institute of Science and Technology, Ikoma 630-0192, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma 630-0192, Japan.
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35
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Uchida Y, Higuchi T, Shirota M, Kagami S, Saigusa D, Koshiba S, Yasuda J, Tamiya G, Kuriyama S, Kinoshita K, Yaegashi N, Yamamoto M, Terasaki T, Sugawara J. Identification and Validation of Combination Plasma Biomarker of Afamin, Fibronectin and Sex Hormone-Binding Globulin to Predict Pre-eclampsia. Biol Pharm Bull 2021; 44:804-815. [PMID: 34078812 DOI: 10.1248/bpb.b20-01043] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The purpose of the present study was to identify a plasma protein biomarker able to predict pre-eclampsia (PE). Comprehensive quantitative proteomics using mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH-MS) was applied to plasma samples of 7 PE and 14 healthy pregnant women (for PE subjects, plasma samples were taken before onset of PE), and 11 proteins were selected as candidates potentially able to differentiate the two groups. Plasmas collected at gestational weeks 14-24 from 36 PE and 120 healthy pregnant women (for PE subjects, plasma samples were taken before onset of PE) were used to conduct selected reaction monitoring quantification analysis, optimize protein combinations and conduct internal validation, which consisted of 30 iterations of 10-fold cross-validation using multivariate logistic regression and receiver operating characteristic (ROC) analysis. The combination of afamin, fibronectin, and sex-hormone-binding globulin was selected as the best candidate. The 3-protein combination predictive model (predictive equation and cut-off value) generated using the internal validation subjects was successfully validated in another group of validation subjects (36 PE and 54 healthy (for PE subjects, plasma samples were taken before onset of PE)) and showed good predictive performance, with the area under the curve (AUC) 0.835 and odds ratio 13.43. In conclusion, we newly identified a 3-protein combination biomarker and established a predictive equation and cut-off value that can predict the onset of PE based on analysis of plasma samples collected during gestational weeks 14-24.
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Affiliation(s)
- Yasuo Uchida
- Faculty of Pharmaceutical Sciences, Tohoku University.,Graduate School of Pharmaceutical Sciences, Tohoku University.,Tohoku Medical Megabank Organization (ToMMo), Tohoku University
| | | | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Satoshi Kagami
- Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Jun Yasuda
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute
| | - Gen Tamiya
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Information Sciences, Tohoku University
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Tetsuya Terasaki
- Faculty of Pharmaceutical Sciences, Tohoku University.,Graduate School of Pharmaceutical Sciences, Tohoku University.,Tohoku Medical Megabank Organization (ToMMo), Tohoku University
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
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36
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Iwama T, Kano K, Saigusa D, Ekroos K, van Echten-Deckert G, Vogt J, Aoki J. Development of an On-Tissue Derivatization Method for MALDI Mass Spectrometry Imaging of Bioactive Lipids Containing Phosphate Monoester Using Phos-tag. Anal Chem 2021; 93:3867-3875. [PMID: 33577289 DOI: 10.1021/acs.analchem.0c04479] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) is an emerging label-free method for mapping the distribution of diverse molecular species in tissue sections. Despite recent progress in MALDI-MSI analyses of lipids, it is still difficult to visualize minor bioactive lipids including lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P). Here, we have developed a novel on-tissue derivatization method using Phos-tag, a zinc complex that specifically binds to a phosphate monoester group. MALDI-MSI with Phos-tag derivatization made it possible to image LPA and S1P in the murine brain. Furthermore, we were able to visualize other low-abundance lipids containing phosphate monoester, such as phosphatidic acid and ceramide-1-phosphate. Compared with conventional MALDI-MS, this derivatization produced LPA images with high spatial accuracy discriminating LPA artificially produced during MALDI-MS analysis. In mice with deficiencies in enzymes that degrade LPA and S1P, we observed marked S1P and/or LPA accumulation in specific regions of the brain. Thus, the present study provides a simple and optimal way to reveal the spatial localization of potent bioactive lipid phosphates such as LPA and S1P in tissues.
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Affiliation(s)
- Taiga Iwama
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan.,Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai980-8577, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan.,Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai980-8577, Japan.,AMED-LEAP, Tokyo100-0004, Japan
| | - Daisuke Saigusa
- AMED-LEAP, Tokyo100-0004, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai980-8577, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai 980-8575, Japan
| | - Kim Ekroos
- Lipidomics Consulting Ltd., 02230 Espoo, Finland
| | | | - Johannes Vogt
- Department of Molecular and Translational Neurosciences, University Medical Hospital, University of Cologne, 50923 Cologne, Germany
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan.,Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai980-8577, Japan.,AMED-LEAP, Tokyo100-0004, Japan
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37
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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38
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Kogaki T, Ohshio I, Ura H, Iyama S, Kitae K, Morie T, Fujii S, Sato S, Nagata T, Takeda AH, Aoki M, Ueda K, Minami K, Yamamoto M, Kawahara K, Furukawa T, Sato M, Ueda Y, Jingushi K, Tozuka Z, Saigusa D, Hase H, Tsujikawa K. Development of a highly sensitive method for the quantitative analysis of modified nucleosides using UHPLC-UniSpray-MS/MS. J Pharm Biomed Anal 2021; 197:113943. [PMID: 33601155 DOI: 10.1016/j.jpba.2021.113943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 01/27/2023]
Abstract
There are more than 150 types of naturally occurring modified nucleosides, which are believed to be involved in various biological processes. Recently, an ultrahigh performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UHPLC-ESI-MS/MS) technique has been developed to measure low levels of modified nucleosides. A comprehensive analysis of modified nucleosides will lead to a better understanding of intracellular ribonucleic acid modification, but this analysis requires high-sensitivity measurements. In this perspective, we established a highly sensitive and quantitative method using the newly developed ion source, UniSpray. A mass spectrometer was used with a UniSpray source in positive ion mode. Our UHPLC-UniSpray-MS/MS methodology separated and detected the four major nucleosides, 42 modified nucleosides, and dG15N5 (internal standard) in 15 min. The UniSpray method provided good correlation coefficients (>0.99) for all analyzed nucleosides, and a wide range of linearity for 35 of the 46 nucleosides. Additionally, the accuracy and precision values satisfied the criteria of <15% for higher concentrations and <20% for the lowest concentrations of all nucleosides. We also investigated whether this method could measure nucleosides in biological samples using mouse tissues and non-small cell lung cancer clinical specimens. We were able to detect 43 and 31 different modified nucleosides from mouse and clinical tissues, respectively. We also found significant differences in the levels of N6-methyl-N6-threonylcarbamoyladenosine (m6t6A), 1-methylinosine (m1I), 2'-O-methylcytidine (Cm), 5-carbamoylmethyluridine (ncm5U), 5-methoxycarbonylmethyl-2-thiouridine (mcm5S2U), and 5-methoxycarbonylmethyl-2'-O-methyluridine (mcm5Um) between cancerous and noncancerous tissues. In conclusion, we developed a highly sensitive methodology using UHPLC-UniSpray-MS/MS to simultaneously detect and quantify modified nucleosides, which can be used for analysis of biological samples.
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Affiliation(s)
- Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ikumi Ohshio
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Hasumi Ura
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Souta Iyama
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiya Morie
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shintarou Fujii
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shohei Sato
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Nagata
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Aya Harada Takeda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Masaya Aoki
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Kazuhiro Ueda
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Kentaro Minami
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Masatatsu Yamamoto
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Kohichi Kawahara
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Tatsuhiko Furukawa
- Department of Molecular Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8544, Japan
| | - Masami Sato
- Department of General Thoracic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, 8-35-1 Sakuragaoka, Kagoshima, Kagoshima 890-8520, Japan
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Zenzaburo Tozuka
- Center for Supporting Drug Discovery and Life Science Research Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, 1-2 Seiryocho, Aobaku, Sendai, Miyagi 980-8573, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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39
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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: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/15/2020] [Accepted: 10/19/2020] [Indexed: 12/30/2022] Open
Abstract
In the Tohoku Medical Megabank project, genome and omics analyses of participants in two cohort studies were performed. A part of the data is available at the Japanese Multi Omics Reference Panel (jMorp; https://jmorp.megabank.tohoku.ac.jp) as a web-based database, as reported in our previous manuscript published in Nucleic Acid Research in 2018. At that time, jMorp mainly consisted of metabolome data; however, now genome, methylome, and transcriptome data have been integrated in addition to the enhancement of the number of samples for the metabolome data. For genomic data, jMorp provides a Japanese reference sequence obtained using de novo assembly of sequences from three Japanese individuals and allele frequencies obtained using whole-genome sequencing of 8,380 Japanese individuals. In addition, the omics data include methylome and transcriptome data from ∼300 samples and distribution of concentrations of more than 755 metabolites obtained using high-throughput nuclear magnetic resonance and high-sensitivity mass spectrometry. In summary, jMorp now provides four different kinds of omics data (genome, methylome, transcriptome, and metabolome), with a user-friendly web interface. This will be a useful scientific data resource on the general population for the discovery of disease biomarkers and personalized disease prevention and early diagnosis.
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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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40
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Kumondai M, Gutiérrez Rico EM, Hishinuma E, Ueda A, Saito S, Saigusa D, Tadaka S, Kinoshita K, Nakayoshi T, Oda A, Abe A, Maekawa M, Mano N, Hirasawa N, Hiratsuka M. Functional Characterization of 40 CYP3A4 Variants by Assessing Midazolam 1'-Hydroxylation and Testosterone 6 β-Hydroxylation. Drug Metab Dispos 2020; 49:212-220. [PMID: 33384383 DOI: 10.1124/dmd.120.000261] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/24/2020] [Indexed: 12/17/2022] Open
Abstract
CYP3A4 is among the most abundant liver and intestinal drug-metabolizing cytochrome P450 enzymes, contributing to the metabolism of more than 30% of clinically used drugs. Therefore, interindividual variability in CYP3A4 activity is a frequent cause of reduced drug efficacy and adverse effects. In this study, we characterized wild-type CYP3A4 and 40 CYP3A4 variants, including 11 new variants, detected among 4773 Japanese individuals by assessing CYP3A4 enzymatic activities for two representative substrates (midazolam and testosterone). The reduced carbon monoxide-difference spectra of wild-type CYP3A4 and 31 CYP3A4 variants produced with our established mammalian cell expression system were determined by measuring the increase in maximum absorption at 450 nm after carbon monoxide treatment. The kinetic parameters of midazolam and testosterone hydroxylation by wild-type CYP3A4 and 29 CYP3A4 variants (K m , k cat , and catalytic efficiency) were determined, and the causes of their kinetic differences were evaluated by three-dimensional structural modeling. Our findings offer insight into the mechanism underlying interindividual differences in CYP3A4-dependent drug metabolism. Moreover, our results provide guidance for improving drug administration protocols by considering the information on CYP3A4 genetic polymorphisms. SIGNIFICANCE STATEMENT: CYP3A4 metabolizes more than 30% of clinically used drugs. Interindividual differences in drug efficacy and adverse-effect rates have been linked to ethnicity-specific differences in CYP3A4 gene variants in Asian populations, including Japanese individuals, indicating the presence of CYP3A4 polymorphisms resulting in the increased expression of loss-of-function variants. This study detected alterations in CYP3A4 activity due to amino acid substitutions by assessing the enzymatic activities of coding variants for two representative CYP3A4 substrates.
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Affiliation(s)
- Masaki Kumondai
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Evelyn Marie Gutiérrez Rico
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Eiji Hishinuma
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Akiko Ueda
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Sakae Saito
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Daisuke Saigusa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Shu Tadaka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Kengo Kinoshita
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Tomoki Nakayoshi
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Akifumi Oda
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Ai Abe
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Masamitsu Maekawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Nariyasu Mano
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (M.K., E.M.G.R., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., D.S., S.T., K.K., M.H.), Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., N.H., M.H.), and Laboratory of Clinical Pharmacy, Faculty of Pharmaceutical Sciences (A.A., M.M., N.M.), Tohoku University, Sendai, Japan; Faculty of Pharmacy, Meijo University, Nagoya, Japan (T.N., A.O.); and Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Miyagi M, Wilson R, Saigusa D, Umeda K, Saijo R, Hager CL, Li Y, McCormick T, Ghannoum MA. Indole-3-acetic acid synthesized through the indole-3-pyruvate pathway promotes Candida tropicalis biofilm formation. PLoS One 2020; 15:e0244246. [PMID: 33332404 PMCID: PMC7746184 DOI: 10.1371/journal.pone.0244246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/04/2020] [Indexed: 12/26/2022] Open
Abstract
We previously found that the elevated abundance of the fungus Candida tropicalis is positively correlated with the bacteria Escherichia coli and Serratia marcescens in Crohn’s disease patients and the three pathogens, when co-cultured, form a robust mixed-species biofilm. The finding suggests that these three pathogens communicate and promote biofilm formation, possibly through secretion of small signaling molecules. To identify candidate signaling molecules, we carried out a metabolomic analysis of the single-species and triple-species cultures of the three pathogens. This analysis identified 15 metabolites that were highly increased in the triple-species culture. One highly induced metabolite was indole-3-acetic acid (IAA), which has been shown to induce filamentation of certain fungi. We thus tested the effect of IAA on biofilm formation of C. tropicalis and demonstrated that IAA promotes biofilm formation of C. tropicalis. Then, we carried out isotope tracing experiments using 13C-labeled-tryptophan as a precursor to uncover the biosynthesis pathway of IAA in C. tropicalis. The results indicated that C. tropicalis synthesizes IAA through the indole-3-pyruvate pathway. Further studies using inhibitors of the indole-3-pyruvate pathway are warranted to decipher the mechanisms by which IAA influences biofilm formation.
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Affiliation(s)
- Masaru Miyagi
- Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (MM); (MAG)
| | - Rachel Wilson
- Department of Dermatology, Center for Medical Mycology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Keiko Umeda
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Reina Saijo
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Christopher L. Hager
- Department of Dermatology, Center for Medical Mycology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Yuejin Li
- Department of Dermatology, Center for Medical Mycology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Thomas McCormick
- Department of Dermatology, Center for Medical Mycology, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - Mahmoud A. Ghannoum
- Department of Dermatology, Center for Medical Mycology, Case Western Reserve University, Cleveland, Ohio, United States of America
- University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
- * E-mail: (MM); (MAG)
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Akiyama T, Saigusa D, Hyodo Y, Umeda K, Saijo R, Koshiba S, Kobayashi K. Metabolic Profiling of the Cerebrospinal Fluid in Pediatric Epilepsy. Acta Med Okayama 2020; 74:65-72. [PMID: 32099251 DOI: 10.18926/amo/57955] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To characterize metabolic profiles within the central nervous system in epilepsy, we performed gas chromatography-tandem mass spectrometry (GC-MS/MS)-based metabolome analysis of the cerebrospinal fluid (CSF) in pediatric patients with and without epilepsy. The CSF samples obtained from 64 patients were analyzed by GC-MS/MS. Multivariate analyses were performed for two age groups, 0-5 years of age and 6-17 years of age, to elucidate the effects of epilepsy and antiepileptic drugs on the metabolites. In patients aged 0-5 years (22 patients with epilepsy, 13 without epilepsy), epilepsy patients had reduced 2-ketoglutaric acid and elevated pyridoxamine and tyrosine. In patients aged 6-17 years (12 with epilepsy, 17 without epilepsy), epilepsy patients had reduced 1,5-anhydroglucitol. Valproic acid was associated with elevated 2-aminobutyric acid, 2-ketoisocaproic acid, 4-hydroxyproline, acetylglycine, methionine, N-acetylserine, and serine. Reduced energy metabolism and alteration of vitamin B6 metabolism may play a role in epilepsy in young children. The roles of 1,5-anhydroglucitol in epilepsy in older children and in levetiracetam and zonisamide treatment remain to be explained. Valproic acid influenced the levels of amino acids and related metabolites involved in the metabolism of serine, methionine, and leucine.
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Affiliation(s)
- Tomoyuki Akiyama
- Department of Child Neurology, Okayama University Hospital, Okayama 700-8558, .,Department of Child Neurology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Yuki Hyodo
- Department of Child Neurology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Keiko Umeda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Reina Saijo
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan
| | - Katsuhiro Kobayashi
- Department of Child Neurology, Okayama University Hospital, Okayama 700-8558, Japan.,Department of Child Neurology, bOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
We performed a metabolome genome-wide association study for the Japanese population in the prospective cohort study of Tohoku Medical Megabank. By combining whole-genome sequencing and nontarget metabolome analyses, we identified a large number of novel associations between genetic variants and plasma metabolites. Of the identified metabolite-associated genes, approximately half have already been shown to be involved in various diseases. We identified metabolite-associated genes involved in the metabolism of xenobiotics, some of which are from intestinal microorganisms, indicating that the identified genetic variants also markedly influence the interaction between the host and symbiotic bacteria. We also identified five associations that appeared to be female-specific. A number of rare variants that influence metabolite levels were also found, and combinations of common and rare variants influenced the metabolite levels more profoundly. These results support our contention that metabolic phenotyping provides important insights into how genetic and environmental factors provoke human diseases.
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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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Nanto-Hara F, Kanemitsu Y, Fukuda S, Kikuchi K, Asaji K, Saigusa D, Iwasaki T, Ho HJ, Mishima E, Suzuki T, Suzuki C, Tsukimi T, Matsuhashi T, Oikawa Y, Akiyama Y, Kure S, Owada Y, Tomioka Y, Soga T, Ito S, Abe T. The guanylate cyclase C agonist linaclotide ameliorates the gut-cardio-renal axis in an adenine-induced mouse model of chronic kidney disease. Nephrol Dial Transplant 2020; 35:250-264. [PMID: 31411705 DOI: 10.1093/ndt/gfz126] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 05/16/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Cardiorenal syndrome is a major cause of mortality in patients with chronic kidney disease (CKD). However, the involvement of detrimental humoral mediators in the pathogenesis of cardiorenal syndrome is still controversial. Trimethylamine-N-oxide (TMAO), a hepatic metabolic product of trimethylamine generated from dietary phosphatidylcholine or carnitine derived by the gut microbiota, has been linked directly with progression of cardiovascular disease and renal dysfunction. Thus, targeting TMAO may be a novel strategy for the prevention of cardiovascular disease and chronic kidney disease. METHODS Linaclotide, a guanylate cyclase C agonist, was administered to adenine-induced renal failure (RF) mice and changes in renal function and levels of gut-derived uremic toxins, as well as the gut microbiota community, were analyzed using metabolomic and metagenomic methods to reveal its cardiorenal effect. RESULTS Linaclotide decreased the plasma levels of TMAO at a clinically used low dose of 10 μg/kg in the adenine-induced RF mouse model. At a high concentration of 100 μg/kg, linaclotide clearly improved renal function and reduced the levels of various uremic toxins. A reduction in TMAO levels following linaclotide treatment was also observed in a choline-fed pro-atherosclerotic model. Linaclotide ameliorated renal inflammation and fibrosis and cardiac fibrosis, as well as decreased the expression of collagen I, transforming growth factor-β, galectin-3 (Gal-3) and ST2 genes. Plasma levels of Gal-3 and ST2 were also reduced. Because exposure of cardiomyocytes to TMAO increased fibronectin expression, these data suggest that linaclotide reduced the levels of TMAO and various uremic toxins and may result in not only renal, but also cardiac, fibrosis. F4/80-positive macrophages were abundant in small intestinal crypts in RF mice, and this increased expression was decreased by linaclotide. Reduced colonic claudin-1 levels were also restored by linaclotide, suggesting that linaclotide ameliorated the 'leaky gut' in RF mice. Metagenomic analysis revealed that the microbial order Clostridiales could be responsible for the change in TMAO levels. CONCLUSION Linaclotide reduced TMAO and uremic toxin levels and could be a powerful tool for the prevention and control of the cardiorenal syndrome by modification of the gut-cardio-renal axis.
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Affiliation(s)
- Fumika Nanto-Hara
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.,Department of Anatomy, Tohoku University Graduate School of Medicine, Sendai, Japan.,Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitomi Kanemitsu
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Koichi Kikuchi
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kei Asaji
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomoyuki Iwasaki
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Hsin-Jung Ho
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.,Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Eikan Mishima
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takehiro Suzuki
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.,Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Chitose Suzuki
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Tetsuro Matsuhashi
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.,Division of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitsugu Oikawa
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.,Division of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukako Akiyama
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shigeo Kure
- Division of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yuji Owada
- Department of Anatomy, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshihisa Tomioka
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Tomoyoshi Soga
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Sadayoshi Ito
- Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takaaki Abe
- Department of Medical Science, Tohoku University Graduate School of Biomedical Engineering, Sendai, Japan.,Division of Nephrology, Endocrinology, and Vascular Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Clinical Biology and Hormonal Regulation, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
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46
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Takahashi Y, Ueki M, Yamada M, Tamiya G, Motoike IN, Saigusa D, Sakurai M, Nagami F, Ogishima S, Koshiba S, Kinoshita K, Yamamoto M, Tomita H. Improved metabolomic data-based prediction of depressive symptoms using nonlinear machine learning with feature selection. Transl Psychiatry 2020; 10:157. [PMID: 32427830 PMCID: PMC7237664 DOI: 10.1038/s41398-020-0831-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 12/15/2022] Open
Abstract
To solve major limitations in algorithms for the metabolite-based prediction of psychiatric phenotypes, a novel prediction model for depressive symptoms based on nonlinear feature selection machine learning, the Hilbert-Schmidt independence criterion least absolute shrinkage and selection operator (HSIC Lasso) algorithm, was developed and applied to a metabolomic dataset with the largest sample size to date. In total, 897 population-based subjects were recruited from the communities affected by the Great East Japan Earthquake; 306 metabolite features (37 metabolites identified by nuclear magnetic resonance measurements and 269 characterized metabolites based on the intensities from mass spectrometry) were utilized to build prediction models for depressive symptoms as evaluated by the Center for Epidemiologic Studies-Depression Scale (CES-D). The nested fivefold cross-validation was used for developing and evaluating the prediction models. The HSIC Lasso-based prediction model showed better predictive power than the other prediction models, including Lasso, support vector machine, partial least squares, random forest, and neural network. L-leucine, 3-hydroxyisobutyrate, and gamma-linolenyl carnitine frequently contributed to the prediction. We have demonstrated that the HSIC Lasso-based prediction model integrating nonlinear feature selection showed improved predictive power for depressive symptoms based on metabolome data as well as on risk metabolites based on nonlinear statistics in the Japanese population. Further studies should use HSIC Lasso-based prediction models with different ethnicities to investigate the generality of each risk metabolite for predicting depressive symptoms.
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Affiliation(s)
- Yuta Takahashi
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
| | - Masao Ueki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Makoto Yamada
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Gen Tamiya
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- RIKEN Center for Advanced Intelligence Project, Tokyo, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Daisuke Saigusa
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Seizo Koshiba
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Institute for Development Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroaki Tomita
- Graduate School of Medicine, Tohoku University, Sendai, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan.
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47
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Rashad S, Saigusa D, Yamazaki T, Matsumoto Y, Tomioka Y, Saito R, Uruno A, Niizuma K, Yamamoto M, Tominaga T. Metabolic basis of neuronal vulnerability to ischemia; an in vivo untargeted metabolomics approach. Sci Rep 2020; 10:6507. [PMID: 32300196 PMCID: PMC7162929 DOI: 10.1038/s41598-020-63483-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 03/27/2020] [Indexed: 02/06/2023] Open
Abstract
Understanding the root causes of neuronal vulnerability to ischemia is paramount to the development of new therapies for stroke. Transient global cerebral ischemia (tGCI) leads to selective neuronal cell death in the CA1 sub-region of the hippocampus, while the neighboring CA3 sub-region is left largely intact. By studying factors pertaining to such selective vulnerability, we can develop therapies to enhance outcome after stroke. Using untargeted liquid chromatography-mass spectrometry, we analyzed temporal metabolomic changes in CA1 and CA3 hippocampal areas following tGCI in rats till the setting of neuronal apoptosis. 64 compounds in CA1 and 74 in CA3 were found to be enriched and statistically significant following tGCI. Pathway analysis showed that pyrimidine and purine metabolism pathways amongst several others to be enriched after tGCI in CA1 and CA3. Metabolomics analysis was able to capture very early changes following ischemia. We detected 6 metabolites to be upregulated and 6 to be downregulated 1 hour after tGCI in CA1 versus CA3. Several metabolites related to apoptosis and inflammation were differentially expressed in both regions after tGCI. We offer a new insight into the process of neuronal apoptosis, guided by metabolomic profiling that was not performed to such an extent previously.
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Affiliation(s)
- Sherif Rashad
- 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.
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Takahiro Yamazaki
- Laboratory of Oncology, Pharmacy Practice and Sciences, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Yotaro Matsumoto
- 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
| | - Ritsumi Saito
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Kuniyasu Niizuma
- 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. .,Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan.
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai, Japan
| | - Teiji Tominaga
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, Sendai, Japan
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48
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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 Commun Mass Spectrom 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] [What about the content of this article? (0)] [Affiliation(s)] [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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49
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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50
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Saigusa D, Motoike IN, Saito S, Zorzi M, Aoki Y, Kitamura H, Suzuki M, Katsuoka F, Ishii H, Kinoshita K, Motohashi H, Yamamoto M. Impacts of NRF2 activation in non-small-cell lung cancer cell lines on extracellular metabolites. Cancer Sci 2020; 111:667-678. [PMID: 31828882 PMCID: PMC7004536 DOI: 10.1111/cas.14278] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 01/09/2023] Open
Abstract
Aberrant activation of NRF2 is as a critical prognostic factor that drives the malignant progression of various cancers. Cancer cells with persistent NRF2 activation heavily rely on NRF2 activity for therapeutic resistance and aggressive tumorigenic capacity. To clarify the metabolic features of NRF2-activated lung cancers, we conducted targeted metabolomic (T-Met) and global metabolomic (G-Met) analyses of non-small-cell lung cancer (NSCLC) cell lines in combination with exome and transcriptome analyses. Exome analysis of 88 cell lines (49 adenocarcinoma, 14 large cell carcinoma, 15 squamous cell carcinoma and 10 others) identified non-synonymous mutations in the KEAP1, NRF2 and CUL3 genes. Judging from the elevated expression of NRF2 target genes, these mutations are expected to result in the constitutive stabilization of NRF2. Out of the 88 cell lines, 52 NSCLC cell lines (29 adenocarcinoma, 10 large cell carcinoma, 9 squamous cell carcinoma and 4 others) were subjected to T-Met analysis. Classification of the 52 cell lines into three groups according to the NRF2 target gene expression enabled us to draw typical metabolomic signatures induced by NRF2 activation. From the 52 cell lines, 18 NSCLC cell lines (14 adenocarcinoma, 2 large cell carcinoma, 1 squamous cell carcinoma and 1 others) were further chosen for G-Met and detailed transcriptome analyses. G-Met analysis of their culture supernatants revealed novel metabolites associated with NRF2 activity, which may be potential diagnostic biomarkers of NRF2 activation. This study also provides useful information for the exploration of new metabolic nodes for selective toxicity towards NRF2-activated NSCLC.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Sakae Saito
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan
| | - Michael Zorzi
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, Italy
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Hiroshi Kitamura
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Mikiko Suzuki
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | | | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | - Hozumi Motohashi
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, Sendai, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
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