1
|
Kozuki R, Sugimoto T, Goto H, Miyamoto N, Hirakawa Y, Umeno A, Idei M, Tagawa S, Namba F, Tani R, Ohmori M, Hamanaka A, Adachi S, Tomita M. Optimal index for detecting splenic involvement on 18F-fluorodeoxyglucose positron emission tomography/computed tomography imaging in diffuse large B-cell lymphoma. Medicine (Baltimore) 2024; 103:e37290. [PMID: 38428864 PMCID: PMC10906632 DOI: 10.1097/md.0000000000037290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024] Open
Abstract
Accurate clinical staging is important in diffuse large B-cell lymphoma (DLBCL) to adapt to optimal therapy. Splenic involvement of DLBCL has been recently more detectable with the advancement of a diagnostic scan by 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET)/computed tomography (CT). Our clinical question is whether splenic involvement was adequately diagnosed by FDG-PET/CT imaging. This retrospective study aimed to determine the optimal index for evaluating splenic involvement in patients with DLBCL. Patients with newly diagnosed DLBCL who were examined with FDG-PET/CT at diagnosis and the end of induction chemotherapy (EOI) was enrolled. The splenic involvement with the splenic FDG uptake value higher than that of the liver at diagnosis or with the decrease of splenic uptake at EOI by visual evaluation was evaluated as positive. The calculative evaluation of splenic involvement, based on the data of standardized uptake value (SUV) of the spleen, used maximum SUV (SUVmax), mean SUV (SUVmean), spleen total lesion glycolysis (spleen TLG), and spleen length. A change in each index following induction chemotherapy was expressed as an index. Receiver operating characteristic analysis was used to set the cutoff value for each index. This study included 52 patients. Spleen TLG (0.904) showed the best accuracy, followed by SUVmax (0.885) and SUVmean (0.885), among the 5 indexes for splenic involvement at diagnosis. Splenic involvement was predicted with a higher accuracy level (0.923) when selecting the cases with values higher than the cutoff level on both spleen TLG and SUVmax. The decision at EOI was more suitable by selecting both positive cases of ∆ TLG and ∆ SUVmax. Obtaining both the positive spleen TLG and SUVmax is recommended at diagnosis to predict splenic involvement. The assessment by ∆ spleen TLG and ∆ SUVmax seems to be optimal.
Collapse
Affiliation(s)
- Ryohei Kozuki
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Takeshi Sugimoto
- Department of Hematology and Oncology, Kita-Harima Medical Center, Hyogo, Japan
| | - Hideaki Goto
- Department of Hematology and Oncology, Kita-Harima Medical Center, Hyogo, Japan
- Department of Oncology and Hematology, Hyogo Prefectural HarimaHimeji General Medical Center, Himeji, Japan
| | - Naokazu Miyamoto
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Yuri Hirakawa
- Department of Hematology and Oncology, Kita-Harima Medical Center, Hyogo, Japan
| | - Akihiro Umeno
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Mari Idei
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Sumire Tagawa
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Fumiko Namba
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Ryuichiro Tani
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Mika Ohmori
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Akihiro Hamanaka
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Shuji Adachi
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| | - Masaru Tomita
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Hyogo, Japan
| |
Collapse
|
2
|
Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
Collapse
Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| |
Collapse
|
3
|
Hirata A, Harada S, Iida M, Kurihara A, Fukai K, Kuwabara K, Kato S, Matsumoto M, Sata M, Miyagawa N, Toki R, Edagawa S, Sugiyama D, Sato A, Hirayama A, Sugimoto M, Soga T, Tomita M, Okamura T, Takebayashi T. Association of Nonalcoholic Fatty Liver Disease with Arterial Stiffness and its Metabolomic Profiling in Japanese Community-Dwellers. J Atheroscler Thromb 2024:64616. [PMID: 38311416 DOI: 10.5551/jat.64616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
AIMS Nonalcoholic fatty liver disease (NAFLD) is known to be associated with atherosclerosis. This study focused on upstream changes in the process by which NAFLD leads to atherosclerosis. The study aimed to confirm the association between NAFLD and the cardio-ankle vascular index (CAVI), an indicator of subclinical atherosclerosis, and explore metabolites involved in both by assessing 94 plasma polar metabolites. METHODS A total of 928 Japanese community-dwellers (306 men and 622 women) were included in this study. The association between NAFLD and CAVI was examined using a multivariable regression model adjusted for confounders. Metabolites commonly associated with NAFLD and CAVI were investigated using linear mixed-effects models in which batch numbers of metabolite measurements were used as a random-effects variable, and false discovery rate-adjusted p-values were calculated. To determine the extent to which these metabolites mediated the association between NAFLD and CAVI, mediation analysis was conducted. RESULTS NAFLD was positively associated with CAVI (coefficients [95% Confidence intervals (CI)]=0.23 [0.09-0.37]; p=0.001). A total of 10 metabolites were involved in NAFLD and CAVI, namely, branched-chain amino acids (BCAAs; valine, leucine, and isoleucine), aromatic amino acids (AAAs; tyrosine and tryptophan), alanine, proline, glutamic acid, glycerophosphorylcholine, and 4-methyl-2-oxopentanoate. Mediation analysis showed that BCAAs mediated more than 20% of the total effect in the association between NAFLD and CAVI. CONCLUSIONS NAFLD was associated with a marker of atherosclerosis, and several metabolites related to insulin resistance, including BCAAs and AAAs, could be involved in the process by which NAFLD leads to atherosclerosis.
Collapse
Affiliation(s)
- Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Kota Fukai
- Department of Preventive Medicine, Tokai University School of Medicine
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Minako Matsumoto
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Mizuki Sata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Naoko Miyagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Ryota Toki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Shun Edagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Daisuke Sugiyama
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Faculty of Nursing and Medical Care, Keio University
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University
| | | | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University
- Institute of Medical Science, Tokyo Medical University
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University
- Faculty of Environment and Information Studies, Keio University
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University
- Faculty of Environment and Information Studies, Keio University
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| |
Collapse
|
4
|
Miyake A, Harada S, Sugiyama D, Matsumoto M, Hirata A, Miyagawa N, Toki R, Edagawa S, Kuwabara K, Okamura T, Sato A, Amano K, Hirayama A, Sugimoto M, Soga T, Tomita M, Arakawa K, Takebayashi T, Iida M. Reliability of Time-Series Plasma Metabolome Data over 6 Years in a Large-Scale Cohort Study. Metabolites 2024; 14:77. [PMID: 38276312 PMCID: PMC10819202 DOI: 10.3390/metabo14010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/16/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Studies examining long-term longitudinal metabolomic data and their reliability in large-scale populations are limited. Therefore, we aimed to evaluate the reliability of repeated measurements of plasma metabolites in a prospective cohort setting and to explore intra-individual concentration changes at three time points over a 6-year period. The study participants included 2999 individuals (1317 men and 1682 women) from the Tsuruoka Metabolomics Cohort Study, who participated in all three surveys-at baseline, 3 years, and 6 years. In each survey, 94 plasma metabolites were quantified for each individual and quality control (QC) sample. The coefficients of variation of QC, intraclass correlation coefficients, and change rates of QC were calculated for each metabolite, and their reliability was classified into three categories: excellent, fair to good, and poor. Seventy-six percent (71/94) of metabolites were classified as fair to good or better. Of the 39 metabolites grouped as excellent, 29 (74%) in men and 26 (67%) in women showed significant intra-individual changes over 6 years. Overall, our study demonstrated a high degree of reliability for repeated metabolome measurements. Many highly reliable metabolites showed significant changes over the 6-year period, suggesting that repeated longitudinal metabolome measurements are useful for epidemiological studies.
Collapse
Affiliation(s)
- Atsuko Miyake
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Daisuke Sugiyama
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
- Faculty of Nursing and Medical Care, Keio University, Kanagawa, Fujisawa 252-0883, Japan
- Graduate School of Health Management, Keio University, Kanagawa, Fujisawa 252-0883, Japan
| | - Minako Matsumoto
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Naoko Miyagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Ryota Toki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Shun Edagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
- Graduate School of Health Management, Keio University, Kanagawa, Fujisawa 252-0883, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Kaori Amano
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka 997-0052, Japan; (A.S.); (K.A.); (A.H.); (M.S.); (T.S.); (M.T.); (K.A.)
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
- Graduate School of Health Management, Keio University, Kanagawa, Fujisawa 252-0883, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan; (A.M.); (S.H.); (D.S.); (M.M.); (A.H.); (N.M.); (R.T.); (S.E.); (K.K.); (T.O.); (T.T.)
| |
Collapse
|
5
|
Harada S, Iida M, Miyagawa N, Hirata A, Kuwabara K, Matsumoto M, Okamura T, Edagawa S, Kawada Y, Miyake A, Toki R, Akiyama M, Kawai A, Sugiyama D, Sato Y, Takemura R, Fukai K, Ishibashi Y, Kato S, Kurihara A, Sata M, Shibuki T, Takeuchi A, Kohsaka S, Sawano M, Shoji S, Izawa Y, Katsumata M, Oki K, Takahashi S, Takizawa T, Maruya H, Nishiwaki Y, Kawasaki R, Hirayama A, Ishikawa T, Saito R, Sato A, Soga T, Sugimoto M, Tomita M, Komaki S, Ohmomo H, Ono K, Otsuka-Yamasaki Y, Shimizu A, Sutoh Y, Hozawa A, Kinoshita K, Koshiba S, Kumada K, Ogishima S, Sakurai-Yageta M, Tamiya G, Takebayashi T. Study Profile of the Tsuruoka Metabolomics Cohort Study (TMCS). J Epidemiol 2024:JE20230192. [PMID: 38191178 DOI: 10.2188/jea.je20230192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
The Tsuruoka Metabolomics Cohort Study (TMCS) is an ongoing population-based cohort study being conducted in the rural area of Yamagata Prefecture, Japan. This study aimed to enhance the precision prevention of multi-factorial, complex diseases, including non-communicable and aging-associated diseases, by improving risk stratification and prediction measures. At baseline, 11,002 participants aged 35-74 years were recruited in Tsuruoka City, Yamagata Prefecture, Japan, between 2012 and 2015, with an ongoing follow-up survey. Participants underwent various measurements, examinations, tests, and questionnaires on their health, lifestyle, and social factors. This study used an integrative approach with deep molecular profiling to identify potential biomarkers linked to phenotypes that underpin disease pathophysiology and provide better mechanistic insights into social health determinants. The TMCS incorporates multi-omics data, including genetic and metabolomic analyses of 10,933 participants and comprehensive data collection ranging from physical, psychological, behavioral, and social to biological data. The metabolome is used as a phenotypic probe because it is sensitive to changes in physiological and external conditions. The TMCS focuses on collecting outcomes for cardiovascular disease, cancer incidence and mortality, disability, functional decline due to aging and disease sequelae, and the variation in health status within the body represented by omics analysis that lies between exposure and disease. It contains several sub-studies on aging, heated tobacco products, and women's health. This study is notable for its robust design, high participation rate (89%), and long-term repeated surveys. Moreover, it contributes to precision prevention in Japan and East Asia as a well-established multi-omics platform.
Collapse
Affiliation(s)
- Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| | - Naoko Miyagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Minako Matsumoto
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Shun Edagawa
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Yoko Kawada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Atsuko Miyake
- Department of Obstetrics and Gynecology, Keio University School of Medicine
| | - Ryota Toki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Miki Akiyama
- Institute for Advanced Biosciences, Keio University
- Faculty of Environment and Information Studies, Keio University
| | - Atsuki Kawai
- Institute for Advanced Biosciences, Keio University
| | - Daisuke Sugiyama
- Faculty of Nursing and Medical Care and Graduate School of Health Management, Keio University
| | - Yasunori Sato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital
| | - Ryo Takemura
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital
| | - Kota Fukai
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Yoshiki Ishibashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Mizuki Sata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Takuma Shibuki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Ayano Takeuchi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
| | - Shun Kohsaka
- Department of Cardiology, Keio University School of Medicine
| | - Mitsuaki Sawano
- Department of Cardiology, Keio University School of Medicine
| | - Satoshi Shoji
- Department of Cardiology, Keio University School of Medicine
- Duke Clinical Research Institute
| | | | | | - Koichi Oki
- Department of Neurology, Keio University School of Medicine
- Department of Neurology, Tokyo Saiseikai Central Hospital
| | - Shinichi Takahashi
- Department of Neurology, Keio University School of Medicine
- Department of Neurology and Stroke, Saitama Medical University International Medical Center
| | | | | | - Yuji Nishiwaki
- Department of Environmental and Occupational Health, School of Medicine, Toho University
| | - Ryo Kawasaki
- Division of Public Health, Department of Social Medicine, Graduate School of Medicine, Osaka University
| | | | | | | | - Asako Sato
- Institute for Advanced Biosciences, Keio University
| | | | | | | | - Shohei Komaki
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences of Iwate Medical University
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences of Iwate Medical University
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Kanako Ono
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Yayoi Otsuka-Yamasaki
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences of Iwate Medical University
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Atsushi Shimizu
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences of Iwate Medical University
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Yoichi Sutoh
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences of Iwate Medical University
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Information Sciences, Tohoku University
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
- Institute of Development, Aging and Cancer, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University
| | | | | | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Center for Advanced Intelligence Project, RIKEN
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| |
Collapse
|
6
|
Ishibashi Y, Harada S, Eitaki Y, Kurihara A, Kato S, Kuwabara K, Iida M, Hirata A, Sata M, Matsumoto M, Shibuki T, Okamura T, Sugiyama D, Sato A, Amano K, Hirayama A, Sugimoto M, Soga T, Tomita M, Takebayashi T. A population-based urinary and plasma metabolomics study of environmental exposure to cadmium. Environ Health Prev Med 2024; 29:22. [PMID: 38556356 PMCID: PMC10992994 DOI: 10.1265/ehpm.23-00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 12/30/2023] [Indexed: 04/02/2024] Open
Abstract
BACKGROUND The application of metabolomics-based profiles in environmental epidemiological studies is a promising approach to refine the process of health risk assessment. We aimed to identify potential metabolomics-based profiles in urine and plasma for the detection of relatively low-level cadmium (Cd) exposure in large population-based studies. METHOD We analyzed 123 urinary metabolites and 94 plasma metabolites detected in fasting urine and plasma samples collected from 1,412 men and 2,022 women involved in the Tsuruoka Metabolomics Cohort Study. Regression analysis was performed for urinary N-acetyl-beta-D-glucosaminidase (NAG), plasma, and urinary metabolites as dependent variables, and urinary Cd (U-Cd, quartile) as an independent variable. The multivariable regression model included age, gender, systolic blood pressure, smoking, rice intake, BMI, glycated hemoglobin, low-density lipoprotein cholesterol, alcohol consumption, physical activity, educational history, dietary energy intake, urinary Na/K ratio, and uric acid. Pathway-network analysis was carried out to visualize the metabolite networks linked to Cd exposure. RESULT Urinary NAG was positively associated with U-Cd, but not at lower concentrations (Q2). Among urinary metabolites in the total population, 45 metabolites showed associations with U-Cd in the unadjusted and adjusted models after adjusting for the multiplicity of comparison with FDR. There were 12 urinary metabolites which showed consistent associations between Cd exposure from Q2 to Q4. Among plasma metabolites, six cations and one anion were positively associated with U-Cd, whereas alanine, creatinine, and isoleucine were negatively associated with U-Cd. Our results were robust by statistical adjustment of various confounders. Pathway-network analysis revealed metabolites and upstream regulator changes associated with mitochondria (ACACB, UCP2, and metabolites related to the TCA cycle). CONCLUSION These results suggested that U-Cd was associated with metabolites related to upstream mitochondrial dysfunction in a dose-dependent manner. Our data will help develop environmental Cd exposure profiles for human populations.
Collapse
Affiliation(s)
- Yoshiki Ishibashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yoko Eitaki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Mizuki Sata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Minako Matsumoto
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Takuma Shibuki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Faculty of Nursing and Medical Care, Keio University, Fujisawa, Kanagawa, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kaori Amano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| |
Collapse
|
7
|
Harada S, Ohmomo H, Matsumoto M, Sata M, Iida M, Hirata A, Miyagawa N, Kuwabara K, Kato S, Toki R, Edagawa S, Sugiyama D, Sato A, Hirayama A, Sugimoto M, Soga T, Tomita M, Shimizu A, Okamura T, Takebayashi T. Metabolomics profiles alterations in cigarette smokers and heated tobacco product users. J Epidemiol 2023:JE20230170. [PMID: 37926518 DOI: 10.2188/jea.je20230170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
BACKGROUND Heated tobacco products (HTPs) have gained global popularity, but their health risks remain unclear. Therefore, the current study aimed to identify plasma metabolites associated with smoking and HTP use in a large Japanese population to improve health risk assessment. METHODS Metabolomics data from 9,922 baseline participants of the Tsuruoka Metabolomics Cohort Study (TMCS) were analyzed to determine the association between smoking habits and plasma metabolites. Moreover, alterations in smoking-related metabolites among HTP users were examined based on data obtained from 3,334 participants involved from April 2018 to June 2019 in a follow-up survey. RESULTS Our study revealed that cigarette smokers had metabolomics profiles distinct from never smokers, with 22 polar metabolites identified as candidate biomarkers for smoking. These biomarker profiles of HTP users were closer to those of cigarette smokers than those of never smokers. The concentration of glutamate was higher in cigarette smokers, and biomarkers involved in glutamate metabolism were also associated with cigarette smoking and HTP use. Network pathway analysis showed that smoking was associated with the glutamate pathway, which could lead to endothelial dysfunction and atherosclerosis of the vessels. CONCLUSIONS Our study showed that the glutamate pathway is affected by habitual smoking. These changes in the glutamate pathway may partly explain the mechanism by which cigarette smoking causes cardiovascular disease. HTP use was also associated with glutamate metabolism, indicating that HTP use may contribute to the development of cardiovascular disease through mechanisms similar to those in cigarette use.
Collapse
Affiliation(s)
- Sei Harada
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| | - Hideki Ohmomo
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University
| | - Minako Matsumoto
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Mizuki Sata
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Miho Iida
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Aya Hirata
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Naoko Miyagawa
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Kazuyo Kuwabara
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Suzuka Kato
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Ryota Toki
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Shun Edagawa
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Daisuke Sugiyama
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University
| | | | | | | | | | - Atsushi Shimizu
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University
| | - Tomonori Okamura
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
| | - Toru Takebayashi
- Department of Public Health and Preventive Medicine, Keio University School of Medicine
- Institute for Advanced Biosciences, Keio University
| |
Collapse
|
8
|
Saito M, Inose R, Sato A, Tomita M, Suzuki H, Kanai A. Systematic Analysis of Diverse Polynucleotide Kinase Clp1 Family Proteins in Eukaryotes: Three Unique Clp1 Proteins of Trypanosoma brucei. J Mol Evol 2023; 91:669-686. [PMID: 37606665 PMCID: PMC10598085 DOI: 10.1007/s00239-023-10128-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 08/01/2023] [Indexed: 08/23/2023]
Abstract
The Clp1 family proteins, consisting of the Clp1 and Nol9/Grc3 groups, have polynucleotide kinase (PNK) activity at the 5' end of RNA strands and are important enzymes in the processing of some precursor RNAs. However, it remains unclear how this enzyme family diversified in the eukaryotes. We performed a large-scale molecular evolutionary analysis of the full-length genomes of 358 eukaryotic species to classify the diverse Clp1 family proteins. The average number of Clp1 family proteins in eukaryotes was 2.3 ± 1.0, and most representative species had both Clp1 and Nol9/Grc3 proteins, suggesting that the Clp1 and Nol9/Grc3 groups were already formed in the eukaryotic ancestor by gene duplication. We also detected an average of 4.1 ± 0.4 Clp1 family proteins in members of the protist phylum Euglenozoa. For example, in Trypanosoma brucei, there are three genes of the Clp1 group and one gene of the Nol9/Grc3 group. In the Clp1 group proteins encoded by these three genes, the C-terminal domains have been replaced by unique characteristics domains, so we designated these proteins Tb-Clp1-t1, Tb-Clp1-t2, and Tb-Clp1-t3. Experimental validation showed that only Tb-Clp1-t2 has PNK activity against RNA strands. As in this example, N-terminal and C-terminal domain replacement also contributed to the diversification of the Clp1 family proteins in other eukaryotic species. Our analysis also revealed that the Clp1 family proteins in humans and plants diversified through isoforms created by alternative splicing.
Collapse
Affiliation(s)
- Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Rerina Inose
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-0882, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-0882, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan.
- Faculty of Environment and Information Studies, Keio University, Fujisawa, 252-0882, Japan.
| |
Collapse
|
9
|
Abhinand CS, Galipon J, Mori M, Ramesh P, Prasad TSK, Raju R, Sudhakaran PR, Tomita M. Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis. J Cell Commun Signal 2023; 17:1067-1079. [PMID: 36881336 PMCID: PMC10409921 DOI: 10.1007/s12079-023-00736-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/17/2023] [Indexed: 03/08/2023] Open
Abstract
Vascular endothelial growth factor-A (VEGF-A) is one of the primary factors promoting angiogenesis in endothelial cells. Although defects in VEGF-A signaling are linked to diverse pathophysiological conditions, the early phosphorylation-dependent signaling events pertinent to VEGF-A signaling remain poorly defined. Hence, a temporal quantitative phosphoproteomic analysis was performed in human umbilical vein endothelial cells (HUVECs) treated with VEGF-A-165 for 1, 5 and 10 min. This led to the identification and quantification of 1971 unique phosphopeptides corresponding to 961 phosphoproteins and 2771 phosphorylation sites in total. Specifically, 69, 153, and 133 phosphopeptides corresponding to 62, 125, and 110 phosphoproteins respectively, were temporally phosphorylated at 1, 5, and 10 min upon addition of VEGF-A. These phosphopeptides included 14 kinases, among others. This study also captured the phosphosignaling events directed through RAC, FAK, PI3K-AKT-MTOR, ERK, and P38 MAPK modules with reference to our previously assembled VEGF-A/VEGFR2 signaling pathway map in HUVECs. Apart from a significant enrichment of biological processes such as cytoskeleton organization and actin filament binding, our results also suggest a role of AAK1-AP2M1 in the regulation of VEGFR endocytosis. Taken together, the temporal quantitative phosphoproteomics analysis of VEGF signaling in HUVECs revealed early signaling events and we believe that this analysis will serve as a starting point for the analysis of differential signaling across VEGF members toward the full elucidation of their role in the angiogenesis processes. Workflow for the identification of early phosphorylation events induced by VEGF-A-165 in HUVEC cells.
Collapse
Affiliation(s)
- Chandran S Abhinand
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India.
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan.
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan.
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Poornima Ramesh
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | | | - Rajesh Raju
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, 575018, India
- Center for Integrative Omics Data Science, Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Perumana R Sudhakaran
- Department of Computational Biology and Bioinformatics, University of Kerala, Thiruvananthapuram, Kerala, 695581, India
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0017, Japan
- Department of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| |
Collapse
|
10
|
Hirayama A, Ishikawa T, Takahashi H, Yamanaka S, Ikeda S, Hirata A, Harada S, Sugimoto M, Soga T, Tomita M, Takebayashi T. Quality Control of Targeted Plasma Lipids in a Large-Scale Cohort Study Using Liquid Chromatography-Tandem Mass Spectrometry. Metabolites 2023; 13:metabo13040558. [PMID: 37110217 PMCID: PMC10146188 DOI: 10.3390/metabo13040558] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/03/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
High-throughput metabolomics has enabled the development of large-scale cohort studies. Long-term studies require multiple batch-based measurements, which require sophisticated quality control (QC) to eliminate unexpected bias to obtain biologically meaningful quantified metabolomic profiles. Liquid chromatography-mass spectrometry was used to analyze 10,833 samples in 279 batch measurements. The quantified profile included 147 lipids including acylcarnitine, fatty acids, glucosylceramide, lactosylceramide, lysophosphatidic acid, and progesterone. Each batch included 40 samples, and 5 QC samples were measured for 10 samples of each. The quantified data from the QC samples were used to normalize the quantified profiles of the sample data. The intra- and inter-batch median coefficients of variation (CV) among the 147 lipids were 44.3% and 20.8%, respectively. After normalization, the CV values decreased by 42.0% and 14.7%, respectively. The effect of this normalization on the subsequent analyses was also evaluated. The demonstrated analyses will contribute to obtaining unbiased, quantified data for large-scale metabolomics.
Collapse
Affiliation(s)
- Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0082, Kanagawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0082, Kanagawa, Japan
| | - Takamasa Ishikawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
| | - Haruka Takahashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
| | - Sanae Yamanaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku 160-8582, Tokyo, Japan
| | - Sei Harada
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku 160-8582, Tokyo, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
- Institute of Medical Research, Tokyo Medical University, Shinjuku 160-0022, Tokyo, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0082, Kanagawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0082, Kanagawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0082, Kanagawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0082, Kanagawa, Japan
| | - Toru Takebayashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku 160-8582, Tokyo, Japan
| |
Collapse
|
11
|
Hayasaka R, Tabata S, Hasebe M, Ikeda S, Hikita T, Oneyama C, Yoshitake J, Onoshima D, Takahashi K, Shibata T, Uchida K, Baba Y, Soga T, Tomita M, Hirayama A. Metabolomics of small extracellular vesicles derived from isocitrate dehydrogenase 1-mutant HCT116 cells collected by semi-automated size exclusion chromatography. Front Mol Biosci 2023; 9:1049402. [PMID: 36710884 PMCID: PMC9873957 DOI: 10.3389/fmolb.2022.1049402] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
Cancer-derived small extracellular vesicles (sEVs) are multifunctional particles with a lipid bilayer structure that are involved in cancer progression, such as malignant proliferation, distant metastasis, and cancer immunity evasion. The separation protocol used to isolate sEVs is an important process and thus, several have been developed, including ultracentrifugation (UC), size exclusion chromatography (SEC), and affinity purification using antibodies against sEV surface antigens. However, the effects of different separation methods on sEV components have not been adequately examined. Here, we developed a semi-automated system for collecting sEVs by combining SEC and preparative high-performance liquid chromatography and applied it to metabolome analysis. The developed SEC system could recover sEVs more efficiently and non-destructively than UC, suggesting that it is an appropriate recovery method for metabolic analysis and reflects biological conditions. Furthermore, using the developed SEC system, we performed metabolome analysis of sEVs from isocitrate dehydrogenase 1 (IDH)-mutated human colon HCT116 cells, which produce the oncogenic metabolite, 2-hydroxyglutaric acid (2-HG). IDH1-mutated HCT116 cells released significantly more sEVs than wild-type (WT) cells. The metabolomic profiles of IDH1 mutant and WT cells showed distinct differences between the cells and their sEVs. Notably, in IDH mutant cells, large amounts of 2-HG were detected not only in cells, but also in sEVs. These results indicate that the SEC system we developed has wide potential applications in sEVs research.
Collapse
Affiliation(s)
- Ryosuke Hayasaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Sho Tabata
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Masako Hasebe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Tomoya Hikita
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Chitose Oneyama
- Division of Cancer Cell Regulation, Aichi Cancer Center Research Institute, Nagoya, Japan,Department of Oncology, Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Japan,Department of Target and Drug Discovery, Graduate School of Medicine, Nagoya University, Nagoya, Japan,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
| | - Jun Yoshitake
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
| | - Daisuke Onoshima
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan
| | | | - Takahiro Shibata
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Koji Uchida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan,Japan Agency for Medical Research and Development, CREST, Tokyo, Japan
| | - Yoshinobu Baba
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan,Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan,Institute of Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan,College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan,Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Japan,*Correspondence: Akiyoshi Hirayama,
| |
Collapse
|
12
|
Matsuta R, Yamamoto H, Tomita M, Saito R. iDMET: network-based approach for integrating differential analysis of cancer metabolomics. BMC Bioinformatics 2022; 23:508. [PMID: 36443658 PMCID: PMC9706903 DOI: 10.1186/s12859-022-05068-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Comprehensive metabolomic analyses have been conducted in various institutes and a large amount of metabolomic data are now publicly available. To help fully exploit such data and facilitate their interpretation, metabolomic data obtained from different facilities and different samples should be integrated and compared. However, large-scale integration of such data for biological discovery is challenging given that they are obtained from various types of sample at different facilities and by different measurement techniques, and the target metabolites and sensitivities to detect them also differ from study to study. RESULTS We developed iDMET, a network-based approach to integrate metabolomic data from different studies based on the differential metabolomic profiles between two groups, instead of the metabolite profiles themselves. As an application, we collected cancer metabolomic data from 27 previously published studies and integrated them using iDMET. A pair of metabolomic changes observed in the same disease from two studies were successfully connected in the network, and a new association between two drugs that may have similar effects on the metabolic reactions was discovered. CONCLUSIONS We believe that iDMET is an efficient tool for integrating heterogeneous metabolomic data and discovering novel relationships between biological phenomena.
Collapse
Affiliation(s)
- Rira Matsuta
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Hiroyuki Yamamoto
- Human Metabolome Technologies, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan
| | - Rintaro Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan
| |
Collapse
|
13
|
Arakawa K, Kono N, Malay AD, Tateishi A, Ifuku N, Masunaga H, Sato R, Tsuchiya K, Ohtoshi R, Pedrazzoli D, Shinohara A, Ito Y, Nakamura H, Tanikawa A, Suzuki Y, Ichikawa T, Fujita S, Fujiwara M, Tomita M, Blamires SJ, Chuah JA, Craig H, Foong CP, Greco G, Guan J, Holland C, Kaplan DL, Sudesh K, Mandal BB, Norma-Rashid Y, Oktaviani NA, Preda RC, Pugno NM, Rajkhowa R, Wang X, Yazawa K, Zheng Z, Numata K. 1000 spider silkomes: Linking sequences to silk physical properties. Sci Adv 2022; 8:eabo6043. [PMID: 36223455 PMCID: PMC9555773 DOI: 10.1126/sciadv.abo6043] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.
Collapse
Affiliation(s)
- Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Ali D. Malay
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Ayaka Tateishi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | - Nao Ifuku
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hiroyasu Masunaga
- Japan Synchrotron Radiation Research Institute, Sayo-gun, Hyogo 679-5198, Japan
| | - Ryota Sato
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | - Rintaro Ohtoshi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | | | | | - Yusuke Ito
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Hiroyuki Nakamura
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Spiber Inc., Tsuruoka, Yamagata 997-0052, Japan
| | - Akio Tanikawa
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan
| | - Yuya Suzuki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
| | - Takeaki Ichikawa
- Kokugakuin Kugayama High School, Suginami, Tokyo 168-0082, Japan
| | - Shohei Fujita
- Graduate School of Agriculture, Saga University, Saga 840-8502, Japan
| | - Masayuki Fujiwara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa 252-8520, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-8520, Japan
| | - Sean J. Blamires
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jo-Ann Chuah
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hamish Craig
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Evolution and Ecology Research Centre, University of New South Wales, Sydney, NSW 2052, Australia
| | - Choon P. Foong
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| | - Gabriele Greco
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano 77, I-38123 Trento, Italy
| | - Juan Guan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Materials Science and Engineering, Beihang University, Beijing 100191, China
| | - Chris Holland
- Natural Materials Group, Department of Materials Science and Engineering, The University of Sheffield, Mappin Street, Sheffield S1 3JD, UK
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Kumar Sudesh
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Biman B. Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati (IITG), Guwahati, 781 039 Assam, India
- Center for Nanotechnology, IITG, Guwahati, 781 039 Assam, India
- School of Health Sciences and Technology, IITG, Guwahati, 781 039 Assam, India
| | - Y. Norma-Rashid
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Nur A. Oktaviani
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Rucsanda C. Preda
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Nicola M. Pugno
- Department of Civil, Environmental and Mechanical Engineering, University of Trento, Via Mesiano 77, I-38123 Trento, Italy
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, E1 4NS London, UK
| | - Rangam Rajkhowa
- Institute for Frontier Materials, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Xiaoqin Wang
- College of Textile and Clothing Engineering, Soochow University, Suzhou 215123, China
| | - Kenjiro Yazawa
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Zhaozhu Zheng
- College of Textile and Clothing Engineering, Soochow University, Suzhou 215123, China
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Nishikyo, Kyoto 615-8510, Japan
| |
Collapse
|
14
|
Tsurumaki M, Saito M, Tomita M, Kanai A. Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis. RNA 2022; 28:1041-1057. [PMID: 35688647 PMCID: PMC9297842 DOI: 10.1261/rna.079103.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 06/06/2022] [Indexed: 06/01/2023]
Abstract
The candidate phyla radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and they often lack ribosomal proteins uL1, bL9, and/or uL30, which are basically ubiquitous in non-CPR bacteria. Here, we comprehensively analyzed the genomic information on CPR bacteria and identified their unique properties. The distribution of protein lengths in CPR bacteria peaks at around 100-150 amino acids, whereas the position of the peak varies in the range of 100-300 amino acids in free-living non-CPR bacteria, and at around 100-200 amino acids in most symbiotic non-CPR bacteria. These results show that the proteins of CPR bacteria are smaller, on average, than those of free-living non-CPR bacteria, like those of symbiotic non-CPR bacteria. We found that ribosomal proteins bL28, uL29, bL32, and bL33 have been lost in CPR bacteria in a taxonomic lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins of CPR differ, in part, from those of non-CPR bacteria, with missing regions or specifically added regions. We also found that several regions in the 16S, 23S, and 5S rRNAs of CPR bacteria are lacking, which presumably caused the total predicted lengths of the three rRNAs of CPR bacteria to be smaller than those of non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than those in free-living non-CPR bacteria, with simplified surface structures.
Collapse
Affiliation(s)
- Megumi Tsurumaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa 252-0882, Japan
| |
Collapse
|
15
|
Kuwabara H, Katsumata K, Iwabuchi A, Udo R, Tago T, Kasahara K, Mazaki J, Enomoto M, Ishizaki T, Soya R, Kaneko M, Ota S, Enomoto A, Soga T, Tomita M, Sunamura M, Tsuchida A, Sugimoto M, Nagakawa Y. Salivary metabolomics with machine learning for colorectal cancer detection. Cancer Sci 2022; 113:3234-3243. [PMID: 35754317 PMCID: PMC9459332 DOI: 10.1111/cas.15472] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/07/2022] [Accepted: 06/15/2022] [Indexed: 11/29/2022] Open
Abstract
As the worldwide prevalence of colorectal cancer (CRC) increases, it is vital to reduce its morbidity and mortality through early detection. Saliva‐based tests are an ideal noninvasive tool for CRC detection. Here, we explored and validated salivary biomarkers to distinguish patients with CRC from those with adenoma (AD) and healthy controls (HC). Saliva samples were collected from patients with CRC, AD, and HC. Untargeted salivary hydrophilic metabolite profiling was conducted using capillary electrophoresis–mass spectrometry and liquid chromatography–mass spectrometry. An alternative decision tree (ADTree)‐based machine learning (ML) method was used to assess the discrimination abilities of the quantified metabolites. A total of 2602 unstimulated saliva samples were collected from subjects with CRC (n = 235), AD (n = 50), and HC (n = 2317). Data were randomly divided into training (n = 1301) and validation datasets (n = 1301). The clustering analysis showed a clear consistency of aberrant metabolites between the two groups. The ADTree model was optimized through cross‐validation (CV) using the training dataset, and the developed model was validated using the validation dataset. The model discriminating CRC + AD from HC showed area under the receiver‐operating characteristic curves (AUC) of 0.860 (95% confidence interval [CI]: 0.828‐0.891) for CV and 0.870 (95% CI: 0.837‐0.903) for the validation dataset. The other model discriminating CRC from AD + HC showed an AUC of 0.879 (95% CI: 0.851‐0.907) and 0.870 (95% CI: 0.838‐0.902), respectively. Salivary metabolomics combined with ML demonstrated high accuracy and versatility in detecting CRC.
Collapse
Affiliation(s)
- Hiroshi Kuwabara
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Kenji Katsumata
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Atsuhiro Iwabuchi
- Center for Health Surveillance and Preventive Medicine, Tokyo Medical University Hospital, Tokyo, Japan
| | - Ryutaro Udo
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Tomoya Tago
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Kenta Kasahara
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Junichi Mazaki
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Masanobu Enomoto
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Tetsuo Ishizaki
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Ryoko Soya
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Miku Kaneko
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Sana Ota
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Ayame Enomoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Makoto Sunamura
- Digestive Surgery and Transplantation Surgery, Tokyo Medical University Hachioji Medical Center, Tokyo, Japan
| | - Akihiko Tsuchida
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Research and Development Center for Minimally Invasive Therapies Health Promotion and Preemptive Medicine, Tokyo Medical University, Shinjuku, Tokyo, Japan
| | - Yuichi Nagakawa
- Department of Gastrointestinal and Pediatric Surgery, Tokyo Medical University, Tokyo, Japan
| |
Collapse
|
16
|
Suzuki Y, Hayasaka R, Hasebe M, Ikeda S, Soga T, Tomita M, Hirayama A, Kuroda H. Comparative Metabolomics of Small Molecules Specifically Expressed in the Dorsal or Ventral Marginal Zones in Vertebrate Gastrula. Metabolites 2022; 12:metabo12060566. [PMID: 35736498 PMCID: PMC9229639 DOI: 10.3390/metabo12060566] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 02/06/2023] Open
Abstract
Many previous studies have reported the various proteins specifically secreted as inducers in the dorsal or ventral regions in vertebrate gastrula. However, little is known about the effect on cell fate of small molecules below 1000 Da. We therefore tried to identify small molecules specifically expressed in the dorsal marginal zone (DMZ) or ventral marginal zone (VMZ) in vertebrate gastrula. Small intracellular and secreted molecules were detected using explants and supernatant samples. Hydrophilic metabolites were analyzed by capillary ion chromatography-mass spectrometry and liquid chromatography-mass spectrometry, and lipids were analyzed by supercritical fluid chromatography-tandem mass spectrometry. In total, 190 hydrophilic metabolites and 396 lipids were identified. The DMZ was found to have high amounts of glycolysis- and glutathione metabolism-related metabolites in explants, and the VMZ was richer in purine metabolism-related metabolites. We also discovered some hydrophilic metabolites and lipids differentially contained in the DMZ or VMZ. Our research would contribute to a deeper understanding of the cellular physiology that regulates early embryogenesis.
Collapse
Affiliation(s)
- Yukako Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
| | - Ryosuke Hayasaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Kanagawa, Japan
| | - Masako Hasebe
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Kanagawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Kanagawa, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Kanagawa, Japan
| | - Hiroki Kuroda
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan; (Y.S.); (R.H.); (M.H.); (S.I.); (T.S.); (M.T.); (A.H.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Kanagawa, Japan
- Correspondence: ; Tel.: +81-466-49-3404
| |
Collapse
|
17
|
Iwai H, Mori M, Tomita M, Kono N, Arakawa K. Molecular Evidence of Chemical Disguise by the Socially Parasitic Spiny Ant Polyrhachis lamellidens (Hymenoptera: Formicidae) When Invading a Host Colony. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.915517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
While most ant species establish a colony independently, some socially parasitic ants build the foundation of their colony by invading other ant (host) colonies and utilizing their labor forces. Many socially parasitic ants disguise their cuticular hydrocarbon (CHC) profile, which is also known as signature mixture for nestmate discrimination, when invading the host colony. Since the strategy of chemical disguise is widespread in socially parasitic ants, elucidating the mechanism of chemical disguise will promote knowledge on the evolutionary history of social parasitism. However, detailed knowledge is still lacking, as the relevant information has only originated from circumstantial evidence, which was obtained from ecological observations. In this study, we investigated the mechanism of chemical disguise in a new queen of a temporary socially parasitic spiny ant (Polyrhachis lamellidens) by measuring its CHC profile, performing a tracing assay with labeled substances, and analyzing gene expression levels. First, after rubbing behavior was observed against the host workers, the CHC profile in P. lamellidens shifted to pronounced peaks that closely resembling that of the host workers. We also observed a reduction in aggressive behaviors by the host ant against P. lamellidens after rubbing behavior was performed. In addition, P. lamellidens acquired artificially-applied labeling substances from host workers through their rubbing behaviors, while gene expression profiling showed the expression of CHC synthesis-related genes did not change during this behavior. These results suggest that P. lamellidens directly obtains host CHCs through rubbing behavior, and these host CHCs enables P. lamellidens to remain disguised during colony invasion.
Collapse
|
18
|
Yoshida Y, Satoh T, Ota C, Tanaka S, Horikawa DD, Tomita M, Kato K, Arakawa K. Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades. BMC Genomics 2022; 23:405. [PMID: 35643424 PMCID: PMC9145152 DOI: 10.1186/s12864-022-08642-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 05/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tardigrades are microscopic animals that are capable of tolerating extreme environments by entering a desiccated state of suspended animation known as anhydrobiosis. While antioxidative stress proteins, antiapoptotic pathways and tardigrade-specific intrinsically disordered proteins have been implicated in the anhydrobiotic machinery, conservation of these mechanisms is not universal within the phylum Tardigrada, suggesting the existence of overlooked components. RESULTS Here, we show that a novel Mn-dependent peroxidase is an important factor in tardigrade anhydrobiosis. Through time-series transcriptome analysis of Ramazzottius varieornatus specimens exposed to ultraviolet light and comparison with anhydrobiosis entry, we first identified several novel gene families without similarity to existing sequences that are induced rapidly after stress exposure. Among these, a single gene family with multiple orthologs that is highly conserved within the phylum Tardigrada and enhances oxidative stress tolerance when expressed in human cells was identified. Crystallographic study of this protein suggested Zn or Mn binding at the active site, and we further confirmed that this protein has Mn-dependent peroxidase activity in vitro. CONCLUSIONS Our results demonstrated novel mechanisms for coping with oxidative stress that may be a fundamental mechanism of anhydrobiosis in tardigrades. Furthermore, localization of these sets of proteins mainly in the Golgi apparatus suggests an indispensable role of the Golgi stress response in desiccation tolerance.
Collapse
Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Tadashi Satoh
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho, Nagoya, 467-8603, Japan
| | - Chise Ota
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho, Nagoya, 467-8603, Japan
| | - Sae Tanaka
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Daiki D Horikawa
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan
| | - Koichi Kato
- Faculty and Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho, Nagoya, 467-8603, Japan
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Nihonkoku, 403-1, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan.
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa, 252-0882, Japan.
- Exploratory Research Center On Life and Living Systems (ExCELLS), National Institute of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.
| |
Collapse
|
19
|
Yoshida Y, Shaikhutdinov N, Kozlova O, Itoh M, Tagami M, Murata M, Nishiyori-Sueki H, Kojima-Ishiyama M, Noma S, Cherkasov A, Gazizova G, Nasibullina A, Deviatiiarov R, Shagimardanova E, Ryabova A, Yamaguchi K, Bino T, Shigenobu S, Tokumoto S, Miyata Y, Cornette R, Yamada TG, Funahashi A, Tomita M, Gusev O, Kikawada T. High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance. NAR Genom Bioinform 2022; 4:lqac029. [PMID: 35387384 PMCID: PMC8982440 DOI: 10.1093/nargab/lqac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Non-biting midges (Chironomidae) are known to inhabit a wide range of environments, and certain species can tolerate extreme conditions, where the rest of insects cannot survive. In particular, the sleeping chironomid Polypedilum vanderplanki is known for the remarkable ability of its larvae to withstand almost complete desiccation by entering a state called anhydrobiosis. Chromosome numbers in chironomids are higher than in other dipterans and this extra genomic resource might facilitate rapid adaptation to novel environments. We used improved sequencing strategies to assemble a chromosome-level genome sequence for P. vanderplanki for deep comparative analysis of genomic location of genes associated with desiccation tolerance. Using whole genome-based cross-species and intra-species analysis, we provide evidence for the unique functional specialization of Chromosome 4 through extensive acquisition of novel genes. In contrast to other insect genomes, in the sleeping chironomid a uniquely high degree of subfunctionalization in paralogous anhydrobiosis genes occurs in this chromosome, as well as pseudogenization in a highly duplicated gene family. Our findings suggest that the Chromosome 4 in Polypedilum is a site of high genetic turnover, allowing it to act as a ‘sandbox’ for evolutionary experiments, thus facilitating the rapid adaptation of midges to harsh environments.
Collapse
Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Nurislam Shaikhutdinov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 21205, Russian Federation
| | - Olga Kozlova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Masayoshi Itoh
- Preventive Medicine & Diagnosis Innovation Program (PMI), RIKEN, Wako, Saitama 351-0198, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Michihira Tagami
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Mitsuyoshi Murata
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | | | - Miki Kojima-Ishiyama
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Shohei Noma
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Alexander Cherkasov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Guzel Gazizova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Aigul Nasibullina
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Elena Shagimardanova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Alina Ryabova
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Takahiro Bino
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Shoko Tokumoto
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
| | - Yugo Miyata
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Richard Cornette
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| | - Takahiro G Yamada
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Akira Funahashi
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Graduate School of Media and Governance, Systems Biology Program, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information studies, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Oleg Gusev
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420012, Russian Federation
- Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
- Department of Regulatory Transcriptomics for Medical Genetic Diagnostics, Graduate School of Medicine, Juntendo University, Tokyo 113-8421, Japan
| | - Takahiro Kikawada
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8562, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-8634, Japan
| |
Collapse
|
20
|
Miura MC, Nagata S, Tamaki S, Tomita M, Kanai A. Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation. Front Microbiol 2022; 13:849080. [PMID: 35295308 PMCID: PMC8919778 DOI: 10.3389/fmicb.2022.849080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/07/2022] [Indexed: 11/23/2022] Open
Abstract
Group II introns (G2Is) are ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are suggested to have been an important evolutionary factor in the prokaryote-to-eukaryote transition, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative genomes had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative genomes had an average of 3.0 G2Is. The greatest number of G2Is per genome was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1-U3) to the previous classification. This analysis suggested that about 30% of all IEPs are non-canonical IEPs. The number of G2Is per genome was defined almost at the phylum level, and at least in the following two phyla, Firmicutes, and Cyanobacteriota, the type of IEP was largely associated as a factor in the G2I increase, i.e., there was an explosive increase in G2Is with bacterial C-type IEPs, mainly in the phylum Firmicutes, and in G2Is with CL-type IEPs, mainly in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.
Collapse
Affiliation(s)
- Masahiro C. Miura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Shohei Nagata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Satoshi Tamaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| |
Collapse
|
21
|
Kurihara Y, Iwai H, Kono N, Tomita M, Arakawa K. Initial parasitic behaviour of the temporary social parasitic ant Polyrhachis lamellidens can be induced by host-like cuticles in laboratory environment. Biol Open 2022; 11:274825. [PMID: 35199830 PMCID: PMC8966776 DOI: 10.1242/bio.058956] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/17/2022] [Indexed: 11/20/2022] Open
Abstract
Polyrhachis lamellidens is a temporary social parasitic species. When a newly mated queen encounters a host worker, it opens its jaws, mounts and rubs the body of the host worker, called rubbing behaviour. This behaviour is different from aggressive behaviour and is considered to be a preparatory action before invasion of the host colony. However, it is unclear what cues trigger rubbing behaviour. Therefore, in this study, we used glass beads that imitated the insect body surfaces and searched for triggers. Although P. lamellidens did not respond to the cuticular compounds only, cuticular compounds and chitin coatings on glass beads elicited responses that were similar to those towards live samples. The rubbing behaviour of P. lamellidens was elicited in response to a cuticle-like surface that mimicked a procuticle by combining the compounds with chitin. These results suggest that host recognition and nest-mate recognition are supported by different mechanisms.
Collapse
Affiliation(s)
- Yu Kurihara
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Hironori Iwai
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Nobuaki Kono
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Kazuharu Arakawa
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| |
Collapse
|
22
|
Fukushima T, Tomita M, Ikeda S, Hattori N. A case of sensory ataxic Guillain-Barré syndrome with immunoglobulin G anti-GM1 antibodies following the first dose of mRNA COVID-19 vaccine BNT162b2 (Pfizer). QJM 2022; 115:25-27. [PMID: 34871447 PMCID: PMC8690109 DOI: 10.1093/qjmed/hcab296] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Indexed: 12/02/2022] Open
Affiliation(s)
- T Fukushima
- Department of Neurology, Toyota Kosei Hospital, 500-1 Ibobara Josui-cho, Toyota City JP470-0396, Japan
- Address correspondence to T. Fukushima, Department of Neurology, Toyota Kosei Hospital, 500-1 Ibobara Josui-cho, Toyota City JP470-0396, Japan.
| | - M Tomita
- Department of Neurology, Toyota Kosei Hospital, 500-1 Ibobara Josui-cho, Toyota City JP470-0396, Japan
| | - S Ikeda
- Department of Neurology, Toyota Kosei Hospital, 500-1 Ibobara Josui-cho, Toyota City JP470-0396, Japan
| | - N Hattori
- Department of Neurology, Toyota Kosei Hospital, 500-1 Ibobara Josui-cho, Toyota City JP470-0396, Japan
| |
Collapse
|
23
|
Okamoto L, Watanabe S, Deno S, Nie X, Maruyama J, Tomita M, Hatano A, Yugi K. Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach. Neurosci Res 2021; 175:82-97. [PMID: 34979163 DOI: 10.1016/j.neures.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/23/2021] [Accepted: 12/23/2021] [Indexed: 01/13/2023]
Abstract
There have been a number of reports about the transcriptional regulatory networks in schizophrenia. However, most of these studies were based on a specific transcription factor or a single dataset, an approach that is inadequate to understand the diverse etiology and underlying common characteristics of schizophrenia. Here we reconstructed and compared the transcriptional regulatory network for lipid metabolism enzymes using 15 public transcriptome datasets of neural cells from schizophrenia patients. Since many of the well-known schizophrenia-related SNPs are in enhancers, we reconstructed a network including enhancer-dependent regulation and found that 53.3 % of the total number of edges (7,577 pairs) involved regulation via enhancers. By examining multiple datasets, we found common and unique transcriptional modes of regulation. Furthermore, enrichment analysis of SNPs that were connected with genes in the transcriptional regulatory networks by eQTL suggested an association with hematological cell counts and some other traits/diseases, whose relationship to schizophrenia was either not or insufficiently reported in previous studies. Based on these results, we suggest that in future studies on schizophrenia, information on genotype, comorbidities and hematological cell counts should be included, along with the transcriptome, for a more detailed genetic stratification and mechanistic exploration of schizophrenia.
Collapse
Affiliation(s)
- Lisa Okamoto
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Soyoka Watanabe
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan
| | - Senka Deno
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Xiang Nie
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Junichi Maruyama
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Atsushi Hatano
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Department of Omics and Systems Biology, Niigata University Graduate School of Medical and Dental Sciences, 757 Ichibancho, Asahimachi-dori, Chuo Ward, Niigata City, 951-8510, Japan
| | - Katsuyuki Yugi
- Laboratory for Integrated Cellular Systems, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan; Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; PRESTO, Japan Science and Technology Agency, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| |
Collapse
|
24
|
Murai Y, Yagi-Utsumi M, Fujiwara M, Tanaka S, Tomita M, Kato K, Arakawa K. Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada. BMC Genomics 2021; 22:813. [PMID: 34763673 PMCID: PMC8582207 DOI: 10.1186/s12864-021-08131-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Background Many limno-terrestrial tardigrades can enter an ametabolic state, known as anhydrobiosis, upon desiccation, in which the animals can withstand extreme environments. Through genomics studies, molecular components of anhydrobiosis are beginning to be elucidated, such as the expansion of oxidative stress response genes, loss of stress signaling pathways, and gain of tardigrade-specific heat-soluble protein families designated CAHS and SAHS. However, to date, studies have predominantly investigated the class Eutardigrada, and molecular mechanisms in the remaining class, Heterotardigrada, still remains elusive. To address this gap in the research, we report a multiomics study of the heterotardigrade Echiniscus testudo, one of the most desiccation-tolerant species which is not yet culturable in laboratory conditions. Results In order to elucidate the molecular basis of anhydrobiosis in E. testudo, we employed a multi-omics strategy encompassing genome sequencing, differential transcriptomics, and proteomics. Using ultra-low input library sequencing protocol from a single specimen, we sequenced and assembled the 153.7 Mbp genome annotated using RNA-Seq data. None of the previously identified tardigrade-specific abundant heat-soluble genes was conserved, while the loss and expansion of existing pathways were partly shared. Furthermore, we identified two families novel abundant heat-soluble proteins, which we named E. testudo Abundant Heat Soluble (EtAHS), that are predicted to contain large stretches of disordered regions. Likewise the AHS families in eutardigrada, EtAHS shows structural changes from random coil to alphahelix as the water content was decreased in vitro. These characteristics of EtAHS proteins are analogous to those of CAHS in eutardigrades, while there is no conservation at the sequence level. Conclusions Our results suggest that Heterotardigrada have partly shared but distinct anhydrobiosis machinery compared with Eutardigrada, possibly due to convergent evolution within Tardigrada. (276/350). Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08131-x.
Collapse
Affiliation(s)
- Yumi Murai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Maho Yagi-Utsumi
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Masayuki Fujiwara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Sae Tanaka
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.,Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, Aichi, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan. .,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan. .,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan. .,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan.
| |
Collapse
|
25
|
Sato Y, Tomita M, Soga T, Ochiai A, Makinoshima H. Upregulation of Thymidylate Synthase Induces Pemetrexed Resistance in Malignant Pleural Mesothelioma. Front Pharmacol 2021; 12:718675. [PMID: 34646134 PMCID: PMC8504579 DOI: 10.3389/fphar.2021.718675] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/14/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is an invasive malignancy that develops in the pleural cavity, and antifolates are used as chemotherapeutics for treating. The majority of antifolates, including pemetrexed (PMX), inhibit enzymes involved in purine and pyrimidine synthesis. MPM patients frequently develop drug resistance in clinical practice, however the associated drug-resistance mechanism is not well understood. This study was aimed to elucidate the mechanism underlying resistance to PMX in MPM cell lines. We found that among the differentially expressed genes associated with drug resistance (determined by RNA sequencing), TYMS expression was higher in the established resistant cell lines than in the parental cell lines. Knocking down TYMS expression significantly reduced drug resistance in the resistant cell lines. Conversely, TYMS overexpression significantly increased drug resistance in the parental cells. Metabolomics analysis revealed that the levels of dTMP were higher in the resistant cell lines than in the parental cell lines; however, resistant cells showed no changes in dTTP levels after PMX treatment. We found that the nucleic acid-biosynthetic pathway is important for predicting the efficacy of PMX in MPM cells. The results of chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) assays suggested that H3K27 acetylation in the 5′-UTR of TYMS may promote its expression in drug-resistant cells. Our findings indicate that the intracellular levels of dTMP are potential biomarkers for the effective treatment of patients with MPM and suggest the importance of regulatory mechanisms of TYMS expression in the disease.
Collapse
Affiliation(s)
- Yuzo Sato
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan.,Shonai Regional Industry Promotion Center, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Tomoyoshi Soga
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Atsushi Ochiai
- Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Hideki Makinoshima
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan.,Division of Translational Information, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| |
Collapse
|
26
|
Saito R, Hirayama A, Akiba A, Kamei Y, Kato Y, Ikeda S, Kwan B, Pu M, Natarajan L, Shinjo H, Akiyama S, Tomita M, Soga T, Maruyama S. Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry. Metabolites 2021; 11:671. [PMID: 34677386 PMCID: PMC8540909 DOI: 10.3390/metabo11100671] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 12/29/2022] Open
Abstract
Acute kidney injury (AKI) is defined as a rapid decline in kidney function. The associated syndromes may lead to increased morbidity and mortality, but its early detection remains difficult. Using capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS), we analyzed the urinary metabolomic profile of patients admitted to the intensive care unit (ICU) after invasive surgery. Urine samples were collected at six time points: before surgery, at ICU admission and 6, 12, 24 and 48 h after. First, urine samples from 61 initial patients (non-AKI: 23, mild AKI: 24, severe AKI: 14) were measured, followed by the measurement of urine samples from 60 additional patients (non-AKI: 40, mild AKI: 20). Glycine and ethanolamine were decreased in patients with AKI compared with non-AKI patients at 6-24 h in the two groups. The linear statistical model constructed at each time point by machine learning achieved the best performance at 24 h (median AUC, area under the curve: 89%, cross-validated) for the 1st group. When cross-validated between the two groups, the AUC showed the best value of 70% at 12 h. These results identified metabolites and time points that show patterns specific to subjects who develop AKI, paving the way for the development of better biomarkers.
Collapse
Affiliation(s)
- Rintaro Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Arisa Akiba
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Yushi Kamei
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Yuyu Kato
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Brian Kwan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA; (B.K.); (M.P.); (L.N.)
| | - Minya Pu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA; (B.K.); (M.P.); (L.N.)
| | - Loki Natarajan
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA 92093, USA; (B.K.); (M.P.); (L.N.)
| | - Hibiki Shinjo
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (H.S.); (S.A.); (S.M.)
| | - Shin’ichi Akiyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (H.S.); (S.A.); (S.M.)
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Japan; (A.H.); (A.A.); (Y.K.); (Y.K.); (S.I.); (M.T.); (T.S.)
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8560, Japan; (H.S.); (S.A.); (S.M.)
| |
Collapse
|
27
|
Ishibashi Y, Harada S, Eitaki Y, Iida M, Kurihara A, Hirata A, Shibuki T, Okamura T, Hirayama A, Sugimoto M, Soga T, Tomita M, Takebayashi T. 1299Association between environmental cadmium exposure and plasma and urinary metabolite profiles in Japanese cohort study. Int J Epidemiol 2021. [DOI: 10.1093/ije/dyab168.312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
The purpose of this study was to identify plasma and urinary metabolites that can be used to better identify the effects of cadmium exposure than N-acetyl-β-D-glucosaminidase (NAG) using capillary electrophoresis - mass spectrometry (CE-MS).
Methods
Urinary cadmium (U-Cd) was measured as an indicator of cadmium exposure. Fasting plasma and urine samples were collected from 1,412 men and 2,022 women in Tsuruoka Metabolomics Cohort Study. Charged 94 plasma and 123 urinary metabolites were detected and determined. Regression analysis was performed for urinary NAG, plasma, and urinary metabolites as dependent variables and U-Cd in quartiles as an independent variable. Multivariate regression model included age, SBP, smoke, rice intake, BMI, HbA1c, LDLc, alcohol consumption, physical activity, educational history, dietary energy intake, urinary Na/K ratio, and uric acid.
Results
The mean U-Cd of the population was 2.65 μg/g creatinine (SD: 1.63). NAG was positively associated with U-Cd, but the association was not significant with lower U-Cd quartiles. In the plasma metabolites, 10 metabolites had significantly negative association with U-Cd in all models and Cd quartiles. Among urinary metabolites, 27 metabolites had significantly positive association with U-Cd. Alanine was negatively associated with U-Cd in urinary metabolites. The trend test also showed significant dose-response trends for 9 plasma and all 28 urinary metabolites (p < 0.05).
Conclusions
We found that the levels of Cd exposure, which did not cause an increase in NAG, caused changes in plasma and urinary metabolites.
Key messages
This study indicated that metabolomics might be promising and useful as markers of Cd exposure.
Collapse
Affiliation(s)
- Yoshiki Ishibashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Yoko Eitaki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Takuma Shibuki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Faculty of Environment and Information Studies Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Faculty of Environment and Information Studies Keio University, Fujisawa, Japan
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Shinjuku-ku, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| |
Collapse
|
28
|
Kono N, Nakamura H, Mori M, Yoshida Y, Ohtoshi R, Malay AD, Pedrazzoli Moran DA, Tomita M, Numata K, Arakawa K. Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk. Proc Natl Acad Sci U S A 2021; 118:e2107065118. [PMID: 34312234 PMCID: PMC8346794 DOI: 10.1073/pnas.2107065118] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dragline silk of golden orb-weaver spiders (Nephilinae) is noted for its unsurpassed toughness, combining extraordinary extensibility and tensile strength, suggesting industrial application as a sustainable biopolymer material. To pinpoint the molecular composition of dragline silk and the roles of its constituents in achieving its mechanical properties, we report a multiomics approach, combining high-quality genome sequencing and assembly, silk gland transcriptomics, and dragline silk proteomics of four Nephilinae spiders. We observed the consistent presence of the MaSp3B spidroin unique to this subfamily as well as several nonspidroin SpiCE proteins. Artificial synthesis and the combination of these components in vitro showed that the multicomponent nature of dragline silk, including MaSp3B and SpiCE, along with MaSp1 and MaSp2, is essential to realize the mechanical properties of spider dragline silk.
Collapse
Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Hiroyuki Nakamura
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Rintaro Ohtoshi
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Ali D Malay
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | | | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Keiji Numata
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Depertment of Material Chemistry, Kyoto University, Kyotodaigaku-Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nihonkoku, Daihouji, Tsuruoka, Yamagata 997-0017, Japan;
- Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| |
Collapse
|
29
|
Miyamoto K, Hirayama A, Sato Y, Ikeda S, Maruyama M, Soga T, Tomita M, Nakamura M, Matsumoto M, Yoshimura N, Miyamoto T. A Metabolomic Profile Predictive of New Osteoporosis or Sarcopenia Development. Metabolites 2021; 11:metabo11050278. [PMID: 33924750 PMCID: PMC8145554 DOI: 10.3390/metabo11050278] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/26/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
The increasing number of patients with osteoporosis and sarcopenia is a global concern among countries with progressively aging societies. The high medical costs of treating those patients suggest that prevention rather than treatment is preferable. We enrolled 729 subjects who attended both the second and third surveys of the Research on Osteoarthritis/Osteoporosis Against Disability (ROAD) study. Blood samples were collected from subjects at the second survey, and then a comprehensive metabolomic analysis was performed. It was found that 35 had newly developed osteoporosis at the third survey performed four years later, and 39 were newly diagnosed with sarcopenia at the third survey. In the second survey, we found that serum Gly levels were significantly higher even after adjustment for age, sex, and BMI in subjects with newly developed osteoporosis relative to those who remained osteoporosis-negative during the four-year follow-up. We also show that serum taurine levels were significantly lower at the second survey, even after adjustment for age, sex, and BMI in subjects with newly developed sarcopenia during the four-year follow-up compared with those not diagnosed with sarcopenia at the second or third surveys. Though our sample size and odds ratios were small, increased Gly and decreased taurine levels were found to be predictive of new development of osteoporosis and sarcopenia, respectively, within four years.
Collapse
Affiliation(s)
- Kana Miyamoto
- Department of Orthopedic Surgery, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan;
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (A.H.); (S.I.); (M.M.); (T.S.); (M.T.)
| | - Yuiko Sato
- Department of Orthopedic Surgery, School of Medicine, Keio University, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.N.); (M.M.)
- Department of Advanced Therapy for Musculoskeletal Disorders II, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
- Department of Musculoskeletal Reconstruction and Regeneration Surgery, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (A.H.); (S.I.); (M.M.); (T.S.); (M.T.)
| | - Midori Maruyama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (A.H.); (S.I.); (M.M.); (T.S.); (M.T.)
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (A.H.); (S.I.); (M.M.); (T.S.); (M.T.)
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (A.H.); (S.I.); (M.M.); (T.S.); (M.T.)
| | - Masaya Nakamura
- Department of Orthopedic Surgery, School of Medicine, Keio University, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.N.); (M.M.)
| | - Morio Matsumoto
- Department of Orthopedic Surgery, School of Medicine, Keio University, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.N.); (M.M.)
| | - Noriko Yoshimura
- Department of Preventive Medicine for Locomotive Organ Disorders, 22nd Century Medical and Research Center, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-8655, Japan;
| | - Takeshi Miyamoto
- Department of Orthopedic Surgery, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan;
- Department of Orthopedic Surgery, School of Medicine, Keio University, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan; (Y.S.); (M.N.); (M.M.)
- Department of Advanced Therapy for Musculoskeletal Disorders II, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
- Department of Musculoskeletal Reconstruction and Regeneration Surgery, Keio University School of Medicine, 35 Shinano-machi, Shinjuku-ku, Tokyo 160-8582, Japan
- Correspondence: ; Tel.: +81-96-373-5226
| |
Collapse
|
30
|
Fujiwara M, Kono N, Hirayama A, Malay AD, Nakamura H, Ohtoshi R, Numata K, Tomita M, Arakawa K. Xanthurenic Acid Is the Main Pigment of Trichonephila clavata Gold Dragline Silk. Biomolecules 2021; 11:563. [PMID: 33921320 PMCID: PMC8070366 DOI: 10.3390/biom11040563] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 11/16/2022] Open
Abstract
Spider silk is a natural fiber with remarkable strength, toughness, and elasticity that is attracting attention as a biomaterial of the future. Golden orb-weaving spiders (Trichonephila clavata) construct large, strong webs using golden threads. To characterize the pigment of golden T. clavata dragline silk, we used liquid chromatography and mass spectrometric analysis. We found that the major pigment in the golden dragline silk of T. clavata was xanthurenic acid. To investigate the possible function of the pigment, we tested the effect of xanthurenic acid on bacterial growth using gram-negative Escherichia coli and gram-positive Bacillus subtilis. We found that xanthurenic acid had a slight antibacterial effect. Furthermore, to investigate the UV tolerance of the T. clavata threads bleached of their golden color, we conducted tensile deformation tests and scanning electron microscope observations. However, in these experiments, no significant effect was observed. We therefore speculate that golden orb-weaving spiders use the pigment for other purposes, such as to attract their prey in the sunlight.
Collapse
Affiliation(s)
- Masayuki Fujiwara
- Institute for Advanced Biosciences, Keio University, Nihonkoku 403-1, Daihoji, Tsuruoka, Yamagata 997-0013, Japan; (M.F.); (N.K.); (A.H.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
| | - Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, Nihonkoku 403-1, Daihoji, Tsuruoka, Yamagata 997-0013, Japan; (M.F.); (N.K.); (A.H.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Nihonkoku 403-1, Daihoji, Tsuruoka, Yamagata 997-0013, Japan; (M.F.); (N.K.); (A.H.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
| | - Ali D. Malay
- Biomacromolecules Research Team: RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (A.D.M.); (K.N.)
| | - Hiroyuki Nakamura
- Spiber Inc.: Mizukami 234-1, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (H.N.); (R.O.)
| | - Rintaro Ohtoshi
- Spiber Inc.: Mizukami 234-1, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan; (H.N.); (R.O.)
| | - Keiji Numata
- Biomacromolecules Research Team: RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; (A.D.M.); (K.N.)
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Nihonkoku 403-1, Daihoji, Tsuruoka, Yamagata 997-0013, Japan; (M.F.); (N.K.); (A.H.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Nihonkoku 403-1, Daihoji, Tsuruoka, Yamagata 997-0013, Japan; (M.F.); (N.K.); (A.H.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
- Faculty of Environment and Information Studies, Keio University, Endo 5322, Fujisawa, Kanagawa 252-0882, Japan
| |
Collapse
|
31
|
Hayasaka R, Tabata S, Hasebe M, Ikeda S, Ohnuma S, Mori M, Soga T, Tomita M, Hirayama A. Metabolomic Analysis of Small Extracellular Vesicles Derived from Pancreatic Cancer Cells Cultured under Normoxia and Hypoxia. Metabolites 2021; 11:metabo11040215. [PMID: 33915936 PMCID: PMC8066639 DOI: 10.3390/metabo11040215] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (EVs) released from cancer cells contribute to various malignant phenotypes of cancer, including metastasis, cachexia, and angiogenesis. Although DNA, mRNAs, miRNAs, and proteins contained in EVs have been extensively studied, the function of metabolites in EVs remains unclear. In this study, we performed a comprehensive metabolomic analysis of pancreatic cancer cells, PANC-1, cultured under different oxygen concentrations, and small EVs (sEVs) released from them, considering the fact that hypoxia contributes to the malignant behavior of cells in pancreatic cancer, which is a poorly diagnosed cancer. sEVs were collected by ultracentrifugation, and hydrophilic metabolites were analyzed using capillary ion chromatography-mass spectrometry and liquid chromatography-mass spectrometry, and lipids were analyzed by supercritical fluid chromatography-tandem mass spectrometry. A total of 140 hydrophilic metabolites and 494 lipids were detected in sEVs, and their profiles were different from those in cells. In addition, the metabolomic profile of sEVs was observed to change under hypoxic stress, and an increase in metabolites involved in angiogenesis was also detected. We reveal the hallmark of the metabolites contained in sEVs and the effect of tumor hypoxia on their profiles, which may help in understanding EV-mediated cancer malignancy.
Collapse
Affiliation(s)
- Ryosuke Hayasaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Sho Tabata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masako Hasebe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
| | - Satsuki Ikeda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
| | - Sumiko Ohnuma
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (R.H.); (S.T.); (M.H.); (S.I.); (S.O.); (M.M.); (T.S.); (M.T.)
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, Aichi 464-8603, Japan
- Correspondence: ; Tel.: +81-235-290-528
| |
Collapse
|
32
|
Ishibashi Y, Harada S, Takeuchi A, Iida M, Kurihara A, Kato S, Kuwabara K, Hirata A, Shibuki T, Okamura T, Sugiyama D, Sato A, Amano K, Hirayama A, Sugimoto M, Soga T, Tomita M, Takebayashi T. Reliability of urinary charged metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry. Sci Rep 2021; 11:7407. [PMID: 33795760 PMCID: PMC8016858 DOI: 10.1038/s41598-021-86600-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/17/2021] [Indexed: 12/19/2022] Open
Abstract
Currently, large-scale cohort studies for metabolome analysis have been launched globally. However, only a few studies have evaluated the reliability of urinary metabolome analysis. This study aimed to establish the reliability of urinary metabolomic profiling in cohort studies. In the Tsuruoka Metabolomics Cohort Study, 123 charged metabolites were identified and routinely quantified using capillary electrophoresis-mass spectrometry (CE-MS). We evaluated approximately 750 quality control (QC) samples and 6,720 participants’ spot urine samples. We calculated inter- and intra-batch coefficients of variation in the QC and participant samples and technical intraclass correlation coefficients (ICC). A correlation of metabolite concentrations between spot and 24-h urine samples obtained from 32 sub-cohort participants was also evaluated. The coefficient of variation (CV) was less than 20% for 87 metabolites (70.7%) and 20–30% for 19 metabolites (15.4%) in the QC samples. There was less than 20% inter-batch CV for 106 metabolites (86.2%). Most urinary metabolites would have reliability for measurement. The 96 metabolites (78.0%) was above 0.75 for the estimated ICC, and those might be useful for epidemiological analysis. Among individuals, the Pearson correlation coefficient of 24-h and spot urine was more than 70% for 59 of the 99 metabolites. These results show that the profiling of charged metabolites using CE-MS in morning spot human urine is suitable for epidemiological metabolomics studies.
Collapse
Affiliation(s)
- Yoshiki Ishibashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Ayano Takeuchi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Aya Hirata
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Takuma Shibuki
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Tomonori Okamura
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan
| | - Daisuke Sugiyama
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan.,Faculty of Nursing And Medical Care, Keio University, Fujisawa, Kanagawa, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kaori Amano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Toru Takebayashi
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, Japan. .,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.
| |
Collapse
|
33
|
Nakamura T, Tomita M, Horikawa N, Ishibashi M, Uematsu K, Hiraki T, Abe T, Uchimura N. Functional connectivity between the amygdala and subgenual cingulate gyrus predicts the antidepressant effects of ketamine in patients with treatment-resistant depression. Neuropsychopharmacol Rep 2021; 41:168-178. [PMID: 33615749 PMCID: PMC8340826 DOI: 10.1002/npr2.12165] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/28/2022] Open
Abstract
Aim Approximately one‐third of patients with major depressive disorder develop treatment‐resistant depression. One‐third of patients with treatment‐resistant depression demonstrate resistance to ketamine, which is a novel antidepressant effective for this disorder. The objective of this study was to examine the utility of resting‐state functional magnetic resonance imaging for the prediction of treatment response to ketamine in treatment‐resistant depression. Methods An exploratory seed‐based resting‐state functional magnetic resonance imaging analysis was performed to examine baseline resting‐state functional connectivity differences between ketamine responders and nonresponders before treatment with multiple intravenous ketamine infusions. Results Fifteen patients with treatment‐resistant depression received multiple intravenous subanesthetic (0.5 mg/kg/40 minutes) ketamine infusions, and nine were identified as responders. The exploratory resting‐state functional magnetic resonance imaging analysis identified a cluster of significant baseline resting‐state functional connectivity differences associating ketamine response between the amygdala and subgenual anterior cingulate gyrus in the right hemisphere. Using anatomical region of interest analysis of the resting‐state functional connectivity, ketamine response was predicted with 88.9% sensitivity and 100% specificity. The resting‐state functional connectivity of significant group differences between responders and nonresponders retained throughout the treatment were considered a trait‐like feature of heterogeneity in treatment‐resistant depression. Conclusion This study suggests the possible clinical utility of resting‐state functional magnetic resonance imaging for predicting the antidepressant effects of ketamine in treatment‐resistant depression patients and implicated resting‐state functional connectivity alterations to determine the trait‐like pathophysiology underlying treatment response heterogeneity in treatment‐resistant depression. This study illustrates that the alteration in the RSFC within the right AN in TRD patients reflects the antidepressant response to ketamine at baseline. The alteration remained throughout the 2‐week treatment with multiple ketamine infusions and seemed to reflect the trait‐like features underlying treatment heterogeneity in TRD. By employing an anatomical ROI of the sc/sgACC, the present study also suggests the possible clinical utility of the rsfMRI to predict the treatment response to ketamine in TRD patients.
![]()
Collapse
Affiliation(s)
- Tomoyuki Nakamura
- Department of Neuropsychiatry, Kurume University School of Medicine, Kurume City, Japan
| | - Masaru Tomita
- Department of Neuropsychiatry, Kurume University School of Medicine, Kurume City, Japan.,Elm-tree Mental Clinic, Ogori City, Japan
| | - Naoki Horikawa
- Department of Neuropsychiatry, Kurume University School of Medicine, Kurume City, Japan.,Nozoe Hills Hospital, Kurume City, Japan
| | - Masatoshi Ishibashi
- Department of Neuropsychiatry, Kurume University School of Medicine, Kurume City, Japan
| | - Ken Uematsu
- Uematsu Mental Clinic, Chikugo City, Japan.,Department of Pharmacology, Kurume University School of Medicine, Kurume City, Japan
| | - Teruyuki Hiraki
- Department of Anaesthesiology, Kurume University School of Medicine, Kurume City, Japan
| | - Toshi Abe
- Department of Radiology, Kurume University School of Medicine, Kurume City, Japan
| | - Naohisa Uchimura
- Department of Neuropsychiatry, Kurume University School of Medicine, Kurume City, Japan
| |
Collapse
|
34
|
Guo J, Satoh K, Tabata S, Mori M, Tomita M, Soga T. Reprogramming of glutamine metabolism via glutamine synthetase silencing induces cisplatin resistance in A2780 ovarian cancer cells. BMC Cancer 2021; 21:174. [PMID: 33596851 PMCID: PMC7891143 DOI: 10.1186/s12885-021-07879-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cisplatin (CDDP) significantly prolongs survival in various cancers, but many patients also develop resistance that results in treatment failure. Thus, this study aimed to elucidate the underlying mechanisms by which ovarian cancer cells acquire CDDP resistance. METHODS We evaluated the metabolic profiles in CDDP-sensitive ovarian cancer A2780 cells and CDDP-resistant A2780cis cells using capillary electrophoresis-time-of-flight mass spectrometry (CE-TOFMS). We further examined the expression of glutamine metabolism enzymes using real-time PCR and Western blot analyses. Cell viability was accessed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. RESULTS The results showed that levels of glutamine, glutamate, and glutathione (GSH), a key drug resistance mediator synthesized from glutamate, were significantly elevated in A2780cis cells than those in A2780 cells. Furthermore, glutamine starvation decreased the GSH levels and CDDP resistance in A2780cis cells. Interestingly, the expression of glutamine synthetase (GS/GLUL), which synthesizes glutamine from glutamate and thereby negatively regulates GSH production, was almost completely suppressed in resistant A2780cis cells. In addition, treatment of A2780cis cells with 5-aza-2'-deoxycytidine, a DNA-demethylating agent, restored GS expression and reduced CDDP resistance. In contrast, GS knockdown in CDDP-sensitive A2780 cells induced CDDP resistance. CONCLUSIONS The results indicate that upregulation of GSH synthesis from glutamine via DNA methylation-mediated silencing of GS causes CDDP resistance in A2780cis cells. Therefore, glutamine metabolism could be a novel therapeutic target against CDDP resistance.
Collapse
Affiliation(s)
- Jing Guo
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan
| | - Kiyotoshi Satoh
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, 997-0052, Japan. .,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan.
| | - Sho Tabata
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, 997-0052, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan.,Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, 997-0052, Japan.,Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan.,Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, 252-0882, Japan
| |
Collapse
|
35
|
Shibutami E, Ishii R, Harada S, Kurihara A, Kuwabara K, Kato S, Iida M, Akiyama M, Sugiyama D, Hirayama A, Sato A, Amano K, Sugimoto M, Soga T, Tomita M, Takebayashi T. Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan. PLoS One 2021; 16:e0246456. [PMID: 33566801 PMCID: PMC7875413 DOI: 10.1371/journal.pone.0246456] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 01/19/2021] [Indexed: 11/18/2022] Open
Abstract
Food intake biomarkers can be critical tools that can be used to objectively assess dietary exposure for both epidemiological and clinical nutrition studies. While an accurate estimation of food intake is essential to unravel associations between the intake and specific health conditions, random and systematic errors affect self-reported assessments. This study aimed to clarify how habitual food intake influences the circulating plasma metabolome in a free-living Japanese regional population and to identify potential food intake biomarkers. To achieve this aim, we conducted a cross-sectional analysis as part of a large cohort study. From a baseline survey of the Tsuruoka Metabolome Cohort Study, 7,012 eligible male and female participants aged 40-69 years were chosen for this study. All data on patients' health status and dietary intake were assessed via a food frequency questionnaire, and plasma samples were obtained during an annual physical examination. Ninety-four charged plasma metabolites were measured using capillary electrophoresis mass spectrometry, by a non-targeted approach. Statistical analysis was performed using partial-least-square regression. A total of 21 plasma metabolites were likely to be associated with long-term food intake of nine food groups. In particular, the influential compounds in each food group were hydroxyproline for meat, trimethylamine-N-oxide for fish, choline for eggs, galactarate for dairy, cystine and betaine for soy products, threonate and galactarate for carotenoid-rich vegetables, proline betaine for fruits, quinate and trigonelline for coffee, and pipecolate for alcohol, and these were considered as prominent food intake markers in Japanese eating habits. A set of circulating plasma metabolites was identified as potential food intake biomarkers in the Japanese community-dwelling population. These results will open the way for the application of new reliable dietary assessment tools not by self-reported measurements but through objective quantification of biofluids.
Collapse
Affiliation(s)
- Eriko Shibutami
- Graduate School of Health Management, Keio University, Fujisawa, Kanagawa, Japan
| | - Ryota Ishii
- Biostatistics Unit, Clinical and Translational Research Center, Keio University Hospital, Tokyo, Japan
| | - Sei Harada
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Ayako Kurihara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Kazuyo Kuwabara
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Suzuka Kato
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Miho Iida
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
| | - Miki Akiyama
- Graduate School of Health Management, Keio University, Fujisawa, Kanagawa, Japan
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Daisuke Sugiyama
- Graduate School of Health Management, Keio University, Fujisawa, Kanagawa, Japan
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Faculty of Nursing and Medical Care, Keio University, Fujisawa, Kanagawa, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Kaori Amano
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Toru Takebayashi
- Graduate School of Health Management, Keio University, Fujisawa, Kanagawa, Japan
- Department of Preventive Medicine and Public Health, Keio University School of Medicine, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- * E-mail:
| |
Collapse
|
36
|
Ohashi Y, Yamamoto Y, Yamada A, Yamamoto K, Arai K, Namba F, Miyamoto N, Tomita M, Fukumoto T, Minamikawa T, Oka M. Aortic Rupture due to Co-localization of Aortic Intimal Myofibroblastic Sarcoma and Urothelial Carcinoma: A Unique Case Report. Intern Med 2021; 60:269-274. [PMID: 32921685 PMCID: PMC7872815 DOI: 10.2169/internalmedicine.5191-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We herein report a unique case of aortic rupture due to co-localization of aortic intimal myofibroblastic sarcoma (IMFS) and urothelial carcinoma (UC). A 76-year-old man who was being followed up after surgery for UC 5 years earlier developed aortic rupture and underwent emergency surgery. Intraoperatively, a tumorous mass on the luminal side of the aortic arch was found near the rupture. A histopathological analysis of the mass revealed aortic IMFS. Furthermore, co-localization of IMFS and UC cells was found near the rupture. The fragility of the aortic wall due to co-localization of IMFS and UC was believed to contribute to the aortic rupture.
Collapse
Affiliation(s)
- Yutaka Ohashi
- Department of Dentistry and Oral Surgery, Kita-Harima Medical Center, Japan
| | - Yuki Yamamoto
- Department of Diagnostic Pathology, Kita-Harima Medical Center, Japan
| | - Akitoshi Yamada
- Department of Cardiovascular Surgery, Kita-Harima Medical Center, Japan
| | - Kazuhiro Yamamoto
- Department of Otorhinolaryngology, Kita-Harima Medical Center, Japan
| | - Keisuke Arai
- Department of Gastroenterology, Kita-Harima Medical Center, Japan
| | - Fumiko Namba
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Japan
| | - Naokazu Miyamoto
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Japan
| | - Masaru Tomita
- Department of Diagnostic Radiology, Kita-Harima Medical Center, Japan
| | - Takeshi Fukumoto
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Japan
| | - Tsutomu Minamikawa
- Department of Dentistry and Oral Surgery, Kita-Harima Medical Center, Japan
| | - Masahiro Oka
- Department of Dermatology, Kita-Harima Medical Center, Japan
| |
Collapse
|
37
|
Ogura T, Wakayama M, Ashino Y, Kadowaki R, Sato M, Soga T, Tomita M. Effects of feed crops and boiling on chicken egg yolk and white determined by a metabolome analysis. Food Chem 2020; 327:127077. [DOI: 10.1016/j.foodchem.2020.127077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/11/2022]
|
38
|
Fujishima H, Okada N, Matsumoto K, Shimizu E, Fukuda S, Tomita M. Conjunctival Injection Reduction in Patients with Atopic Keratoconjunctivitis Due to Synergic Effect of Bovine Enteric-Coated Lactoferrin in 0.1% Tacrolimus Ophthalmic Suspension. J Clin Med 2020; 9:jcm9103093. [PMID: 32992801 PMCID: PMC7599790 DOI: 10.3390/jcm9103093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 01/03/2023] Open
Abstract
Lactoferrin (LF), a multifunctional glycoprotein found in mammalian milk, is reported to have immunoregulatory effects. The present study aimed to evaluate whether enteric-coated LF (eLF) could improve symptoms in patients with atopic keratoconjunctivitis (AKC). This randomized double-blind placebo-controlled single-center trial comprised Japanese patients (n = 20; aged 22–60 years) with AKC. Patients treated with 0.1% tacrolimus ophthalmic suspension (TALYMUS®) were administered eLF (400 mg/d of bovine LF) or placebo tablets for 12 weeks. Conjunctival injection was examined, papillae formation in the palpebral conjunctiva was evaluated, and corneal fluorescein score, itchy sensation in end-point itching scale, and serum allergic parameters were assessed. Conjunctival injection was significantly reduced in the LF group than in the placebo group (p = 0.0017, Mann–Whitney U-test). Papillae formation in the palpebral conjunctiva showed a statistical decrease in the LF group than in the placebo group (p = 0.010, unpaired T-test). LF combined with TALYMUS® could be a promising treatment strategy to mitigate AKC.
Collapse
Affiliation(s)
- Hiroshi Fujishima
- Department of Ophthalmology, Tsurumi University School of Dental Medicine, Tsurumi, Yokohama 230-8501, Japan;
- Correspondence: ; Tel.: +81-45-580-8599
| | - Naoko Okada
- Department of Ophthalmology, Tsurumi University School of Dental Medicine, Tsurumi, Yokohama 230-8501, Japan;
- Department of Pharmaceutical Sciences, Nihon Pharmaceutical University, Saitama 362-0806, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan;
| | - Eisuke Shimizu
- Department of Ophthalmology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (S.F.); (M.T.)
- Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki 210-0821, Kanagawa, Japan
- Transborder Medical Research Center, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; (S.F.); (M.T.)
| |
Collapse
|
39
|
Kono N, Nakamura H, Mori M, Tomita M, Arakawa K. Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies. Sci Rep 2020; 10:15721. [PMID: 32973264 PMCID: PMC7515903 DOI: 10.1038/s41598-020-72888-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 09/08/2020] [Indexed: 01/29/2023] Open
Abstract
Orb-weaving spiders have two main methods of prey capture: cribellate spiders use dry, sticky capture threads, and ecribellate spiders use viscid glue droplets. Predation behaviour is a major evolutionary driving force, and it is important on spider phylogeny whether the cribellate and ecribellate spiders each evolved the orb architecture independently or both strategies were derived from an ancient orb web. These hypotheses have been discussed based on behavioural and morphological characteristics, with little discussion on this subject from the perspective of molecular materials of orb web, since there is little information about cribellate spider-associated spidroin genes. Here, we present in detail a spidroin catalogue of six uloborid species of cribellate orb-weaving spiders, including cribellate and pseudoflagelliform spidroins, with transcriptome assembly complemented with long read sequencing, where silk composition is confirmed by proteomics. Comparative analysis across families (Araneidae and Uloboridae) shows that the gene architecture, repetitive domains, and amino acid frequencies of the orb web constituting silk proteins are similar among orb-weaving spiders regardless of the prey capture strategy. Notably, the fact that there is a difference only in the prey capture thread proteins strongly supports the monophyletic origin of the orb web.
Collapse
Affiliation(s)
- Nobuaki Kono
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan.
| | - Hiroyuki Nakamura
- Spiber Inc., 234-1 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata, 997-0017, Japan
| |
Collapse
|
40
|
Yang J, Yang Y, Ishii M, Nagata M, Aw W, Obana N, Tomita M, Nomura N, Fukuda S. Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms? Microbes Environ 2020; 35. [PMID: 32624527 PMCID: PMC7511787 DOI: 10.1264/jsme2.me20037] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Microbes inhabit various environments, such as soil, water environments, plants, and animals. Humans harbor a complex commensal microbial community in the gastrointestinal tract, which is known as the gut microbiota. The gut microbiota participates not only in various metabolic processes in the human body, it also plays a critical role in host immune responses. Gut microbes that inhabit the intestinal epithelial surface form polymicrobial biofilms. In the last decade, it has been widely reported that gut microbial biofilms and gut microbiota-derived products, such as metabolites and bacterial membrane vesicles, not only directly affect the host intestinal environment, but also indirectly influence the health of the host. In this review, we discuss the most recent findings from human and animal studies on the interactions between the gut microbiota and hosts, and their associations with various disorders, including inflammatory diseases, atopic dermatitis, metabolic disorders, and psychiatric and neurological diseases. The integrated approach of metabologenomics together with biofilm imaging may provide valuable insights into the gut microbiota and suggest remedies that may lead to a healthier society.
Collapse
Affiliation(s)
- Jiayue Yang
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University
| | | | - Manami Ishii
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University
| | - Mayuko Nagata
- Institute for Advanced Biosciences, Keio University.,Faculty of Environment and Information Studies, Keio University
| | - Wanping Aw
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University
| | - Nozomu Obana
- Transborder Medical Research Center, University of Tsukuba
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University.,Faculty of Environment and Information Studies, Keio University
| | - Nobuhiko Nomura
- Microbiology Research Center for Sustainability, University of Tsukuba.,Faculty of Life and Environmental Sciences, University of Tsukuba
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University.,Systems Biology Program, Graduate School of Media and Governance, Keio University.,Transborder Medical Research Center, University of Tsukuba.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology.,Metabologenomics, Inc
| |
Collapse
|
41
|
Kondo K, Mori M, Tomita M, Arakawa K. Pre-treatment with D942, a furancarboxylic acid derivative, increases desiccation tolerance in an anhydrobiotic tardigrade Hypsibius exemplaris. FEBS Open Bio 2020; 10:1774-1781. [PMID: 32623826 PMCID: PMC7459401 DOI: 10.1002/2211-5463.12926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/18/2020] [Accepted: 06/30/2020] [Indexed: 11/25/2022] Open
Abstract
The tardigrade Hypsibius exemplaris can undergo anhydrobiosis. Several chemicals that inhibit successful anhydrobiosis in H. exemplaris have been identified, and these chemicals inhibit the activity of signaling molecules. In the present study, we investigated whether upregulation of the activity of these signaling molecules could improve desiccation tolerance of H. exemplaris. Pre‐treatment with an indirect activator of AMP‐activated protein kinase [AMPK; which directly inhibits mammalian NAD(P)H dehydrogenase [quinone] 1 [NQO1] of mitochondrial complex I (D942)] significantly improved desiccation tolerance of H. exemplaris, whereas a direct activator of AMPK did not. To elucidate the underlying molecular mechanisms, we examined the proteome of tardigrades treated with D942. Two proteins, putative glutathione S‐transferase and pirin‐like protein, were upregulated by treatment. Both of these proteins are known to be associated with the response to oxidative stress. One of the downregulated proteins was serine/threonine‐proteinphosphatase 2A (PP2A) 65‐kDa regulatory subunit A alpha isoform, and it is interesting to note that PP2A activity was previously suggested to be required for successful anhydrobiosis in H. exemplaris. Taken together, our results suggest that D942 treatment may partially induce responses common to those of desiccation stress. The identification of a chemical that improves desiccation tolerance of H. exemplaris may facilitate further investigation into desiccation tolerance mechanisms.
Collapse
Affiliation(s)
- Koyuki Kondo
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| |
Collapse
|
42
|
Ozawa H, Hirayama A, Ishikawa T, Kudo R, Maruyama M, Shoji F, Doke T, Ishimoto T, Maruyama S, Soga T, Tomita M. Comprehensive Dipeptide Profiling and Quantitation by Capillary Electrophoresis and Liquid Chromatography Coupled with Tandem Mass Spectrometry. Anal Chem 2020; 92:9799-9806. [DOI: 10.1021/acs.analchem.0c01258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Hitoshi Ozawa
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Takamasa Ishikawa
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Ryuhei Kudo
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
- Nissin Pharmaceutical Co., Ltd., 2-3-1 Shogehigashi, Tendo, Yamagata 994-0069, Japan
| | - Midori Maruyama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Futaba Shoji
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| | - Tomohito Doke
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Takuji Ishimoto
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Shoichi Maruyama
- Department of Nephrology, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Aichi 466-8550, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami,
Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa 252-0882, Japan
| |
Collapse
|
43
|
Islam MZ, Arifuzzaman M, Banik S, Hossain MA, Ferdous J, Khalequzzaman M, Pittendrigh BR, Tomita M, Ali MP. Mapping QTLs underpin nutrition components in aromatic rice germplasm. PLoS One 2020; 15:e0234395. [PMID: 32525930 PMCID: PMC7289389 DOI: 10.1371/journal.pone.0234395] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
As rice is an important staple food globally, research for development and enhancement of its nutritional value it is an imperative task. Identification of nutrient enriched rice germplasm and exploiting them for breeding programme is the easiest way to develop better quality rice. In this study, we analyzed 113 aromatic rice germplasm in order to identify quantitative trait loci (QTL) underpinning nutrition components and determined by measuring the normal frequency distribution for Fe, Zn, amylose, and protein content in those rice germplasm. Comparatively, the germplasm Radhuni pagal, Kalobakri, Thakurbhog (26.6 ppm) and Hatisail exhibited the highest mean values for Fe (16.9 ppm), Zn (34.1 ppm), amylose (26.6 ppm) and protein content (11.0 ppm), respectively. Moreover, a significant linear relationship (R2 = 0.693) was observed between Fe and Zn contents. Cluster analysis based on Mahalanobis D2 distances revealed four major clusters of 113 rice germplasm, with cluster III containing a maximum 37 germplasm and a maximum inter-cluster distance between clusters III and IV. The 45 polymorphic SSRs and four trait associations exhibited eight significant quantitative trait loci (QTL) located on eight different chromosomes using composite interval mapping (CIM). The highly significant QTL (variance 7.89%, LOD 2.02) for protein content (QTL.pro.1) was observed on chromosome 1 at 94.9cM position. Also, four QTLs for amylose content were observed with the highly significant QTL.amy.8 located on chromosome 8 exhibiting 7.2% variance with LOD 1.83. Only one QTL (QTL.Fe.9) for Fe content was located on chromosome 9 (LOD 1.24), and two (QTL.Zn.4 and QTL.Zn.5) for Zn on chromosome 4 (LOD 1.71) and 5 (LOD 1.18), respectively. Overall, germplasm from clusters III and IV might offer higher heterotic response with the identified QTLs playing a significant role in any rice biofortification breeding program and released with development of new varieties.
Collapse
Affiliation(s)
- M. Z. Islam
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
| | - M. Arifuzzaman
- Department of Genetics and Plant Breeding, Hajee Mohammad Danesh Science and Technology University, Dinajpur, Bangladesh
| | - S. Banik
- Grain Quality and Nutrition Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. A. Hossain
- Regional Station, Barisal, Bangladesh Rice Research Institute, Gazipur, Bangladesh
| | - J. Ferdous
- Biotechnology Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - M. Khalequzzaman
- Genetic Resources and Seed Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | - B. R. Pittendrigh
- Department of Entomology, Michigan State University, East Lansing, Michigan, United States of America
| | - M. Tomita
- Genetics and Genome Engineering Laboratory, Green Biology Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka City, Shizuoka, Japan
- * E-mail: (MZI); (MPA); (MT)
| | - M. P. Ali
- Entomolgy Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
- * E-mail: (MZI); (MPA); (MT)
| |
Collapse
|
44
|
Sakata RC, Ishiguro S, Mori H, Tanaka M, Tatsuno K, Ueda H, Yamamoto S, Seki M, Masuyama N, Nishida K, Nishimasu H, Arakawa K, Kondo A, Nureki O, Tomita M, Aburatani H, Yachie N. Base editors for simultaneous introduction of C-to-T and A-to-G mutations. Nat Biotechnol 2020; 38:865-869. [PMID: 32483365 DOI: 10.1038/s41587-020-0509-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 04/03/2020] [Indexed: 12/20/2022]
Abstract
We describe base editors that combine both cytosine and adenine base-editing functions. A codon-optimized fusion of the cytosine deaminase PmCDA1, the adenosine deaminase TadA and a Cas9 nickase (Target-ACEmax) showed a high median simultaneous C-to-T and A-to-G editing activity at 47 genomic targets. On-target as well as DNA and RNA off-target activities of Target-ACEmax were similar to those of existing single-function base editors.
Collapse
Affiliation(s)
- Rina C Sakata
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,College of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Soh Ishiguro
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Hideto Mori
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Mamoru Tanaka
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Kenji Tatsuno
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Hiroki Ueda
- Biological Data Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Shogo Yamamoto
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Motoaki Seki
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Nanami Masuyama
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Keiji Nishida
- Engineering Biology Research Center, Kobe University, Kobe, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Hiroshi Nishimasu
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, Kobe, Japan.,Graduate School of Science, Technology and Innovation, Kobe University, Kobe, Japan.,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Osamu Nureki
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan
| | - Masaru Tomita
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan
| | - Nozomu Yachie
- Synthetic Biology Division, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan. .,College of Arts and Sciences, University of Tokyo, Tokyo, Japan. .,Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan. .,Graduate School of Media and Governance, Keio University, Fujisawa, Japan. .,Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan. .,PRESTO, Japan Science and Technology Agency (JST), Tokyo, Japan.
| |
Collapse
|
45
|
Hikichi S, Sugimoto M, Tomita M. Correlation-centred variable selection of a gene expression signature to predict breast cancer metastasis. Sci Rep 2020; 10:7923. [PMID: 32404965 PMCID: PMC7220948 DOI: 10.1038/s41598-020-64870-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 04/23/2020] [Indexed: 12/20/2022] Open
Abstract
Predictions of distant cancer metastasis based on gene signatures are studied intensively to realise precise diagnosis and treatments. Gene selection i.e. feature selection is a cornerstone to both establish accurate predictions and understand underlying pathologies. Here, we developed a simple but robust feature selection method using a correlation-centred approach to select minimal gene sets that have both high predictive and generalisation abilities. A multiple logistic regression model was used to predict 5-year metastases of patients with breast cancer. Gene expression data obtained from tumour samples of lymph node-negative breast cancer patients were randomly split into training and validation data. Our method selected 12 genes using training data and this showed a higher area under the receiver operating characteristic curve of 0.730 compared with 0.579 yielded by previously reported 76 genes. The signature with the predictive model was validated in an independent dataset, and its higher generalization ability was observed. Gene ontology analyses revealed that our method consistently selected genes with identical functions which frequently selected by the 76 genes. Taken together, our method identifies fewer gene sets bearing high predictive abilities, which would be versatile and applicable to predict other factors such as the outcomes of medical treatments and prognoses of other cancer types.
Collapse
Affiliation(s)
- Shiori Hikichi
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan.,Research Fellow of Japan Society for the Promotion of Science, Chiyoda, Tokyo, 102-0083, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0811, Japan. .,Research and Development Center for Minimally Invasive Therapies, Institute of Medical Science, Tokyo Medical University, Shinjuku, Tokyo, 160-0022, Japan.
| | - Masaru Tomita
- Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-8520, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, 997-0811, Japan
| |
Collapse
|
46
|
Hamid SS, Wakayama M, Ashino Y, Kadowaki R, Soga T, Tomita M. Effect of blanching on the concentration of metabolites in two parts of Undaria pinnatifida, Wakame (leaf) and Mekabu (sporophyll). ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101829] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
47
|
Tsukimi T, Watabe T, Tanaka K, Sato MP, Suzuki H, Tomita M, Fukuda S. Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals. J Genomics 2020; 8:37-42. [PMID: 32328204 PMCID: PMC7171383 DOI: 10.7150/jgen.38516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/20/2019] [Indexed: 11/05/2022] Open
Abstract
Bifidobacterium species are well recognized as probiotics and colonized in various parts of the human body. Here, we report the draft genome sequences of Bifidobacterium animalis isolated from two healthy Japanese volunteers, one of which was sampled twice before and after a 10-year interval. A core genome phylogeny analysis indicated that the strains isolated from the same volunteer were closely related. This paper is the first report of multiple draft genome sequences of B. animalis independently isolated from the same individual and provides insight into the probiotic potential of a member of this species.
Collapse
Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Tsubasa Watabe
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Kazuki Tanaka
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Mitsuhiko P Sato
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka 812-8582, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,Faculty of Environment and Information Studies, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, 5322 Endo, Fujisawa, Kanagawa 252-0882, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki, Kanagawa 210-0821, Japan.,Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan.,Metabologenomics, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
| |
Collapse
|
48
|
Saito M, Sato A, Nagata S, Tamaki S, Tomita M, Suzuki H, Kanai A. Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life. Genome Biol Evol 2020; 11:2713-2726. [PMID: 31513263 PMCID: PMC6777427 DOI: 10.1093/gbe/evz195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2019] [Indexed: 01/13/2023] Open
Abstract
Clp1, a polyribonucleotide 5′-hydroxyl kinase in eukaryotes, is involved in pretRNA splicing and mRNA 3′-end formation. Enzymes similar in amino acid sequence to Clp1, Nol9, and Grc3, are present in some eukaryotes and are involved in prerRNA processing. However, our knowledge of how these Clp1 family proteins evolved and diversified is limited. We conducted a large-scale molecular evolutionary analysis of the Clp1 family proteins in all living organisms for which protein sequences are available in public databases. The phylogenetic distribution and frequencies of the Clp1 family proteins were investigated in complete genomes of Bacteria, Archaea and Eukarya. In total, 3,557 Clp1 family proteins were detected in the three domains of life, Bacteria, Archaea, and Eukarya. Many were from Archaea and Eukarya, but a few were found in restricted, phylogenetically diverse bacterial species. The domain structures of the Clp1 family proteins also differed among the three domains of life. Although the proteins were, on average, 555 amino acids long (range, 196–2,728), 122 large proteins with >1,000 amino acids were detected in eukaryotes. These novel proteins contain the conserved Clp1 polynucleotide kinase domain and various other functional domains. Of these proteins, >80% were from Fungi or Protostomia. The polyribonucleotide kinase activity of Thermus scotoductus Clp1 (Ts-Clp1) was characterized experimentally. Ts-Clp1 preferentially phosphorylates single-stranded RNA oligonucleotides (Km value for ATP, 2.5 µM), or single-stranded DNA at higher enzyme concentrations. We propose a comprehensive assessment of the diversification of the Clp1 family proteins and the molecular evolution of their functional domains.
Collapse
Affiliation(s)
- Motofumi Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Asako Sato
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Shohei Nagata
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Satoshi Tamaki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Haruo Suzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Akio Kanai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan.,Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan.,Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| |
Collapse
|
49
|
Hirayama A, Tabata S, Kudo R, Hasebe M, Suzuki K, Tomita M, Soga T. The use of a double coaxial electrospray ionization sprayer improves the peak resolutions of anionic metabolites in capillary ion chromatography-mass spectrometry. J Chromatogr A 2020; 1619:460914. [PMID: 32008820 DOI: 10.1016/j.chroma.2020.460914] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 01/03/2023]
Abstract
Recently, ion chromatography coupled with mass spectrometry has been used for the determination of anionic metabolites. However, connection with a mass spectrometer in this method is not straightforward because backpressure produced by the addition of a make-up solution often affects the peak resolutions of the target metabolites. To overcome this problem, we developed a capillary ion chromatography-mass spectrometry method utilizing a double coaxial electrospray ionization sprayer. This method was not affected by backpressure and the number of theoretical plates was about three times that of a conventional sprayer. Under optimized conditions, 44 anionic metabolites, including organic acids, sugar phosphates, nucleotides, and cofactors, were successfully separated and selectively detected with a Q Exactive mass spectrometer. The calibration curves of the tested metabolites showed excellent linearity within the range of 1-100,000 nmol/L and the correlation coefficient was greater than 0.991. The detection limits for these metabolites were between 1 and 500 nmol/L (0.4 and 200 fmol). The developed method was applied to the quantitation of anionic metabolites in cultured cancer cell samples with tumor necrosis factor (TNF)-α stimulation. This allowed for the successful determination of 105 metabolites. The levels of tricarboxylic acid cycle intermediates changed significantly after TNF-α stimulation. These results demonstrate that the developed method is a promising new tool for comprehensive analysis of anionic metabolites.
Collapse
Affiliation(s)
- Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Sho Tabata
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Ryuhei Kudo
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Masako Hasebe
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Kumi Suzuki
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| |
Collapse
|
50
|
Yoshida Y, Sugiura K, Tomita M, Matsumoto M, Arakawa K. Comparison of the transcriptomes of two tardigrades with different hatching coordination. BMC Dev Biol 2019; 19:24. [PMID: 31864287 PMCID: PMC6925440 DOI: 10.1186/s12861-019-0205-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 11/11/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND Tardigrades are microscopic organisms, famous for their tolerance against extreme environments. The establishment of rearing systems of multiple species has allowed for comparison of tardigrade physiology, in particular in embryogenesis. Interestingly, in-lab cultures of limnic species showed smaller variation in hatching timing than terrestrial species, suggesting a hatching regulation mechanism acquired by adaptation to their habitat. RESULTS To this end, we screened for coordinated gene expression during the development of two species of tardigrades, Hypsibius exemplaris and Ramazzottius varieornatus, and observed induction of the arthropod molting pathway. Exposure of ecdysteroids and juvenile hormone analog affected egg hatching but not embryonic development in only the limnic H. exemplaris. CONCLUSION These observations suggest a hatching regulation mechanism by the molting pathway in H. exemplaris.
Collapse
Affiliation(s)
- Yuki Yoshida
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Kenta Sugiura
- Graduate School of Science and Technology, Keio University, Fujisawa, Yokohama, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan
| | - Midori Matsumoto
- Graduate School of Science and Technology, Keio University, Fujisawa, Yokohama, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Mizukami 246-2, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, Japan.
| |
Collapse
|