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Takano Y, Naraoka H, Dworkin JP, Koga T, Sasaki K, Sato H, Oba Y, Ogawa NO, Yoshimura T, Hamase K, Ohkouchi N, Parker ET, Aponte JC, Glavin DP, Furukawa Y, Aoki J, Kano K, Nomura SIM, Orthous-Daunay FR, Schmitt-Kopplin P, Yurimoto H, Nakamura T, Noguchi T, Okazaki R, Yabuta H, Sakamoto K, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Watanabe SI, Tsuda Y, Tachibana S. Primordial aqueous alteration recorded in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu. Nat Commun 2024; 15:5708. [PMID: 38987536 PMCID: PMC11237059 DOI: 10.1038/s41467-024-49237-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 05/29/2024] [Indexed: 07/12/2024] Open
Abstract
We report primordial aqueous alteration signatures in water-soluble organic molecules from the carbonaceous asteroid (162173) Ryugu by the Hayabusa2 spacecraft of JAXA. Newly identified low-molecular-weight hydroxy acids (HO-R-COOH) and dicarboxylic acids (HOOC-R-COOH), such as glycolic acid, lactic acid, glyceric acid, oxalic acid, and succinic acid, are predominant in samples from the two touchdown locations at Ryugu. The quantitative and qualitative profiles for the hydrophilic molecules between the two sampling locations shows similar trends within the order of ppb (parts per billion) to ppm (parts per million). A wide variety of structural isomers, including α- and β-hydroxy acids, are observed among the hydrophilic molecules. We also identify pyruvic acid and dihydroxy and tricarboxylic acids, which are biochemically important intermediates relevant to molecular evolution, such as the primordial TCA (tricarboxylic acid) cycle. Here, we find evidence that the asteroid Ryugu samples underwent substantial aqueous alteration, as revealed by the presence of malonic acid during keto-enol tautomerism in the dicarboxylic acid profile. The comprehensive data suggest the presence of a series for water-soluble organic molecules in the regolith of Ryugu and evidence of signatures in coevolutionary aqueous alteration between water and organics in this carbonaceous asteroid.
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Affiliation(s)
- Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan.
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Jason P Dworkin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Kazunori Sasaki
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hajime Sato
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8 Kita-ku, Sapporo, 060-0819, Japan
| | - Nanako O Ogawa
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Toshihiro Yoshimura
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Kenji Hamase
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-0054, Japan
| | - Naohiko Ohkouchi
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Eric T Parker
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - José C Aponte
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Daniel P Glavin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Yoshihiro Furukawa
- Department of Earth Material Science, Tohoku University, Sendai, 980-8578, Japan
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Tokyo, 113-0033, Japan
| | - Shin-Ichiro M Nomura
- Department of Robotics Graduate school of Engineering, Tohoku University, Sendai, 980-8579, Japan
| | - Francois-Regis Orthous-Daunay
- Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Centre National d'Etudes Spatiales, L'Institut de Planétologie et d'Astrophysique de Grenoble, 38000, Grenoble, France
| | - Philippe Schmitt-Kopplin
- Technische Universitӓt München, Analytische Lebensmittel Chemie, 85354, Freising, Germany
- Max Planck Institute for Extraterrestrial Physics, 85748, Garching bei München, Germany
- Center for Research and Exploration in Space Science and Technology, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Hisayoshi Yurimoto
- Department of Earth and Planetary Sciences, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tomoki Nakamura
- Department of Earth Material Science, Tohoku University, Sendai, 980-8578, Japan
| | - Takaaki Noguchi
- Department of Earth and Planetary Sciences, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuji Okazaki
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hikaru Yabuta
- Department of Earth and Planetary Sciences, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Kanako Sakamoto
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Toru Yada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masahiro Nishimura
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Aiko Nakato
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Akiko Miyazaki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Kasumi Yogata
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masanao Abe
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tatsuaki Okada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tomohiro Usui
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Makoto Yoshikawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Takanao Saiki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Satoshi Tanaka
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Fuyuto Terui
- Kanagawa Institute of Technology, Atsugi, 243-0292, Japan
| | - Satoru Nakazawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Sei-Ichiro Watanabe
- Department of Earth and Environment Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yuichi Tsuda
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Shogo Tachibana
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
- UTokyo Organization for Planetary and Space Science (UTOPS), University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
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Prieto‐Vila M, Yoshioka Y, Kuriyama N, Okamura A, Yamamoto Y, Muranaka A, Ochiya T. Adult cardiomyocytes-derived EVs for the treatment of cardiac fibrosis. J Extracell Vesicles 2024; 13:e12461. [PMID: 38940266 PMCID: PMC11211925 DOI: 10.1002/jev2.12461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 04/15/2024] [Accepted: 05/06/2024] [Indexed: 06/29/2024] Open
Abstract
Cardiac fibrosis is a common pathological feature of cardiovascular diseases that arises from the hyperactivation of fibroblasts and excessive extracellular matrix (ECM) deposition, leading to impaired cardiac function and potentially heart failure or arrhythmia. Extracellular vesicles (EVs) released by cardiomyocytes (CMs) regulate various physiological functions essential for myocardial homeostasis, which are disrupted in cardiac disease. Therefore, healthy CM-derived EVs represent a promising cell-free therapy for the treatment of cardiac fibrosis. To this end, we optimized the culture conditions of human adult CMs to obtain a large yield of EVs without compromising cellular integrity by using a defined combination of small molecules. EVs were isolated by ultracentrifugation, and their characteristics were analysed. Finally, their effect on fibrosis was tested. Treatment of TGFβ-activated human cardiac fibroblasts with EVs derived from CMs using our culture system resulted in a decrease in fibroblast activation markers and ECM accumulation. The rescued phenotype was associated with specific EV cargo, including multiple myocyte-specific and antifibrotic microRNAs, although their effect individually was not as effective as the EV treatment. Notably, pathway analysis showed that EV treatment reverted the transcription of activated fibroblasts and decreased several signalling pathways, including MAPK, mTOR, JAK/STAT, TGFβ, and PI3K/Akt, all of which are involved in fibrosis development. Intracardiac injection of CM-derived EVs in an animal model of cardiac fibrosis reduced fibrotic area and increased angiogenesis, which correlated with improved cardiac function. These findings suggest that EVs derived from human adult CMs may offer a targeted and effective treatment for cardiac fibrosis, owing to their antifibrotic properties and the specificity of cargo.
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Affiliation(s)
- Marta Prieto‐Vila
- Department of Molecular and Cellular MedicineTokyo Medical UniversityTokyoJapan
| | - Yusuke Yoshioka
- Department of Molecular and Cellular MedicineTokyo Medical UniversityTokyoJapan
| | - Naoya Kuriyama
- Department of Molecular and Cellular MedicineTokyo Medical UniversityTokyoJapan
- Department of Vascular SurgeryAsahikawa Medical UniversityAsahikawaHokkaidoJapan
| | - Akihiko Okamura
- Department of Molecular and Cellular MedicineTokyo Medical UniversityTokyoJapan
- Department of Cardiovascular MedicineNara Medical UniversityNaraJapan
| | - Yusuke Yamamoto
- Laboratory of Integrative OncologyNational Cancer Center Research InstituteTokyoJapan
| | - Asao Muranaka
- Department of Molecular and Cellular MedicineTokyo Medical UniversityTokyoJapan
| | - Takahiro Ochiya
- Department of Molecular and Cellular MedicineTokyo Medical UniversityTokyoJapan
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Oharazawa A, Maimaituxun G, Watanabe K, Nishiyasu T, Fujii N. Metabolome analyses of skin dialysate: Insights into skin interstitial fluid biomarkers. J Dermatol Sci 2024; 114:141-147. [PMID: 38740531 DOI: 10.1016/j.jdermsci.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/27/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Metabolites in biofluids can serve as biomarkers for diagnosing diseases and monitoring body conditions. Among the available biofluids, interstitial fluid (ISF) in the skin has garnered considerable attention owing to its advantages, which include inability to clot, easy access to the skin, and possibility of incorporating wearable devices. However, the scientific understanding of skin ISF composition is limited. OBJECTIVE In this study, we aimed to compare metabolites between skin dialysate containing metabolites from the skin ISF and venous blood (plasma) samples, both collected under resting states. METHODS We collected forearm skin dialysate using intradermal microdialysis alongside venous blood (plasma) samples from 12 healthy young adults. We analyzed these samples using capillary electrophoresis-fourier transform mass spectrometry-based metabolomics (CE-FTMS). RESULTS Significant positive correlations were observed in 39 metabolites between the skin dialysate and plasma, including creatine (a mitochondrial disease biomarker), 1-methyladenosine (an early detection of cancer biomarker), and trimethylamine N-oxide (a posterior predictor of heart failure biomarker). Based on the Human Metabolome Technologies database, we identified 12 metabolites unique to forearm skin dialysate including nucleic acids, benzoate acids, fatty acids, amino acids, ascorbic acid, 3-methoxy-4-hydroxyphenylethyleneglycol (an Alzheimer's disease biomarker), and cysteic acid (an acute myocardial infarction biomarker). CONCLUSION We show that some venous blood biomarkers may be predicted from skin dialysate or skin ISF, and that these fluids may serve as diagnostic and monitoring tools for health and clinical conditions.
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Affiliation(s)
| | - Gulinu Maimaituxun
- Institute of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Koichi Watanabe
- Institute of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takeshi Nishiyasu
- Institute of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan; Advanced Research Initiative for Human High Performance (ARIHHP), Japan
| | - Naoto Fujii
- Institute of Health and Sport Sciences, University of Tsukuba, Tsukuba, Japan; Advanced Research Initiative for Human High Performance (ARIHHP), Japan.
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4
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Matsui S, Ri C, Bolanos LC, Choi K, Shibamiya A, Ishii A, Takaishi K, Oshima-Hasegawa N, Tsukamoto S, Takeda Y, Mimura N, Yoshimi A, Yokote K, Starczynowski DT, Sakaida E, Muto T. Metabolic reprogramming regulated by TRAF6 contributes to the leukemia progression. Leukemia 2024; 38:1032-1045. [PMID: 38609495 DOI: 10.1038/s41375-024-02245-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/31/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
TNF receptor associated factor 6 (TRAF6) is an E3 ubiquitin ligase that has been implicated in myeloid malignancies. Although altered TRAF6 expression is observed in human acute myeloid leukemia (AML), its role in the AML pathogenesis remains elusive. In this study, we showed that the loss of TRAF6 in AML cells significantly impairs leukemic function in vitro and in vivo, indicating its functional importance in AML subsets. Loss of TRAF6 induces metabolic alterations, such as changes in glycolysis, TCA cycle, and nucleic acid metabolism as well as impaired mitochondrial membrane potential and respiratory capacity. In leukemic cells, TRAF6 expression shows a positive correlation with the expression of O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT), which catalyzes the addition of O-GlcNAc to target proteins involved in metabolic regulation. The restoration of growth capacity and metabolic activity in leukemic cells with TRAF6 loss, achieved through either forced expression of OGT or pharmacological inhibition of O-GlcNAcase (OGA) that removes O-GlcNAc, indicates the significant role of O-GlcNAc modification in the TRAF6-related cellular and metabolic dynamics. Our findings highlight the oncogenic function of TRAF6 in leukemia and illuminate the novel TRAF6/OGT/O-GlcNAc axis as a potential regulator of metabolic reprogramming in leukemogenesis.
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Affiliation(s)
- Shinichiro Matsui
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Chihiro Ri
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Lyndsey C Bolanos
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kwangmin Choi
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Asuka Shibamiya
- Department of Hematology, Chiba University Hospital, Chiba, Japan
| | - Arata Ishii
- Department of Hematology, Chiba University Hospital, Chiba, Japan
| | - Koji Takaishi
- Department of Hematology, Chiba University Hospital, Chiba, Japan
| | - Nagisa Oshima-Hasegawa
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Department of Transfusion Medicine and Cell Therapy, Chiba University Hospital, Chiba, Japan
| | | | - Yusuke Takeda
- Department of Hematology, Chiba University Hospital, Chiba, Japan
| | - Naoya Mimura
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Department of Transfusion Medicine and Cell Therapy, Chiba University Hospital, Chiba, Japan
| | - Akihide Yoshimi
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, Japan
| | - Koutaro Yokote
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Daniel T Starczynowski
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Emiko Sakaida
- Department of Hematology, Chiba University Hospital, Chiba, Japan
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan
- Department of Transfusion Medicine and Cell Therapy, Chiba University Hospital, Chiba, Japan
| | - Tomoya Muto
- Department of Hematology, Chiba University Hospital, Chiba, Japan.
- Department of Endocrinology, Hematology and Gerontology, Chiba University Graduate School of Medicine, Chiba, Japan.
- Division of Cancer RNA Research, National Cancer Center Research Institute, Tokyo, Japan.
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Muroya S, Horiuchi Y, Iguchi K, Higuchi T, Sakamoto S, Ojima K, Matsukawa K. Depth of Interbreed Difference in Postmortem Bovine Muscle Determined by CE-FT/MS and LC-FT/MS Metabolomics. Metabolites 2024; 14:261. [PMID: 38786738 PMCID: PMC11123161 DOI: 10.3390/metabo14050261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Japanese Brown (JBR) cattle have moderately marbled beef compared to the highly marbled beef of Japanese Black (JBL) cattle; however, their skeletal muscle properties remain poorly characterized. To unveil interbreed metabolic differences over the previous results, we explored the metabolome network changes before and after postmortem 7-day aging in the trapezius muscle of the two cattle breeds by employing a deep and high-coverage metabolomics approach. Using both capillary electrophoresis (CE) and ultra-high-performance liquid chromatography (UHPLC)-Fourier transform mass spectrometry (FT/MS), we detected 522 and 384 annotated peaks, respectively, across all muscle samples. The CE-based results showed that the cattle were clearly separated by breed and postmortem age in multivariate analyses. The metabolism related to glutathione, glycolysis, vitamin K, taurine, and arachidonic acid was enriched with differentially abundant metabolites in aged muscles, in addition to amino acid (AA) metabolisms. The LC-based results showed that the levels of bile-acid-related metabolites, such as tauroursodeoxycholic acid (TUDCA), were high in fresh JBR muscle and that acylcarnitines were enriched in aged JBR muscle, compared to JBL muscle. Postmortem aging resulted in an increase in fatty acids and a decrease in acylcarnitine in the muscles of both cattle breeds. In addition, metabolite set enrichment analysis revealed that JBR muscle was distinctive in metabolisms related to pyruvate, glycerolipid, cardiolipin, and mitochondrial energy production, whereas the metabolisms related to phosphatidylethanolamine, nucleotide triphosphate, and AAs were characteristic of JBL. This suggests that the interbreed differences in postmortem trapezius muscle are associated with carnitine/acylcarnitine transport, β-oxidation, tricarboxylic acid cycle, and mitochondrial membrane stability, in addition to energy substrate and AA metabolisms. These interbreed differences may characterize beef quality traits such as the flavor intensity and oxidative stability.
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Affiliation(s)
- Susumu Muroya
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Tsukuba 305-0901, Ibaraki, Japan
- Faculty of Veterinary Medicine, Kagoshima University, Korimoto 890-0065, Kagoshima, Japan
| | - Yuta Horiuchi
- Human Metabolome Technologies Inc., Tsuruoka 997-0052, Yamagata, Japan
| | - Kazuki Iguchi
- Human Metabolome Technologies Inc., Tsuruoka 997-0052, Yamagata, Japan
| | - Takuma Higuchi
- Science Research Center, Kochi University, Nankoku 783-8505, Kochi, Japan
| | - Shuji Sakamoto
- Science Research Center, Kochi University, Nankoku 783-8505, Kochi, Japan
| | - Koichi Ojima
- Division of Animal Products Research, NARO Institute of Livestock and Grassland Science (NILGS), Tsukuba 305-0901, Ibaraki, Japan
| | - Kazutsugu Matsukawa
- Department of Agriculture and Marine Science, Kochi University, Nankoku 783-8502, Kochi, Japan
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Ren Y, Liu Y, Zhang W, Ran J, Li L, Zhang Z. Sheathless CESI-MS versus LC-MS: Results of qualitative and quantitative analyses of the primary and secondary metabolites of Pleioblastus amarus bamboo shoots. Electrophoresis 2024; 45:266-274. [PMID: 37817363 DOI: 10.1002/elps.202300030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 09/05/2023] [Accepted: 09/11/2023] [Indexed: 10/12/2023]
Abstract
The bamboo shoot of Pleioblastus amarus (Keng) Keng f. is a medicinal and edible resource in China. In this study, three separation techniques were applied to identify the primary and secondary metabolites component of P. amarus bamboo shoots, including sheathless capillary electrophoresis electrospray ionization-mass spectrometry (CESI-MS), reverse-phase liquid chromatography-MS (RPLC-MS), and hydrophilic interaction liquid chromatography-MS (HILIC-MS). A total of 201 metabolites were identified by the three methods. Among those metabolites, 146 were identified by RPLC-MS, 85 were identified by HILIC-MS, and 46 were identified by sheathless CESI-MS. These methods were complementary and had a linear coefficient. CESI-MS presented advantages in the identification of isomers, high sensitivity, very low sample usage, and good detection of polar and nonpolar metabolites, showing its unique applications in food analysis and prospects in metabolic research.
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Affiliation(s)
- Yan Ren
- College of Pharmacy, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Ying Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Analytical Instrumentation Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, P. R. China
| | - Wenming Zhang
- College of Pharmacy, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Junfeng Ran
- College of Pharmacy, Southwest Minzu University, Chengdu, Sichuan, P. R. China
| | - Li Li
- The Sixth People's Hospital of Hengshui, Hengshui, Hebei, P. R. China
| | - Zhidan Zhang
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Systems Biology Centre, Technical Support Core Facilities, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, P. R. China
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Oishi K, Yajima Y, Yoshida Y, Hagihara H, Miyakawa T, Higo-Yamamoto S, Toyoda A. Metabolic profiles of saliva in male mouse models of chronic sleep disorders induced by psychophysiological stress. Sci Rep 2023; 13:11156. [PMID: 37429932 PMCID: PMC10333369 DOI: 10.1038/s41598-023-38289-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 07/06/2023] [Indexed: 07/12/2023] Open
Abstract
Disordered sleep is a global social problem and an established significant risk factor for psychological and metabolic diseases. We profiled non-targeted metabolites in saliva from mouse models of chronic sleep disorder (CSD). We identified 288 and 55 metabolites using CE-FTMS and LC-TOFMS, respectively, among which concentrations of 58 (CE-FTMS) and three (LC-TOFMS) were significantly changed by CSD. Pathway analysis revealed that CSD significantly suppressed glycine, serine and threonine metabolism. Arginine and proline metabolic pathways were among those that were both upregulated and downregulated. Pathways of alanine, aspartate and glutamate metabolism, genetic information processing, and the TCA cycle tended to be downregulated, whereas histidine metabolism tended to be upregulated in mice with CSD. Pyruvate, lactate, malate, succinate and the glycemic amino acids alanine, glycine, methionine, proline, and threonine were significantly decreased, whereas 3-hydroxybutyric and 2-hydroxybutyric acids associated with ketosis were significantly increased, suggesting abnormal glucose metabolism in mice with CSD. Increases in the metabolites histamine and kynurenic acid that are associated with the central nervous system- and decreased glycine, might be associated with sleep dysregulation and impaired cognitive dysfunction in mice with CSD. Our findings suggested that profiling salivary metabolites could be a useful strategy for diagnosing CSD.
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Affiliation(s)
- Katsutaka Oishi
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan.
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.
- School of Integrative and Global Majors (SIGMA), University of Tsukuba, Tsukuba, Ibaraki, Japan.
| | - Yuhei Yajima
- College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
- Ibaraki Prefecture Livestock Research Center, Ishioka, Ibaraki, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Yuta Yoshida
- College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
| | - Hideo Hagihara
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Tsuyoshi Miyakawa
- Division of Systems Medical Science, Center for Medical Science, Fujita Health University, Toyoake, Aichi, Japan
| | - Sayaka Higo-Yamamoto
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Atsushi Toyoda
- College of Agriculture, Ibaraki University, Ami, Ibaraki, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
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Sugishita T, Tokunaga M, Kami K, Terai K, Yamamoto H, Shinohara H, Kinugasa Y. Determination of the Minimum Sample Amount for Capillary Electrophoresis-Fourier Transform Mass Spectrometry (CE-FTMS)-Based Metabolomics of Colorectal Cancer Biopsies. Biomedicines 2023; 11:1706. [PMID: 37371800 DOI: 10.3390/biomedicines11061706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
The minimum sample volume for capillary electrophoresis-Fourier transform mass spectrometry (CE-FTMS) useful for analyzing hydrophilic metabolites was investigated using samples obtained from colorectal cancer patients. One, two, five, and ten biopsies were collected from tumor and nontumor parts of the surgically removed specimens from each of the five patients who had undergone colorectal cancer surgery. Metabolomics was performed on the collected samples using CE-FTMS. To determine the minimum number of specimens based on data volume and biological interpretability, we compared the number of annotated metabolites in each sample with different numbers of biopsies and conducted principal component analysis (PCA), hierarchical cluster analysis (HCA), quantitative enrichment analysis (QEA), and random forest analysis (RFA). The number of metabolites detected in one biopsy was significantly lower than those in 2, 5, and 10 biopsies, whereas those detected among 2, 5, and 10 pieces were not significantly different. Moreover, a binary classification model developed by RFA based on 2-biopsy data perfectly distinguished tumor and nontumor samples with 5- and 10-biopsy data. Taken together, two biopsies would be sufficient for CE-FTMS-based metabolomics from a data content and biological interpretability viewpoint, which opens the gate of biopsy metabolomics for practical clinical applications.
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Affiliation(s)
- Tetsuo Sugishita
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Masanori Tokunaga
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Kenjiro Kami
- Human Metabolome Technologies, Inc., Tsuruoka 997-0052, Japan
| | - Kozue Terai
- Human Metabolome Technologies, Inc., Tsuruoka 997-0052, Japan
| | | | - Hajime Shinohara
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo 113-8510, Japan
| | - Yusuke Kinugasa
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University, 1-5-45, Yushima, Bunkyo, Tokyo 113-8510, Japan
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9
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Naito Y, Koyama S, Masuhiro K, Hirai T, Uenami T, Inoue T, Osa A, Machiyama H, Watanabe G, Sax N, Villa J, Kinugasa-Katayama Y, Nojima S, Yaga M, Hosono Y, Okuzaki D, Satoh S, Tsuda T, Nakanishi Y, Suga Y, Morita T, Fukushima K, Nishide M, Shiroyama T, Miyake K, Iwahori K, Hirata H, Nagatomo I, Yano Y, Tamiya M, Kumagai T, Takemoto N, Inohara H, Yamasaki S, Yamashita K, Aoshi T, Akbay EA, Hosen N, Shintani Y, Takamatsu H, Mori M, Takeda Y, Kumanogoh A. Tumor-derived semaphorin 4A improves PD-1-blocking antibody efficacy by enhancing CD8 + T cell cytotoxicity and proliferation. SCIENCE ADVANCES 2023; 9:eade0718. [PMID: 37205755 DOI: 10.1126/sciadv.ade0718] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have caused revolutionary changes in cancer treatment, but low response rates remain a challenge. Semaphorin 4A (Sema4A) modulates the immune system through multiple mechanisms in mice, although the role of human Sema4A in the tumor microenvironment remains unclear. This study demonstrates that histologically Sema4A-positive non-small cell lung cancer (NSCLC) responded significantly better to anti-programmed cell death 1 (PD-1) antibody than Sema4A-negative NSCLC. Intriguingly, SEMA4A expression in human NSCLC was mainly derived from tumor cells and was associated with T cell activation. Sema4A promoted cytotoxicity and proliferation of tumor-specific CD8+ T cells without terminal exhaustion by enhancing mammalian target of rapamycin complex 1 and polyamine synthesis, which led to improved efficacy of PD-1 inhibitors in murine models. Improved T cell activation by recombinant Sema4A was also confirmed using isolated tumor-infiltrating T cells from patients with cancer. Thus, Sema4A might be a promising therapeutic target and biomarker for predicting and promoting ICI efficacy.
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Affiliation(s)
- Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Kashiwa,Chiba, and Tokyo, Japan
| | - Kentaro Masuhiro
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Takashi Hirai
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takeshi Uenami
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Akio Osa
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hirotomo Machiyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Go Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research and Clinical Trial Center (EPOC), National Cancer Center, Kashiwa,Chiba, and Tokyo, Japan
| | - Nicolas Sax
- KOTAI Biotechnologies Inc., Suita, Osaka, Japan
| | | | - Yumi Kinugasa-Katayama
- Department of Cellular Immunology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Moto Yaga
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Yuki Hosono
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Molecular Immunology, WPI, IFReC, Osaka University, Suita, Osaka, Japan
- Department of Molecular Immunology, RIMD, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Single Cell Genomics, Human Immunology, WPI, IFReC, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Takeshi Tsuda
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yoshimitsu Nakanishi
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Yasuhiko Suga
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takayoshi Morita
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Kiyoharu Fukushima
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Host Defense, WPI, IFReC, Osaka University, Suita, Osaka, Japan
| | - Masayuki Nishide
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kota Iwahori
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yukihiro Yano
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Toru Kumagai
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Norihiko Takemoto
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Sho Yamasaki
- Laboratory of Molecular Immunology, WPI, IFReC, Osaka University, Suita, Osaka, Japan
- Department of Molecular Immunology, RIMD, Osaka University, Suita, Osaka, Japan
| | | | - Taiki Aoshi
- Department of Cellular Immunology, Research Institute for Microbial Diseases (RIMD), Osaka University, Suita, Osaka, Japan
| | - Esra A Akbay
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Naoki Hosen
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Laboratory of Cellular Immunotherapy, WPI, IFReC, Osaka University, Suita, Osaka, Japan
| | - Yasushi Shintani
- Department of General Thoracic Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hyota Takamatsu
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
| | - Masahide Mori
- Department of Thoracic Oncology, National Hospital Organization, Osaka Toneyama Medical Center, Toyonaka, Osaka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunology and Molecular Medicine, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immunopathology, World Premier International Research Center (WPI), Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
- Center for Infectious Diseases for Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology (AMED-CREST), Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS (CAMaD), Osaka University, Suita, Osaka, Japan
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10
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Oba Y, Koga T, Takano Y, Ogawa NO, Ohkouchi N, Sasaki K, Sato H, Glavin DP, Dworkin JP, Naraoka H, Tachibana S, Yurimoto H, Nakamura T, Noguchi T, Okazaki R, Yabuta H, Sakamoto K, Yada T, Nishimura M, Nakato A, Miyazaki A, Yogata K, Abe M, Okada T, Usui T, Yoshikawa M, Saiki T, Tanaka S, Terui F, Nakazawa S, Watanabe SI, Tsuda Y. Uracil in the carbonaceous asteroid (162173) Ryugu. Nat Commun 2023; 14:1292. [PMID: 36944653 PMCID: PMC10030641 DOI: 10.1038/s41467-023-36904-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/15/2023] [Indexed: 03/23/2023] Open
Abstract
The pristine sample from the near-Earth carbonaceous asteroid (162173) Ryugu collected by the Hayabusa2 spacecraft enabled us to analyze the pristine extraterrestrial material without uncontrolled exposure to the Earth's atmosphere and biosphere. The initial analysis team for the soluble organic matter reported the detection of wide variety of organic molecules including racemic amino acids in the Ryugu samples. Here we report the detection of uracil, one of the four nucleobases in ribonucleic acid, in aqueous extracts from Ryugu samples. In addition, nicotinic acid (niacin, a B3 vitamer), its derivatives, and imidazoles were detected in search for nitrogen heterocyclic molecules. The observed difference in the concentration of uracil between A0106 and C0107 may be related to the possible differences in the degree of alteration induced by energetic particles such as ultraviolet photons and cosmic rays. The present study strongly suggests that such molecules of prebiotic interest commonly formed in carbonaceous asteroids including Ryugu and were delivered to the early Earth.
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Affiliation(s)
- Yasuhiro Oba
- Institute of Low Temperature Science (ILTS), Hokkaido University, N19W8, Kita-ku, Sapporo, 060-0819, Japan.
| | - Toshiki Koga
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Yoshinori Takano
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan.
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Nanako O Ogawa
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Naohiko Ohkouchi
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima, Yokosuka, 237-0061, Japan
| | - Kazunori Sasaki
- Institute for Advanced Biosciences (IAB), Keio University, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hajime Sato
- Human Metabolome Technologies Inc., Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Daniel P Glavin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Jason P Dworkin
- Solar System Exploration Division, NASA Goddard Space Flight Center, Greenbelt, MD, 20771, USA
| | - Hiroshi Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Shogo Tachibana
- UTokyo Organization for Planetary and Space Science (UTOPS), University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Hisayoshi Yurimoto
- Department of Earth and Planetary Sciences, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tomoki Nakamura
- Department of Earth Material Science, Tohoku University, Sendai, 980-8578, Japan
| | - Takaaki Noguchi
- Department of Earth and Planetary Sciences, Kyoto University, Kyoto, 606-8502, Japan
| | - Ryuji Okazaki
- Department of Earth and Planetary Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hikaru Yabuta
- Department of Earth and Planetary Systems Science, Hiroshima University, 739-8526, Higashi-Hiroshima, Japan
| | - Kanako Sakamoto
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Toru Yada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masahiro Nishimura
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Aiko Nakato
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Akiko Miyazaki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Kasumi Yogata
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Masanao Abe
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tatsuaki Okada
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Tomohiro Usui
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Makoto Yoshikawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Takanao Saiki
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Satoshi Tanaka
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Fuyuto Terui
- Kanagawa Institute of Technology, Atsugi, 243-0292, Japan
| | - Satoru Nakazawa
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
| | - Sei-Ichiro Watanabe
- Graduate School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Yuichi Tsuda
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, 252-5210, Japan
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11
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Advances in capillary electrophoresis mass spectrometry for metabolomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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12
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Yoshida Y, Yajima Y, Kawakami K, Nakamura SI, Tsukahara T, Oishi K, Toyoda A. Salivary microRNA and Metabolic Profiles in a Mouse Model of Subchronic and Mild Social Defeat Stress. Int J Mol Sci 2022; 23:ijms232214479. [PMID: 36430957 PMCID: PMC9692636 DOI: 10.3390/ijms232214479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Identification of early biomarkers of stress is important for preventing mood and anxiety disorders. Saliva is an easy-to-collect and non-invasive diagnostic target. The aim of this study was to characterize the changes in salivary whole microRNAs (miRNAs) and metabolites in mice subjected to subchronic and mild social defeat stress (sCSDS). In this study, we identified seven upregulated and one downregulated miRNAs/PIWI-interacting RNA (piRNA) in the saliva of sCSDS mice. One of them, miR-208b-3p, which is reported as a reliable marker for myocardial infarction, was upregulated in the saliva of sCSDS mice. Histological analysis showed frequent myocardial interstitial fibrosis in the heart of such mice. In addition, gene ontology and pathway analyses suggested that the pathways related to energy metabolism, such as the oxidative phosphorylation and the pentose phosphate pathway, were significantly related to the miRNAs affected by sCSDS in saliva. In contrast, salivary metabolites were not significantly changed in the sCSDS mice, which is consistent with our previous metabolomic study on the plasma of sCSDS mice. Taken in the light of previous studies, the present study provides novel potential stress biomarkers for future diagnosis using saliva.
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Affiliation(s)
- Yuta Yoshida
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Mito 300-0393, Japan
| | - Yuhei Yajima
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Mito 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
| | - Kina Kawakami
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Mito 300-0393, Japan
| | | | | | - Katsutaka Oishi
- Healthy Food Science Research Group, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba 305-8566, Japan
- Department of Applied Biological Science, Graduate School of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Atsushi Toyoda
- Department of Food and Life Sciences, College of Agriculture, Ibaraki University, Mito 300-0393, Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo 183-8509, Japan
- Correspondence: ; Tel.: +81-29-888-8584; Fax: +81-29-888-8584
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13
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Noso S, Babaya N, Hiromine Y, Taketomo Y, Niwano F, Yoshida S, Ikegami H. Metabolic signatures of β-cell destruction in type 1 diabetes. J Diabetes Investig 2022; 14:48-57. [PMID: 36227003 PMCID: PMC9807153 DOI: 10.1111/jdi.13926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/24/2022] [Accepted: 09/27/2022] [Indexed: 01/07/2023] Open
Abstract
AIMS/INTRODUCTION In the development of type 1 diabetes, metabolites are significantly altered and might be involved in β-cell destruction and protection. We aimed to identify new metabolic markers of β-cell destruction in type 1 diabetes patients. MATERIALS AND METHODS A total of 33 participants were recruited for this cross-sectional observational study: 23 with type 1 diabetes, seven with type 2 diabetes and three healthy controls. Those with type 1 diabetes were further subdivided into three groups: new-onset, microsecretors and complete lack of endogenous insulin in type 1 diabetes. RESULTS Metabolomic analysis identified a total of 737 peaks, and partial least square analysis was successful in discriminating between the three groups of type 1 diabetes. Among the factor loadings discriminating type 1 diabetes, 3-phenylpropionic acid (r = 0.80, P = 4.7E-6 ) and hypotaurine (r = -0.484, P = 1.9E-2 ) strongly contributed to identifying new-onset type 1 diabetes, and 5-methylcytosine to identifying complete-lack type 1 diabetes (r = 0.586, P = 6.5E-3 ). Reporter operating characteristics analysis, including all type 1 diabetes, type 2 diabetes and healthy controls, showed that high 3-phenylpropionic acid (Pc <0.0001) and low hypotaurine (Pc <0.0001) were useful for identifying new-onset type 1 diabetes, and high 5-methylcytosine (Pc = 0.002) for the complete-lack type 1 diabetes. CONCLUSIONS In the present study, metabolic signatures were shown to be useful in identifying type 1 diabetes at different clinical stages, and 3-phenylpropionic acid and hypotaurine are novel biomarkers for identifying new-onset type 1 diabetes, suggesting the involvement of the gut bacterial environment, anti-oxidant mechanisms through the hypotaurine-taurine pathway and methylated deoxyribonucleic acid fragmentation in the process of β-cell destruction.
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Affiliation(s)
- Shinsuke Noso
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
| | - Naru Babaya
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
| | - Yoshihisa Hiromine
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
| | - Yasunori Taketomo
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
| | - Fumimaru Niwano
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
| | - Sawa Yoshida
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
| | - Hiroshi Ikegami
- Department of Endocrinology, Metabolism and DiabetesKindai University Faculty of MedicineOsakaJapan
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14
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Ohno K, Abdelhamid M, Zhou C, Jung CG, Michikawa M. Bifidobacterium breve MCC1274 Supplementation Increased the Plasma Levels of Metabolites with Potential Anti-Oxidative Activity in APP Knock-In Mice. J Alzheimers Dis 2022; 89:1413-1425. [DOI: 10.3233/jad-220479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: We previously reported the effects of a probiotic strain, Bifidobacterium breve MCC1274, in improving cognitive function in preclinical and clinical studies. Recently, we demonstrated that supplementation of this strain led to decreased amyloid-β production, attenuated microglial activation, and suppressed inflammation reaction in the brain of APP knock-in (App NL - G - F ) mice. Objective: In this study, we investigated the plasma metabolites to reveal the mechanism of action of this probiotic strain in this Alzheimer’s disease (AD)-like model. Methods: Three-month-old mice were orally supplemented with B. breve MCC1274 or saline for four months and their plasma metabolites were comprehensively analyzed using CE-FTMS and LC-TOFMS. Results: Principal component analysis showed a significant difference in the plasma metabolites between the probiotic and control groups (PERMANOVA, p = 0.03). The levels of soy isoflavones (e.g., genistein) and indole derivatives of tryptophan (e.g., 5-methoxyindoleacetic acid), metabolites with potent anti-oxidative activities were significantly increased in the probiotic group. Moreover, there were increased levels of glutathione-related metabolites (e.g., glutathione (GSSG)_divalent, ophthalmic acid) and TCA cycle-related metabolites (e.g., 2-Oxoglutaric acid, succinic acid levels) in the probiotic group. Similar alternations were observed in the wild-type mice by the probiotic supplementation. Conclusion: These results suggest that the supplementation of B. breve MCC1274 enhanced the bioavailability of potential anti-oxidative metabolites from the gut and addressed critical gaps in our understanding of the gut-brain axis underlying the mechanisms of the probiotic action of this strain in the improvement of cognitive function.
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Affiliation(s)
- Kazuya Ohno
- Department of Medicine for Community-Based Medical Education, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Mona Abdelhamid
- Department of Biochemistry, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Chunyu Zhou
- Department of Biochemistry, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Cha-Gyun Jung
- Department of Biochemistry, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Makoto Michikawa
- Department of Biochemistry, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
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15
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Elshamy YS, Strein TG, Holland LA, Li C, DeBastiani A, Valentine SJ, Li P, Lucas JA, Shaffer TA. Nanoflow Sheath Voltage-Free Interfacing of Capillary Electrophoresis and Mass Spectrometry for the Detection of Small Molecules. Anal Chem 2022; 94:11329-11336. [PMID: 35913997 PMCID: PMC9387528 DOI: 10.1021/acs.analchem.2c02074] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Coupling capillary electrophoresis (CE) to mass spectrometry (MS) is a powerful strategy to leverage a high separation efficiency with structural identification. Traditional CE-MS interfacing relies upon voltage to drive this process. Additionally, sheathless interfacing requires that the electrophoresis generates a sufficient volumetric flow to sustain the ionization process. Vibrating sharp-edge spray ionization (VSSI) is a new method to interface capillary electrophoresis to mass analyzers. In contrast to traditional interfacing, VSSI is voltage-free, making it straightforward for CE and MS. New nanoflow sheath CE-VSSI-MS is introduced in this work to reduce the reliance on the separation flow rate to facilitate the transfer of analyte to the MS. The nanoflow sheath VSSI spray ionization functions from 400 to 900 nL/min. Using the new nanoflow sheath reported here, volumetric flow rate through the separation capillary is less critical, allowing the use of a small (i.e., 20 to 25 μm) inner diameter separation capillary and enabling the use of higher separation voltages and faster analysis. Moreover, the use of a nanoflow sheath enables greater flexibility in the separation conditions. The nanoflow sheath is operated using aqueous solutions in the background electrolyte and in the sheath, demonstrating the separation can be performed under normal and reversed polarity in the presence or absence of electroosmotic flow. This includes the use of a wider pH range as well. The versatility of nanoflow sheath CE-VSSI-MS is demonstrated by separating cationic, anionic, and zwitterionic molecules under a variety of separation conditions. The detection sensitivity observed with nanoflow sheath CE-VSSI-MS is comparable to that obtained with sheathless CE-VSSI-MS as well as CE-MS separations with electrospray ionization interfacing. A bare fused silica capillary is used to separate cationic β-blockers with a near-neutral background electrolyte at concentrations ranging from 1.0 nM to 1.0 μM. Under acidic conditions, 13 amino acids are separated with normal polarity at a concentration ranging from 0.25 to 5 μM. Finally, separations of anionic compounds are demonstrated using reversed polarity under conditions of suppressed electroosmotic flow through the use of a semipermanent surface coating. With a near-neutral separation electrolyte, anionic nonsteroidal anti-inflammatory drugs are detected over a concentration range of 0.1 to 5.0 μM.
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Affiliation(s)
- Yousef S Elshamy
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Timothy G Strein
- Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Lisa A Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - John A Lucas
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
| | - Tyler A Shaffer
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26505, United States
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16
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Adil N, Siddiqui AJ, Musharraf SG. Metabolomics‐based Researches in Autoimmune Liver Disease: A
Mini‐Review. Scand J Immunol 2022. [DOI: 10.1111/sji.13208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nurmeen Adil
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
| | - Amna Jabbar Siddiqui
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
| | - Syed Ghulam Musharraf
- H. E. J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi Karachi Pakistan
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17
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Kumagai S, Koyama S, Itahashi K, Tanegashima T, Lin YT, Togashi Y, Kamada T, Irie T, Okumura G, Kono H, Ito D, Fujii R, Watanabe S, Sai A, Fukuoka S, Sugiyama E, Watanabe G, Owari T, Nishinakamura H, Sugiyama D, Maeda Y, Kawazoe A, Yukami H, Chida K, Ohara Y, Yoshida T, Shinno Y, Takeyasu Y, Shirasawa M, Nakama K, Aokage K, Suzuki J, Ishii G, Kuwata T, Sakamoto N, Kawazu M, Ueno T, Mori T, Yamazaki N, Tsuboi M, Yatabe Y, Kinoshita T, Doi T, Shitara K, Mano H, Nishikawa H. Lactic acid promotes PD-1 expression in regulatory T cells in highly glycolytic tumor microenvironments. Cancer Cell 2022; 40:201-218.e9. [PMID: 35090594 DOI: 10.1016/j.ccell.2022.01.001] [Citation(s) in RCA: 283] [Impact Index Per Article: 141.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/07/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
The balance of programmed death-1 (PD-1)-expressing CD8+ T cells and regulatory T (Treg) cells in the tumor microenvironment (TME) determines the clinical efficacy of PD-1 blockade therapy through the competition of their reactivation. However, factors that determine this balance remain unknown. Here, we show that Treg cells gain higher PD-1 expression than effector T cells in highly glycolytic tumors, including MYC-amplified tumors and liver tumors. Under low-glucose environments via glucose consumption by tumor cells, Treg cells actively absorbed lactic acid (LA) through monocarboxylate transporter 1 (MCT1), promoting NFAT1 translocation into the nucleus, thereby enhancing the expression of PD-1, whereas PD-1 expression by effector T cells was dampened. PD-1 blockade invigorated the PD-1-expressing Treg cells, resulting in treatment failure. We propose that LA in the highly glycolytic TME is an active checkpoint for the function of Treg cells in the TME via upregulation of PD-1 expression.
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MESH Headings
- Animals
- Biomarkers, Tumor
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/pathology
- Cell Line, Tumor
- Disease Models, Animal
- Fluorescent Antibody Technique
- Gene Expression Regulation, Neoplastic/drug effects
- Glycolysis
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Immune Checkpoint Inhibitors/therapeutic use
- Immune Checkpoint Proteins/metabolism
- Immunophenotyping
- Lactic Acid/metabolism
- Lactic Acid/pharmacology
- Lymphocyte Activation
- Lymphocyte Count
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphocytes, Tumor-Infiltrating/pathology
- Mice
- Molecular Targeted Therapy
- Prognosis
- Programmed Cell Death 1 Receptor/antagonists & inhibitors
- Programmed Cell Death 1 Receptor/genetics
- Programmed Cell Death 1 Receptor/metabolism
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Treatment Outcome
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/genetics
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Affiliation(s)
- Shogo Kumagai
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan; Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shohei Koyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan.
| | - Kota Itahashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Tokiyoshi Tanegashima
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Yi-Tzu Lin
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yosuke Togashi
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takahiro Kamada
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takuma Irie
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Genki Okumura
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Hidetoshi Kono
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Daisuke Ito
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Rika Fujii
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Sho Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Atsuo Sai
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shota Fukuoka
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Eri Sugiyama
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Go Watanabe
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Takuya Owari
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Hitomi Nishinakamura
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Daisuke Sugiyama
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Yuka Maeda
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan
| | - Akihito Kawazoe
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Hiroki Yukami
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Keigo Chida
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Yuuki Ohara
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuki Shinno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Yuki Takeyasu
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Masayuki Shirasawa
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Kenta Nakama
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Keiju Aokage
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Jun Suzuki
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Genichiro Ishii
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Takeshi Kuwata
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Naoya Sakamoto
- Pathology and Clinical Laboratories, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Masahito Kawazu
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Toshihide Ueno
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Taisuke Mori
- Department of Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Naoya Yamazaki
- Department of Dermatologic Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Masahiro Tsuboi
- Department of Thoracic Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Yasushi Yatabe
- Department of Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Takahiro Kinoshita
- Department of Gastric Surgery, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Toshihiko Doi
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Kohei Shitara
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Chiba 277-8577, Japan
| | - Hiroyuki Mano
- Division of Cellular Signaling, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroyoshi Nishikawa
- Division of Cancer Immunology, Research Institute/Exploratory Oncology Research & Clinical Trial Center (EPOC), National Cancer Center, Tokyo 104-0045/Chiba 277-8577, Japan; Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan.
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18
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Ly R, Ly N, Sasaki K, Suzuki M, Kami K, Ohashi Y, Britz-McKibbin P. Nontargeted Serum Lipid Profiling of Nonalcoholic Steatohepatitis by Multisegment Injection-Nonaqueous Capillary Electrophoresis-Mass Spectrometry: A Multiplexed Separation Platform for Resolving Ionic Lipids. J Proteome Res 2021; 21:768-777. [PMID: 34676758 DOI: 10.1021/acs.jproteome.1c00682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New methods are needed for global lipid profiling due to the complex chemical structures and diverse physicochemical properties of lipids. Herein we introduce a robust data workflow to unambiguously select lipid features from serum ether extracts by multisegment injection-nonaqueous capillary electrophoresis-mass spectrometry (MSI-NACE-MS). An iterative three-stage screening strategy is developed for nontargeted lipid analyses when using multiplexed electrophoretic separations coupled to an Orbitrap mass analyzer under negative ion mode. This approach enables the credentialing of 270 serum lipid features annotated based on their accurate mass and relative migration time, including 128 ionic lipids reliably measured (median CV ≈ 13%) in most serum samples (>75%) from nonalcoholic steatohepatitis (NASH) patients (n = 85). A mobility map is introduced to classify charged lipid classes over a wide polarity range with selectivity complementary to chromatographic separations, including lysophosphatidic acids, phosphatidylcholines, phosphatidylinositols, phosphatidylethanolamines, and nonesterified fatty acids (NEFAs). Serum lipidome profiles were also used to differentiate high- from low-risk NASH patients using a k-means clustering algorithm, where elevated circulating NEFAs (e.g., palmitic acid) were associated with increased glucose intolerance, more severe liver fibrosis, and greater disease burden. MSI-NACE-MS greatly expands the metabolome coverage of conventional aqueous-based CE-MS protocols and is a promising platform for large-scale lipidomic studies.
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Affiliation(s)
- Ritchie Ly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Nicholas Ly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Kazunori Sasaki
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Makoto Suzuki
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Kenjiro Kami
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Yoshiaki Ohashi
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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19
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Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
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Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
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20
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Twenty years of amino acid determination using capillary electrophoresis: A review. Anal Chim Acta 2021; 1174:338233. [DOI: 10.1016/j.aca.2021.338233] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 01/14/2021] [Accepted: 01/16/2021] [Indexed: 12/28/2022]
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21
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Diederen T, Delabrière A, Othman A, Reid ME, Zamboni N. Metabolomics. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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De novo deoxyribonucleotide biosynthesis regulates cell growth and tumor progression in small-cell lung carcinoma. Sci Rep 2021; 11:13474. [PMID: 34188151 PMCID: PMC8242079 DOI: 10.1038/s41598-021-92948-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/07/2021] [Indexed: 11/09/2022] Open
Abstract
Deoxyribonucleotide biosynthesis from ribonucleotides supports the growth of active cancer cells by producing building blocks for DNA. Although ribonucleotide reductase (RNR) is known to catalyze the rate-limiting step of de novo deoxyribonucleotide triphosphate (dNTP) synthesis, the biological function of the RNR large subunit (RRM1) in small-cell lung carcinoma (SCLC) remains unclear. In this study, we established siRNA-transfected SCLC cell lines to investigate the anticancer effect of silencing RRM1 gene expression. We found that RRM1 is required for the full growth of SCLC cells both in vitro and in vivo. In particular, the deletion of RRM1 induced a DNA damage response in SCLC cells and decreased the number of cells with S phase cell cycle arrest. We also elucidated the overall changes in the metabolic profile of SCLC cells caused by RRM1 deletion. Together, our findings reveal a relationship between the deoxyribonucleotide biosynthesis axis and key metabolic changes in SCLC, which may indicate a possible link between tumor growth and the regulation of deoxyribonucleotide metabolism in SCLC.
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23
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Lichtenberg S, Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Metabolomic Laboratory-Developed Tests: Current Status and Perspectives. Metabolites 2021; 11:423. [PMID: 34206934 PMCID: PMC8305461 DOI: 10.3390/metabo11070423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Laboratory-developed tests (LDTs) are a subset of in vitro diagnostic devices, which the US Food and Drug Administration defines as "tests that are manufactured by and used within a single laboratory". The review describes the emergence and history of LDTs. The current state and development prospects of LDTs based on metabolomics are analyzed. By comparing LDTs with the scientific metabolomics study of human bio samples, the characteristic features of metabolomic LDT are shown, revealing its essence, strengths, and limitations. The possibilities for further developments and scaling of metabolomic LDTs and their potential significance for healthcare are discussed. The legal aspects of LDT regulation in the United States, European Union, and Singapore, demonstrating different approaches to this issue, are also provided. Based on the data presented in the review, recommendations were made on the feasibility and ways of further introducing metabolomic LDTs into practice.
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Affiliation(s)
- Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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24
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Shimada M, Miyagawa T, Kodama T, Toyoda H, Tokunaga K, Honda M. Metabolome analysis using cerebrospinal fluid from narcolepsy type 1 patients. Sleep 2021; 43:5837570. [PMID: 32412602 DOI: 10.1093/sleep/zsaa095] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/25/2020] [Indexed: 12/14/2022] Open
Abstract
Narcolepsy type 1 (NT1) is a hypersomnia characterized by excessive daytime sleepiness and cataplexy. Inappropriate regulation of fatty acid metabolism has been suggested to be involved in the pathophysiology of NT1, but the detailed mechanisms remain uncertain. Here we performed a metabolomic analysis of cerebrospinal fluid samples from 14 NT1 and 17 control subjects using a novel capillary electrophoresis coupled with Fourier transform mass spectrometry. A total of 268 metabolites were identified and the amount of histidine was the most significantly increased in NT1 patients (p = 4.0 × 10-4). Validation analysis using high-performance liquid chromatography (HPLC) including independent replication samples also identified the association of histidine (p = 2.02 × 10-3). Further, levels of histamine, which is synthesized from histidine, were also examined using HPLC and were found to be significantly decreased in NT1 patients (p = 6.12 × 10-4). Pathway analysis with nominally significant metabolites identified several pathways related to the metabolism of glycogenic amino acids, suggesting that glycogenesis is enhanced in NT1 as a compensatory mechanism for fatty acid metabolism. We performed further exploratory analysis, searching for metabolites associated with sleep variables from polysomnography and the multiple sleep latency test. As a result, 5'-deoxy-5'-methylthioadenosine showed a significant association with apnea-hypopnea index (p = 2.66 ×10-6). Moreover, gamma aminobutyric acid displayed a negative correlation with rapid eye movement sleep latency (REML), and thus might represent an intriguing target for future studies to elucidate how the controlling circuit of REM sleep is associated with abnormally short REML in NT1.
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Affiliation(s)
- Mihoko Shimada
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taku Miyagawa
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tohru Kodama
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hiromi Toyoda
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Makoto Honda
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.,Seiwa Hospital, Institute of Neuropsychiatry, Tokyo, Japan
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25
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Multiblock metabolomics: An approach to elucidate whole-body metabolism with multiblock principal component analysis. Comput Struct Biotechnol J 2021; 19:1956-1965. [PMID: 33995897 PMCID: PMC8086023 DOI: 10.1016/j.csbj.2021.04.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/20/2021] [Accepted: 04/04/2021] [Indexed: 12/16/2022] Open
Abstract
“Multiblock metabolomics” elucidates the global metabolic network in a whole body. “Multiblock metabolomics” combines LC/MS-based metabolomics with multiblock PCA. “Multiblock metabolomics” highlights and elicits organ-specific metabolism. TGs with less unsaturated fatty acids were highly accumulated in the diabetic liver.
Principal component analysis (PCA) is a useful tool for omics analysis to identify underlying factors and visualize relationships between biomarkers. However, this approach is limited in addressing life complexity and further improvement is required. This study aimed to develop a new approach that combines mass spectrometry-based metabolomics with multiblock PCA to elucidate the whole-body global metabolic network, thereby generating comparable metabolite maps to clarify the metabolic relationships among several organs. To evaluate the newly developed method, Zucker diabetic fatty (ZDF) rats (n = 6) were used as type 2 diabetic models and Sprague Dawley (SD) rats (n = 6) as controls. Metabolites in the heart, kidney, and liver were analyzed by capillary electrophoresis and liquid chromatography mass spectrometry, respectively, and the detected metabolites were analyzed by multiblock PCA. More than 300 metabolites were detected in the heart, kidney, and liver. When the metabolites obtained from the three organs were analyzed with multiblock PCA, the score and loading maps obtained were highly synchronized and their metabolism patterns were visually comparable. A significant finding in this study was the different expression patterns in lipid metabolism among the three organs; notably triacylglycerols with polyunsaturated fatty acids or less unsaturated fatty acids showed specific accumulation patterns depending on the organs.
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Key Words
- AMP, adenosine monophosphate
- Biomarkers
- CE/MS, capillary electrophoresis mass spectrometry
- CV, coefficient of variation
- ESI, electrospray ionization
- FABP, fatty acid-binding protein
- GC/MS, gas chromatography mass spectrometry
- LC/MS, liquid chromatography mass spectrometry
- Mass spectrometry
- Metabolomics
- Multiblock PCA
- PCA, principal component analysis
- PPAR, peroxisome proliferator-activated receptor
- QC, quality control
- SD, Sprague Dawley
- TCA, tricarboxylic acid. CoA, coenzyme A
- TG, triacylglycerol
- Type 2 Diabetes
- UPLC, ultra-performance liquid chromatography
- ZDF, Zucker diabetic fatty
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26
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Shanmuganathan M, Kroezen Z, Gill B, Azab S, de Souza RJ, Teo KK, Atkinson S, Subbarao P, Desai D, Anand SS, Britz-McKibbin P. The maternal serum metabolome by multisegment injection-capillary electrophoresis-mass spectrometry: a high-throughput platform and standardized data workflow for large-scale epidemiological studies. Nat Protoc 2021; 16:1966-1994. [PMID: 33674789 DOI: 10.1038/s41596-020-00475-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/24/2020] [Indexed: 01/31/2023]
Abstract
A standardized data workflow is described for large-scale serum metabolomic studies using multisegment injection-capillary electrophoresis-mass spectrometry. Multiplexed separations increase throughput (<4 min/sample) for quantitative determination of 66 polar/ionic metabolites in serum filtrates consistently detected (coefficient of variance (CV) <30%) with high frequency (>75%) from a multi-ethnic cohort of pregnant women (n = 1,004). We outline a validated protocol implemented in four batches over a 7-month period that includes details on preventive maintenance, sample workup, data preprocessing and metabolite authentication. We achieve stringent quality control (QC) and robust batch correction of long-term signal drift with good mutual agreement for a wide range of metabolites, including serum glucose as compared to a clinical chemistry analyzer (mean bias = 11%, n = 668). Control charts for a recovery standard (mean CV = 12%, n = 2,412) and serum metabolites in QC samples (median CV = 13%, n = 202) demonstrate acceptable intermediate precision with a median intraclass coefficient of 0.87. We also report reference intervals for 53 serum metabolites from a diverse population of women in their second trimester of pregnancy.
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Affiliation(s)
- Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zachary Kroezen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Biban Gill
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Sandi Azab
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Russell J de Souza
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada.,Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - Koon K Teo
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Stephanie Atkinson
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Padmaja Subbarao
- Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Dipika Desai
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Sonia S Anand
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada.,Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada.,Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada.
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27
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Recent (2018-2020) development in capillary electrophoresis. Anal Bioanal Chem 2021; 414:115-130. [PMID: 33754195 PMCID: PMC7984737 DOI: 10.1007/s00216-021-03290-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 12/14/2022]
Abstract
Development of new capillary electrophoresis (CE) methodology and instrumentation, as well as application of CE to solve new problems, remains an active research area because of the attractive features of CE compared to other separation techniques. In this review, we focus on the representative works about sample preconcentration, separation media or capillary coating development, detector construction, and multidimensional separation in CE, which are judiciously selected from the papers published in 2018–2020.
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28
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Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Mass spectrometry-based metabolomics diagnostics - myth or reality? Expert Rev Proteomics 2021; 18:7-12. [PMID: 33653222 DOI: 10.1080/14789450.2021.1893695] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
ABSTACTIntroduction: Metabolomics, one of the most high-promising technologies, is the most recently developed post-genomics discipline for developing new diagnostic tests for future implementation in medicine. More than 2,000 scientific papers, using mass spectrometry-based (MS-based) metabolomics analysis for human disease diagnostics, have been published during the past two decades, and almost every metabolomics study shows high diagnostic accuracy. However, despite the great results and promising perspectives, there are currently no diagnostic tests based on metabolomics that have been approved and introduced into clinics.Areas covered: In this report, the advantages and challenges of MS-based metabolomics are discussed with a focus on its developing role in diagnostics, and the current trends in implementing metabolomics diagnostics in the clinic.Expert opinion: In the development of new clinical diagnostics tests, MS-based metabolomics has potential as both a preliminary discovery base for routine testing and a multi-test prototype, which is hoped to be introduced into clinical practice in the near future. A laboratory-developed test (LDT) is one possible way that multi-testing could be developed.
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Affiliation(s)
- Oxana P Trifonova
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Dmitri L Maslov
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Elena E Balashova
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
| | - Petr G Lokhov
- Analytical Branch, Laboratory of Mass Spectrometry-based Metabolomic Diagnostic, Institute of Biomedical Chemistry, Moscow, Russia
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29
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Someya S, Tohyama S, Kameda K, Tanosaki S, Morita Y, Sasaki K, Kang MI, Kishino Y, Okada M, Tani H, Soma Y, Nakajima K, Umei T, Sekine O, Moriwaki T, Kanazawa H, Kobayashi E, Fujita J, Fukuda K. Tryptophan Metabolism Regulates Proliferative Capacity of Human Pluripotent Stem Cells. iScience 2021; 24:102090. [PMID: 33615198 PMCID: PMC7878994 DOI: 10.1016/j.isci.2021.102090] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/09/2020] [Accepted: 01/18/2021] [Indexed: 11/27/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have a unique metabolic signature for maintenance of pluripotency, self-renewal, and survival. Although hPSCs could be potentially used in regenerative medicine, the prohibitive cost associated with large-scale cell culture presents a major barrier to the clinical application of hPSC. Moreover, without a fully characterized metabolic signature, hPSC culture conditions are not optimized. Here, we performed detailed amino acid profiling and found that tryptophan (TRP) plays a key role in the proliferation with maintenance of pluripotency. In addition, metabolome analyses revealed that intra- and extracellular kynurenine (KYN) is decreased under TRP-supplemented conditions, whereas N-formylkynurenine (NFK), the upstream metabolite of KYN, is increased thereby contributing to proliferation promotion. Taken together, we demonstrate that TRP is indispensable for survival and proliferation of hPSCs. A deeper understanding of TRP metabolism will enable cost-effective large-scale production of hPSCs, leading to advances in regenerative medicine. TRP is the only AA that enables enhanced hPSC proliferation by supplementation hPSCs proliferate with pluripotency after long-term culture in TRP supplementation The proliferative properties of hPSCs are independent of AhR signaling TRP-derived NFK contributes to enhanced hPSC proliferation
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Affiliation(s)
- Shota Someya
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Shugo Tohyama
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Department of Organ Fabrication, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Kotaro Kameda
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Sho Tanosaki
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Yuika Morita
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Kazunori Sasaki
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Moon-Il Kang
- Human Metabolome Technologies, Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Yoshikazu Kishino
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Marina Okada
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Hidenori Tani
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Yusuke Soma
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Kazuaki Nakajima
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Tomohiko Umei
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Otoya Sekine
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Taijun Moriwaki
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Hideaki Kanazawa
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Eiji Kobayashi
- Department of Organ Fabrication, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Jun Fujita
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Endowed Course for Severe Heart Failure Treatment II, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
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30
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Okamoto N, Ikenouchi A, Watanabe K, Igata R, Fujii R, Yoshimura R. A Metabolomics Study of Serum in Hospitalized Patients With Chronic Schizophrenia. Front Psychiatry 2021; 12:763547. [PMID: 34975570 PMCID: PMC8714673 DOI: 10.3389/fpsyt.2021.763547] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/15/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose: Metabolomics has attracted attention as a new method for understanding the molecular mechanisms of psychiatric disorders. Current metabolomics technology allows us to measure over hundreds of metabolites at a time and is a useful indicator of the consequences of complex and continuous changes in metabolic profiles due to the execution of genomic information and external factors of biological activity. Therefore, metabolomics is imperative to the discovery of biomarkers and mechanisms associated with pathophysiological processes. In this study, we investigated metabolites changes in hospitalized patients with chronic schizophrenia compared to that in healthy controls, and examined the correlations between the metabolites and psychiatric symptoms. Patients and Methods: Thirty patients with schizophrenia and ten healthy controls participated in this study between September 2019 and June 2020. The mean duration of disease in patients with schizophrenia was 26 years. Clinical and neuropsychiatric symptoms of patients with schizophrenia were assessed using the Positive and Negative Syndrome Scale (PANSS). Metabolomics was conducted using Capillary Electrophoresis Fourier Transform Mass Spectrometry (CE-FTMS), using serum samples from patients with schizophrenia and healthy controls. Metabolomics assigned a candidate compound to the 446 (cation 279, anion 167) peaks. Hierarchical cluster analysis (HCA), principal component analysis (PCA), logistic regression analysis, receiver operating characteristic (ROC) analysis, and linear regression analysis were used to analyze the metabolites changes, identifying the disease and the relationship between metabolites and psychiatric symptoms. Results: HCA showed that approximately 60% of metabolites had lower peak values in patients with schizophrenia than in healthy controls. Glutamate metabolism and the urea cycle had the highest proportions in the metabolic pathway, which decreased in patients with schizophrenia. PCA showed a clear separation between patients with schizophrenia and healthy controls in the first principal component (the contribution ratio of the first principal component was 15.9%). Logistic regression analysis suggested that the first principal component was a predictor of disease (odds = 1.36, 95%CI = 1.11-1.67, p = 0.0032). ROC analysis showed a sensitivity of 93% and a specificity of 100% for the diagnosis of schizophrenia with a cut-off value of the first principal component; -3.33 (AUC = 0.95). We extracted the high factor loading for the first principal component. Gamma-glutamyl-valine (γ-Glu-Val) was significantly negatively correlated with PANSS total scores (r = -0.45, p = 0.012) and PANSS general scores (r = -0.49, p = 0.0055). Gamma-glutamyl-phenylalanine (γ-Glu-Phe) was significantly negatively correlated with PANSS total score (r = -0.40, p = 0.031) and PANSS general score (r = -0.41, p = 0.025). Tetrahydrouridine was significantly positively correlated with PANSS negative scores (r = 0.53, p = 0.0061). Conclusion: Metabolites changes in hospitalized patients with chronic schizophrenia showed extensive and generalized declines. Glutamate metabolism and the urea cycle had the highest proportions in the metabolic pathway, which decreased in the schizophrenia group. Metabolomic analysis was useful to identify chronic schizophrenia. Some glutamate compound metabolites had a relationship with psychiatric symptoms.
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Affiliation(s)
- Naomichi Okamoto
- Medical Center for Dementia, University Hospital, University of Occupational and Environmental Health, Kitakyushu, Japan.,Department of Psychiatry, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Atsuko Ikenouchi
- Medical Center for Dementia, University Hospital, University of Occupational and Environmental Health, Kitakyushu, Japan.,Department of Psychiatry, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Keita Watanabe
- Open Innovation Laboratory, Kyoto University, Kyoto, Japan
| | - Ryohei Igata
- Department of Psychiatry, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Rintaro Fujii
- Department of Psychiatry, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Reiji Yoshimura
- Department of Psychiatry, University of Occupational and Environmental Health, Kitakyushu, Japan
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31
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Identification of intracellular cadmium transformation in HepG2 and MCF-7 cells. Talanta 2020; 218:121065. [PMID: 32797863 DOI: 10.1016/j.talanta.2020.121065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 01/14/2023]
Abstract
It is of significance to elucidate or understand the intracellular transformation & migration behaviors of heavy metals in specific cells. Herein, we report the fast and efficient separation of cadmium-metallothioneins (Cd-MTs) and Cd2+in cell lysate by a short column capillary electrophoresis (SC-CE), followed by coupling with inductively coupled plasma mass spectrometry (ICP-MS) to facilitate the speciation of intracellular cadmium species. The incorporation of sodium dodecyl sulfate (SDS) in running buffer significantly reduces the peak width of Cd2+from 170 s to 26 s in the electrophoretogram, causing a 5.3-fold improvement on the sensitivity. Linear ranges of 0.5-50 mg L-1,0.056-5.6 mg L-1 and 0.1-10 mg L-1 are achieved for MTs, Cd-MTs (Cd) and Cd2+, respectively, along with detection limits of 0.013 mg L-1 for Cd-MTs (Cd) and 0.020 mg L-1 for Cd2+. The transformation of cadmium in HepG2 and MCF-7 cells is evaluated after their incubation with Cd2+ reinforced culture medium. Intracellular free Cd2+ cation and Cd-MTs are identified, along with Cd2+ transformation to Cd-glutathione (GSH) adduct/complex, as further demonstrated by ESI-MS.
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Roberts JA, Varma VR, Huang CW, An Y, Oommen A, Tanaka T, Ferrucci L, Elango P, Takebayashi T, Harada S, Iida M, Thambisetty M. Blood Metabolite Signature of Metabolic Syndrome Implicates Alterations in Amino Acid Metabolism: Findings from the Baltimore Longitudinal Study of Aging (BLSA) and the Tsuruoka Metabolomics Cohort Study (TMCS). Int J Mol Sci 2020; 21:ijms21041249. [PMID: 32070008 PMCID: PMC7072861 DOI: 10.3390/ijms21041249] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/07/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Rapid lifestyle and dietary changes have contributed to a rise in the global prevalence of metabolic syndrome (MetS), which presents a potential healthcare crisis, owing to its association with an increased burden of multiple cardiovascular and neurological diseases. Prior work has identified the role that genetic, lifestyle, and environmental factors can play in the prevalence of MetS. Metabolomics is an important tool to study alterations in biochemical pathways intrinsic to the pathophysiology of MetS. We undertook a metabolomic study of MetS in serum samples from two ethnically distinct, well-characterized cohorts—the Baltimore Longitudinal Study of Aging (BLSA) from the U.S. and the Tsuruoka Metabolomics Cohort Study (TMCS) from Japan. We used multivariate logistic regression to identify metabolites that were associated with MetS in both cohorts. Among the top 25 most significant (lowest p-value) metabolite associations with MetS in each cohort, we identified 18 metabolites that were shared between TMCS and BLSA, the majority of which were classified as amino acids. These associations implicate multiple biochemical pathways in MetS, including branched-chain amino acid metabolism, glutathione production, aromatic amino acid metabolism, gluconeogenesis, and the tricarboxylic acid cycle. Our results suggest that fundamental alterations in amino acid metabolism may be central features of MetS.
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Affiliation(s)
- Jackson A. Roberts
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (J.A.R.); (V.R.V.)
| | - Vijay R. Varma
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (J.A.R.); (V.R.V.)
| | - Chiung-Wei Huang
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (C.-W.H.); (Y.A.)
| | - Yang An
- Brain Aging and Behavior Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (C.-W.H.); (Y.A.)
| | - Anup Oommen
- Glycoscience Group, National Centre for Biomedical Engineering Science, National University of Ireland Galway, Galway H91-TK33, Ireland;
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (T.T.); (L.F.); (P.E.)
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (T.T.); (L.F.); (P.E.)
| | - Palchamy Elango
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (T.T.); (L.F.); (P.E.)
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University, Tokyo 160-8282, Japan; (T.T.); (S.H.); (M.I.)
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University, Tokyo 160-8282, Japan; (T.T.); (S.H.); (M.I.)
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University, Tokyo 160-8282, Japan; (T.T.); (S.H.); (M.I.)
| | - Madhav Thambisetty
- Clinical and Translational Neuroscience Section, Laboratory of Behavioral Neuroscience, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (J.A.R.); (V.R.V.)
- Correspondence: ; Tel.: +1-(410)-558-8572; Fax: +1-(410)-558-8302
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33
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Teclemariam ET, Pergande MR, Cologna SM. Considerations for mass spectrometry-based multi-omic analysis of clinical samples. Expert Rev Proteomics 2020; 17:99-107. [PMID: 31996049 DOI: 10.1080/14789450.2020.1724540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction: The role of mass spectrometry in biomolecule analysis has become paramount over the last several decades ranging in the analysis across model systems and human specimens. Accordingly, the presence of mass spectrometers in clinical laboratories has also expanded alongside the number of researchers investigating the protein, lipid, and metabolite composition of an array of biospecimens. With this increase in the number of omic investigations, it is important to consider the entire experimental strategy from sample collection and storage, data collection and analysis.Areas covered: In this short review, we outline considerations for working with clinical (e.g. human) specimens including blood, urine, and cerebrospinal fluid, with emphasis on sample handling, profiling composition, targeted measurements and relevance to disease. Discussions of integrated genomic or transcriptomic datasets are not included. A brief commentary is also provided regarding new technologies with clinical relevance.Expert opinion: The role of mass spectrometry to investigate clinically related specimens is on the rise and the ability to integrate multiple omics datasets from mass spectrometry measurements will be crucial to further understanding human health and disease.
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Affiliation(s)
- Esei T Teclemariam
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Melissa R Pergande
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA.,Laboratory of Integrated Neuroscience, University of Illinois at Chicago, Chicago, IL, USA
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34
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Kristoff CJ, Bwanali L, Veltri LM, Gautam GP, Rutto PK, Newton EO, Holland LA. Challenging Bioanalyses with Capillary Electrophoresis. Anal Chem 2020; 92:49-66. [PMID: 31698907 PMCID: PMC6995690 DOI: 10.1021/acs.analchem.9b04718] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Courtney J. Kristoff
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lloyd Bwanali
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lindsay M. Veltri
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Gayatri P. Gautam
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Patrick K. Rutto
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Ebenezer O. Newton
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
| | - Lisa A. Holland
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia 26506, United States
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35
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Zhang XW, Li QH, Xu ZD, Dou JJ. Mass spectrometry-based metabolomics in health and medical science: a systematic review. RSC Adv 2020; 10:3092-3104. [PMID: 35497733 PMCID: PMC9048967 DOI: 10.1039/c9ra08985c] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/14/2019] [Indexed: 01/15/2023] Open
Abstract
Metabolomics is the study of the investigation of small molecules derived from cellular and organism metabolism, which reflects the outcomes of the complex network of biochemical reactions in living systems.
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Affiliation(s)
- Xi-wu Zhang
- Institute of Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Qiu-han Li
- Institute of Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Zuo-di Xu
- Institute of Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Jin-jin Dou
- Institute of Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
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36
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Dysregulation of multiple metabolic networks related to brain transmethylation and polyamine pathways in Alzheimer disease: A targeted metabolomic and transcriptomic study. PLoS Med 2020; 17:e1003012. [PMID: 31978055 PMCID: PMC6980402 DOI: 10.1371/journal.pmed.1003012] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 12/20/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND There is growing evidence that Alzheimer disease (AD) is a pervasive metabolic disorder with dysregulation in multiple biochemical pathways underlying its pathogenesis. Understanding how perturbations in metabolism are related to AD is critical to identifying novel targets for disease-modifying therapies. In this study, we test whether AD pathogenesis is associated with dysregulation in brain transmethylation and polyamine pathways. METHODS AND FINDINGS We first performed targeted and quantitative metabolomics assays using capillary electrophoresis-mass spectrometry (CE-MS) on brain samples from three groups in the Baltimore Longitudinal Study of Aging (BLSA) (AD: n = 17; Asymptomatic AD [ASY]: n = 13; Control [CN]: n = 13) (overall 37.2% female; mean age at death 86.118 ± 9.842 years) in regions both vulnerable and resistant to AD pathology. Using linear mixed-effects models within two primary brain regions (inferior temporal gyrus [ITG] and middle frontal gyrus [MFG]), we tested associations between brain tissue concentrations of 26 metabolites and the following primary outcomes: group differences, Consortium to Establish a Registry for Alzheimer's Disease (CERAD) (neuritic plaque burden), and Braak (neurofibrillary pathology) scores. We found significant alterations in concentrations of metabolites in AD relative to CN samples, as well as associations with severity of both CERAD and Braak, mainly in the ITG. These metabolites represented biochemical reactions in the (1) methionine cycle (choline: lower in AD, p = 0.003; S-adenosyl methionine: higher in AD, p = 0.005); (2) transsulfuration and glutathione synthesis (cysteine: higher in AD, p < 0.001; reduced glutathione [GSH]: higher in AD, p < 0.001); (3) polyamine synthesis/catabolism (spermidine: higher in AD, p = 0.004); (4) urea cycle (N-acetyl glutamate: lower in AD, p < 0.001); (5) glutamate-aspartate metabolism (N-acetyl aspartate: lower in AD, p = 0.002); and (6) neurotransmitter metabolism (gamma-amino-butyric acid: lower in AD, p < 0.001). Utilizing three Gene Expression Omnibus (GEO) datasets, we then examined mRNA expression levels of 71 genes encoding enzymes regulating key reactions within these pathways in the entorhinal cortex (ERC; AD: n = 25; CN: n = 52) and hippocampus (AD: n = 29; CN: n = 56). Complementing our metabolomics results, our transcriptomics analyses also revealed significant alterations in gene expression levels of key enzymatic regulators of biochemical reactions linked to transmethylation and polyamine metabolism. Our study has limitations: our metabolomics assays measured only a small proportion of all metabolites participating in the pathways we examined. Our study is also cross-sectional, limiting our ability to directly test how AD progression may impact changes in metabolite concentrations or differential-gene expression. Additionally, the relatively small number of brain tissue samples may have limited our power to detect alterations in all pathway-specific metabolites and their genetic regulators. CONCLUSIONS In this study, we observed broad dysregulation of transmethylation and polyamine synthesis/catabolism, including abnormalities in neurotransmitter signaling, urea cycle, aspartate-glutamate metabolism, and glutathione synthesis. Our results implicate alterations in cellular methylation potential and increased flux in the transmethylation pathways, increased demand on antioxidant defense mechanisms, perturbations in intermediate metabolism in the urea cycle and aspartate-glutamate pathways disrupting mitochondrial bioenergetics, increased polyamine biosynthesis and breakdown, as well as abnormalities in neurotransmitter metabolism that are related to AD.
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Abstract
In this chapter, we summarize data preprocessing and data analysis strategies used for analysis of NMR data for metabolomics studies. Metabolomics consists of the analysis of the low molecular weight compounds in cells, tissues, or biological fluids, and has been used to reveal biomarkers for early disease detection and diagnosis, to monitor interventions, and to provide information on pathway perturbations to inform mechanisms and identifying targets. Metabolic profiling (also termed metabotyping) involves the analysis of hundreds to thousands of molecules using mainly state-of-the-art mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy technologies. While NMR is less sensitive than mass spectrometry, NMR does provide a wealth of complex and information rich metabolite data. NMR data together with the use of conventional statistics, modeling methods, and bioinformatics tools reveals biomarker and mechanistic information. A typical NMR spectrum, with up to 64k data points, of a complex biological fluid or an extract of cells and tissues consists of thousands of sharp signals that are mainly derived from small molecules. In addition, a number of advanced NMR spectroscopic methods are available for extracting information on high molecular weight compounds such as lipids or lipoproteins. There are numerous data preprocessing, data reduction, and analysis methods developed and evolving in the field of NMR metabolomics. Our goal is to provide an extensive summary of NMR data preprocessing and analysis strategies by providing examples and open source and commercially available analysis software and bioinformatics tools.
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Affiliation(s)
- Wimal Pathmasiri
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA.
| | - Kristine Kay
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan McRitchie
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Susan Sumner
- Department of Nutrition, School of Public Health, NIH Eastern Regional Comprehensive Metabolomics Resource Core (ERCMRC), Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
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Kartsova L, Makeeva D, Davankov V. Nano-sized polymer and polymer-coated particles in electrokinetic separations. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ferré S, González-Ruiz V, Guillarme D, Rudaz S. Analytical strategies for the determination of amino acids: Past, present and future trends. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1132:121819. [PMID: 31704619 DOI: 10.1016/j.jchromb.2019.121819] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/25/2019] [Accepted: 09/27/2019] [Indexed: 12/27/2022]
Abstract
This review describes the analytical methods that have been developed over the years to tackle the high polarity and non-chromophoric nature of amino acids (AAs). First, the historical methods are briefly presented, with a strong focus on the use of derivatization reagents to make AAs detectable with spectroscopic techniques (ultraviolet and fluorescence) and/or sufficiently retained in reversed phase liquid chromatography. Then, an overview of the current analytical strategies for achiral separation of AAs is provided, in which mass spectrometry (MS) becomes the most widely used detection mode in combination with innovative liquid chromatography or capillary electrophoresis conditions to detect AAs at very low concentration in complex matrixes. Finally, some future trends of AA analysis are provided in the last section of the review, including the use of supercritical fluid chromatography (SFC), multidimensional liquid chromatography and electrophoretic separations, hyphenation of ion exchange chromatography to mass spectrometry, and use of ion mobility spectrometry mass spectrometry (IM-MS). Various application examples will also be presented throughout the review to highlight the benefits and limitations of these different analytical approaches for AAs determination.
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Affiliation(s)
- Sabrina Ferré
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland
| | - Víctor González-Ruiz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
| | - Davy Guillarme
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland.
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CMU - Rue Michel Servet 1, 1211 Geneva 4, Switzerland; Swiss Centre for Applied Human Toxicology (SCAHT), Switzerland
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40
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Pang H, Jia W, Hu Z. Emerging Applications of Metabolomics in Clinical Pharmacology. Clin Pharmacol Ther 2019; 106:544-556. [DOI: 10.1002/cpt.1538] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/18/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Huanhuan Pang
- School of Pharmaceutical Sciences Tsinghua University Beijing China
| | - Wei Jia
- Cancer Biology Program University of Hawaii Cancer Center Honolulu Hawaii USA
| | - Zeping Hu
- School of Pharmaceutical Sciences Tsinghua University Beijing China
- Tsinghua‐Peking Joint Center for Life Sciences Tsinghua University Beijing China
- Beijing Frontier Research Center for Biological Structure Tsinghua University Beijing China
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