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Nakane K, Yagi K, Yajima S, Nomura S, Sugimoto M, Seto Y. Salivary metabolomic biomarkers for esophageal and gastric cancers by liquid chromatography-mass spectrometry. Cancer Sci 2024. [PMID: 39004809 DOI: 10.1111/cas.16256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/24/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
Early detection of esophageal and gastric cancers is essential for patients' prognosis; however, optimal noninvasive screening tests are currently not available. Saliva is a biofluid that is readily available, allowing for frequent screening tests. Thus, we explored salivary diagnostic biomarkers for esophageal and gastric cancers using metabolomic analyses. Saliva samples were collected from patients with esophageal (n = 50) and gastric cancer (n = 63), and patients without cancer as controls (n = 20). Salivary metabolites were analyzed by liquid chromatography-mass spectrometry to identify salivary biomarkers. We also examined the metabolic profiles of gastric cancer tissues and compared them with the salivary biomarkers. The sensitivity of the diagnostic models based on salivary biomarkers was assessed by comparing it with that of serum tumor markers. Additionally, using postoperative saliva samples collected from patients with gastric cancer, we analyzed the changes in the biomarkers' concentrations before and after surgery. Cytosine was detected as a salivary biomarker for gastric cancer, and cytosine, 2-oxoglutarate, and arginine were detected as salivary biomarkers for esophageal cancer. Cytidine, a cytosine nucleotide, showed decreased concentrations in gastric cancer tissues. The sensitivity of the diagnostic models for esophageal and gastric cancers was 66.0% and 47.6%, respectively, while that of serum tumor markers was 40%. Salivary cytosine concentration increased significantly postoperatively relative to the preoperative value. In summary, we identified salivary biomarkers for esophageal and gastric cancers, which showed diagnostic sensitivity at least comparable to that of serum tumor markers. Salivary metabolomic tests could be promising screening tests for these types of cancer.
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Affiliation(s)
- Kosuke Nakane
- Department of Gastrointestinal Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Koichi Yagi
- Department of Gastrointestinal Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Sho Yajima
- Department of Gastrointestinal Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Sachiyo Nomura
- Department of Gastrointestinal Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Imamura R, Sugimoto M, Horike SI, Terakawa J, Fujita K, Tamai I, Daikoku T, Kato Y, Arakawa H. Role of Organic Anion Transporter NPT4 in Renal Handling of Uremic Toxin 3-indoxyl Sulfate. J Pharm Sci 2024; 113:1996-2000. [PMID: 38641061 DOI: 10.1016/j.xphs.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
Sodium-phosphate transporter NPT4 (SLC17A3) is a membrane transporter for organic anionic compounds localized on the apical membranes of kidney proximal tubular epithelial cells and plays a role in the urinary excretion of organic anionic compounds. However, its physiological role has not been sufficiently elucidated because its substrate specificity is yet to be determined. The present study aimed to comprehensively explore the physiological substrates of NPT4 in newly developed Slc17a3-/- mice using a metabolomic approach. Metabolomic analysis showed that the plasma concentrations of 11 biological substances, including 3-indoxyl sulfate, were more than two-fold higher in Slc17a3-/- mice than in wild-type mice. Moreover, urinary excretion of 3-indoxyl sulfate was reduced in Slc17a3-/- mice compared to that in wild-type mice. The uptake of 3-indoxyl sulfate by NPT4-expressing Xenopus oocytes was significantly higher than that by water-injected oocytes. The calculated Km and Vmax values for NPT4-mediated 3-indoxyl sulfate uptake were 4.52 ± 1.18 mM and 1.45 ± 0.14 nmol/oocyte/90 min, respectively. In conclusion, the present study revealed that 3-indoxyl sulfate is a novel substrate of NPT4 based on the metabolomic analysis of Slc17a3-/- mice, suggesting that NPT4 regulates systemic exposure to 3-indoxyl sulfate by regulating its urinary excretion.
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Affiliation(s)
- Rikako Imamura
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Shin-Ichi Horike
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-0934, Japan
| | - Jumpei Terakawa
- Laboratory of Toxicology, School of Veterinary Medicine, Azabu University, Sagamihara, Kanagawa 252-5201, Japan
| | - Kazuki Fujita
- Faculty of Pharmaceutical Science, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Ikumi Tamai
- Faculty of Pharmaceutical Science, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Takiko Daikoku
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa 920-0934, Japan
| | - Yukio Kato
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroshi Arakawa
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan.
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3
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Okinaka Y, Kageyama S, Goto T, Sugimoto M, Tomita A, Aizawa Y, Kobayashi K, Wada A, Kawauchi A, Kataoka Y. Metabolomic profiling of cancer-related fatigue involved in cachexia and chemotherapy. Sci Rep 2024; 14:8329. [PMID: 38594321 PMCID: PMC11004174 DOI: 10.1038/s41598-024-57747-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Patients with advanced cancer are frequently burdened with a severe sensation of fatigue called cancer-related fatigue (CRF). CRF is induced at various stages and treatments, such as cachexia and chemotherapy, and reduces the overall survival of patients. Objective and quantitative assessment of CRF could contribute to the diagnosis and prediction of treatment efficacy. However, such studies have not been intensively performed, particularly regarding metabolic profiles. Here, we conducted plasma metabolomics of 15 patients with urological cancer. The patients with and without fatigue, including those with cachexia or chemotherapy-induced fatigue, were compared. Significantly lower concentrations of valine and tryptophan were observed in fatigued patients than in non-fatigued patients. In addition, significantly higher concentrations of polyamine pathway metabolites were observed in patients with fatigue and cachexia than in those without cachexia. Patients with exacerbated fatigue due to chemotherapy showed significantly decreased cysteine and methionine metabolism before chemotherapy compared with those without fatigue exacerbation. These findings suggest that plasma metabolic profiles could help improve the diagnosis and monitoring of CRF.
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Affiliation(s)
- Yuki Okinaka
- Department of Urology, Shiga University of Medical Science, Shiga, 520-2192, Japan
- RIKEN Center for Biosystems Dynamics Research, Hyogo, 650-0047, Japan
| | - Susumu Kageyama
- Department of Urology, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Toshiyuki Goto
- RIKEN Center for Biosystems Dynamics Research, Hyogo, 650-0047, Japan
- Graduate School of Science, Technology and Innovation, Kobe University, Hyogo, 650-0047, Japan
| | - Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, 160-8402, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0052, Japan
| | - Atsumi Tomita
- Institute of Medical Science, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Yumi Aizawa
- Institute of Medical Science, Tokyo Medical University, Tokyo, 160-8402, Japan
| | - Kenichi Kobayashi
- Department of Urology, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Akinori Wada
- Department of Urology, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Akihiro Kawauchi
- Department of Urology, Shiga University of Medical Science, Shiga, 520-2192, Japan
| | - Yosky Kataoka
- RIKEN Center for Biosystems Dynamics Research, Hyogo, 650-0047, Japan.
- Graduate School of Science, Technology and Innovation, Kobe University, Hyogo, 650-0047, Japan.
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Pucchio A, Krance SH, Pur DR, Bhatti J, Bassi A, Manichavagan K, Brahmbhatt S, Aggarwal I, Singh P, Virani A, Stanley M, Miranda RN, Felfeli T. Applications of artificial intelligence and bioinformatics methodologies in the analysis of ocular biofluid markers: a scoping review. Graefes Arch Clin Exp Ophthalmol 2024; 262:1041-1091. [PMID: 37421481 DOI: 10.1007/s00417-023-06100-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 07/10/2023] Open
Abstract
PURPOSE This scoping review summarizes the applications of artificial intelligence (AI) and bioinformatics methodologies in analysis of ocular biofluid markers. The secondary objective was to explore supervised and unsupervised AI techniques and their predictive accuracies. We also evaluate the integration of bioinformatics with AI tools. METHODS This scoping review was conducted across five electronic databases including EMBASE, Medline, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Web of Science from inception to July 14, 2021. Studies pertaining to biofluid marker analysis using AI or bioinformatics were included. RESULTS A total of 10,262 articles were retrieved from all databases and 177 studies met the inclusion criteria. The most commonly studied ocular diseases were diabetic eye diseases, with 50 papers (28%), while glaucoma was explored in 25 studies (14%), age-related macular degeneration in 20 (11%), dry eye disease in 10 (6%), and uveitis in 9 (5%). Supervised learning was used in 91 papers (51%), unsupervised AI in 83 (46%), and bioinformatics in 85 (48%). Ninety-eight papers (55%) used more than one class of AI (e.g. > 1 of supervised, unsupervised, bioinformatics, or statistical techniques), while 79 (45%) used only one. Supervised learning techniques were often used to predict disease status or prognosis, and demonstrated strong accuracy. Unsupervised AI algorithms were used to bolster the accuracy of other algorithms, identify molecularly distinct subgroups, or cluster cases into distinct subgroups that are useful for prediction of the disease course. Finally, bioinformatic tools were used to translate complex biomarker profiles or findings into interpretable data. CONCLUSION AI analysis of biofluid markers displayed diagnostic accuracy, provided insight into mechanisms of molecular etiologies, and had the ability to provide individualized targeted therapeutic treatment for patients. Given the progression of AI towards use in both research and the clinic, ophthalmologists should be broadly aware of the commonly used algorithms and their applications. Future research may be aimed at validating algorithms and integrating them in clinical practice.
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Affiliation(s)
- Aidan Pucchio
- Department of Ophthalmology, Queen's University, Kingston, ON, Canada
- Queens School of Medicine, Kingston, ON, Canada
| | - Saffire H Krance
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Daiana R Pur
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Jasmine Bhatti
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Arshpreet Bassi
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Shaily Brahmbhatt
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Priyanka Singh
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Aleena Virani
- Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | | | - Rafael N Miranda
- The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - Tina Felfeli
- The Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, University of Toronto, 340 College Street, Suite 400, Toronto, ON, M5T 3A9, Canada.
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Arakawa H, Kawanishi T, Shengyu D, Nishiuchi T, Meguro-Horike M, Horike SI, Sugimoto M, Kato Y. Renal Pharmacokinetic Adaptation to Cholestasis Causes Increased Nephrotoxic Drug Accumulation by Mrp6 Downregulation in Mice. J Pharm Sci 2023; 112:3209-3215. [PMID: 37611664 DOI: 10.1016/j.xphs.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/13/2023] [Accepted: 08/13/2023] [Indexed: 08/25/2023]
Abstract
In hepatic dysfunction, renal pharmacokinetic adaptation can be observed, although information on the changes in drug exposure and the interorgan regulation of membrane transporters in kidney in liver diseases is limited. This study aimed to clarify the effects of renal exposure to nephrotoxic drugs during cholestasis induced by bile duct ligation (BDL). Among the 11 nephrotoxic drugs examined, the tissue accumulation of imatinib and cisplatin in kidney slices obtained from mice 2 weeks after BDL operation was higher than that in sham-operated mice. The uptake of imatinib in the kidney slices of BDL mice was slightly higher, whereas its efflux from the slices was largely decreased compared to that in sham-operated mice. Proteomic analysis revealed a reduction in renal expression of the efflux transporter multidrug resistance-associated protein 6 (Mrp6/Abcc6) in BDL mice, and both imatinib and cisplatin were identified as Mrp6 substrates. Survival probability after cisplatin administration was reduced in BDL mice. In conclusion, the present study demonstrated that BDL-induced cholestasis leads to the downregulation of the renal basolateral efflux transporter Mrp6, resulting in drug accumulation in renal cells and promoting drug-induced renal injury.
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Affiliation(s)
- Hiroshi Arakawa
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takumi Kawanishi
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Dai Shengyu
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Takumi Nishiuchi
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Makiko Meguro-Horike
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Shin-Ichi Horike
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa 920-0934, Japan
| | - Masahiro Sugimoto
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0052, Yamagata, Japan
| | - Yukio Kato
- Faculty of Pharmacy, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan.
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Li H, Tan H, Liu Z, Pan S, Tan S, Zhu Y, Wang Q, Su G, Zhou C, Cao Q, Yang P. Succinic acid exacerbates experimental autoimmune uveitis by stimulating neutrophil extracellular traps formation via SUCNR1 receptor. Br J Ophthalmol 2023; 107:1744-1749. [PMID: 35346946 DOI: 10.1136/bjophthalmol-2021-320880] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/08/2022] [Indexed: 12/26/2022]
Abstract
AIMS To investigate the effect of succinic acid on the development of experimental autoimmune uveitis (EAU) and the underlying mechanism. METHODS Succinic acid was administrated intraperitoneally to evaluate its effects on immune response and EAU in mice. Intraocular inflammation was evaluated by histopathological scoring. Frequencies of Th1/Th17 cells were measured by flow cytometry. Concentrations of IFN-γ/IL-17A, neutrophil elastase (NE) and myeloperoxidase (MPO) were determined by enzyme-linked immunosorbent test. Infiltration of neutrophils and generation of neutrophil extracellular traps (NETs) within the eye were assessed by immumofluorescence. NETs formation in extracellular matrix was visualised by laser scanning confocal microscopy. Succinate receptor (SUCNR1) antagonist was used to investigate its effect on the generation of NETs. RESULTS Intraperitoneal injection of succinic acid exacerbated EAU severity as evidenced by severe histological changes in association with elevated frequencies of splenic Th1/Th17 cells, and upregulated levels of IFN-γ/IL-17A and NETs in plasma. In vitro experiments showed that succinic acid could promote the generation of NETs by neutrophils as shown by increased expression of NE and MPO.NETs could increase the frequencies of Th1/Th17 cells in CD4+ T cells and their expression of IFN-γ/IL-17A. In the experiment of receptor antagonism, the upregulatory effect of succinic acid on NETs could be significantly blocked by SUCNR1 antagonist. CONCLUSIONS Succinic acid could worsen EAU induced by IRBP in mice. This effect was possibly mediated by its upregulation on NETs generation and frequencies of Th1/Th17 cells in affiliation with increased production of IFN-γ/IL-17A through succinic acid-SUCNR1 axis.
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Affiliation(s)
- Hongxi Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Handan Tan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhangluxi Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Su Pan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Shiyao Tan
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yunyun Zhu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qingfeng Wang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunjiang Zhou
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Kim J, Lee S, Moodley Y, Yagnik L, Birnie D, Dwivedi G. The role of the host-microbiome and metabolomics in sarcoidosis. Am J Physiol Cell Physiol 2023; 325:C1336-C1353. [PMID: 37746695 DOI: 10.1152/ajpcell.00316.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023]
Abstract
Sarcoidosis is a complex inflammatory fibrotic disease that affects multiple organ systems. It is characterized by the infiltration of lymphocytes and mononuclear phagocytes, which form non-caseating granulomas in affected organs. The lungs and intrathoracic lymph nodes are the most commonly affected organs. The underlying cause of sarcoidosis is unknown, but it is believed to occur in genetically predisposed individuals who are exposed to pathogenic organisms, environmental contaminants, or self and non-self-antigens. Recent research has suggested that the microbiome may play a role in the development of respiratory conditions, including sarcoidosis. Additionally, metabolomic studies have identified potential biomarkers for monitoring sarcoidosis progression. This review will focus on recent microbiome and metabolomic findings in sarcoidosis, with the goal of shedding light on the pathogenesis and possible diagnostic and therapeutic approaches.
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Affiliation(s)
- Junwoo Kim
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Silvia Lee
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Yuben Moodley
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Respiratory Internal Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Lokesh Yagnik
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Department of Respiratory Internal Medicine, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - David Birnie
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Division of Cardiology, Department of Medicine, University of Ottawa, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Girish Dwivedi
- Department of Advanced Clinical and Translational Cardiovascular Imaging, Harry Perkins Institute of Medical Research, Murdoch, Western Australia, Australia
- School of Medicine, The University of Western Australia, Crawley, Western Australia, Australia
- Division of Cardiology, Department of Medicine, University of Ottawa, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
- Department of Cardiology, Fiona Stanley Hospital, Murdoch, Western Australia, Australia
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8
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Qiu S, Cai Y, Yao H, Lin C, Xie Y, Tang S, Zhang A. Small molecule metabolites: discovery of biomarkers and therapeutic targets. Signal Transduct Target Ther 2023; 8:132. [PMID: 36941259 PMCID: PMC10026263 DOI: 10.1038/s41392-023-01399-3] [Citation(s) in RCA: 112] [Impact Index Per Article: 112.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/22/2023] Open
Abstract
Metabolic abnormalities lead to the dysfunction of metabolic pathways and metabolite accumulation or deficiency which is well-recognized hallmarks of diseases. Metabolite signatures that have close proximity to subject's phenotypic informative dimension, are useful for predicting diagnosis and prognosis of diseases as well as monitoring treatments. The lack of early biomarkers could lead to poor diagnosis and serious outcomes. Therefore, noninvasive diagnosis and monitoring methods with high specificity and selectivity are desperately needed. Small molecule metabolites-based metabolomics has become a specialized tool for metabolic biomarker and pathway analysis, for revealing possible mechanisms of human various diseases and deciphering therapeutic potentials. It could help identify functional biomarkers related to phenotypic variation and delineate biochemical pathways changes as early indicators of pathological dysfunction and damage prior to disease development. Recently, scientists have established a large number of metabolic profiles to reveal the underlying mechanisms and metabolic networks for therapeutic target exploration in biomedicine. This review summarized the metabolic analysis on the potential value of small-molecule candidate metabolites as biomarkers with clinical events, which may lead to better diagnosis, prognosis, drug screening and treatment. We also discuss challenges that need to be addressed to fuel the next wave of breakthroughs.
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Affiliation(s)
- Shi Qiu
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China
| | - Ying Cai
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Hong Yao
- First Affiliated Hospital, Harbin Medical University, Harbin, 150081, China
| | - Chunsheng Lin
- Second Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, 150001, China
| | - Yiqiang Xie
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Songqi Tang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
| | - Aihua Zhang
- International Advanced Functional Omics Platform, Scientific Experiment Center, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), College of Chinese Medicine, Hainan Medical University, Xueyuan Road 3, Haikou, 571199, China.
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.
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9
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Sugimoto M, Aizawa Y, Tomita A. Data Processing and Analysis in Liquid Chromatography-Mass Spectrometry-Based Targeted Metabolomics. Methods Mol Biol 2023; 2571:241-255. [PMID: 36152165 DOI: 10.1007/978-1-0716-2699-3_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Mass spectrometry (MS)-based metabolomics provides high-dimensional datasets; that is, the data include various metabolite features. Data analysis begins by converting the raw data obtained from the MS to produce a data matrix (metabolite × concentrations). This is followed by several steps, such as peak integration, alignment of multiple data, metabolite identification, and calculation of metabolite concentrations. Each step yields the analytical results and the accompanying information used for the quality assessment of the anterior steps. Thus, the measurement quality can be analyzed through data processing. Here, we introduce a typical data processing procedure and describe a method to utilize the intermediate data as quality control. Subsequently, commonly used data analysis methods for metabolomics data, such as statistical analyses, are also introduced.
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Affiliation(s)
- Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
- Institute for Advanced Biosciences, Yamagata, Japan.
| | - Yumi Aizawa
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Atsumi Tomita
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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10
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Clinical Comparative Study of Different Fundus Imaging Methods in the Acute Phase of Vogt-Koyanagi-Harada Disease. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:5812090. [PMID: 36262163 PMCID: PMC9576379 DOI: 10.1155/2022/5812090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 09/20/2022] [Indexed: 11/05/2022]
Abstract
Background The diversification of follow-up ophthalmic imaging examination methods, and whether there are differences in clinical characteristics of VKH at the acute stage under different images. Our study aims to compare the imaging characteristics of the acute phase of Vogt-Koyanagi-Harada disease (VKH) under different fundus imaging methods to deepen clinical knowledge. Methods A retrospective case study was performed on fundus images of 62 eyes from 31 patients with acute phase VKH and a disease duration ≤2 months who were treated at Ganzhou People's Hospital from January 2013 to December 2020. Fundus photography (FP), optical coherence tomography (OCT), and fundus fluorescein angiography (FFA) were performed on all 62 eyes. The fundus presentations were divided into an optic disc swelling (ODS) group, a serous retinal detachment (SRD) group, and a mixed type (MT) group (both ODS and SRD), and the proportions of patients in these groups and the coincidence rate of ODS, SRD, and MT identified by the three fundus imaging modes were determined. Results The proportion of patients with ODS was highest under FP, and the proportion of patients with MT was highest under OCT. The proportions of patients with ODS and MT in the three fundus imaging modes differed significantly (P < 0.05), while the proportion of patients with SRD did not (P > 0.05). The proportion of patients with subretinal fluid with positive OCT results was significantly higher than those with positive FFA results (81.08% vs. 59.46%) (P < 0.05). Conclusion Clinically significant positive signs could be obtained for acute VKH under different imaging methods. However, compared with FP and FFA, OCT tomography is more intuitive for the observation of lesions.
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11
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Ding J, Su G, Wang H, Tian X, Xu J, Li N, Luo X, Yang P. Comparison of metabolic profiles in aqueous humor of Fuchs' syndrome and presumed viral-induced anterior uveitis patients. Clin Exp Ophthalmol 2022; 50:1065-1081. [PMID: 35849327 DOI: 10.1111/ceo.14138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/30/2022] [Accepted: 07/16/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE To investigate and compare the metabolic profiles in the aqueous humor of Han Chinese patients with Fuchs' syndrome and presumed viral-induced anterior uveitis (PVIAU). METHODS The metabolites in the aqueous humor of 20 Fuchs' syndrome patients, 20 PVIAU patients and 20 senile cataract control patients were detected by liquid chromatography with mass spectrometry. Differential metabolites were analyzed by Student's t-test, multivariate analysis, cluster analysis and correlation analysis. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was applied to explore the potential disrupted metabolic pathways in Fuchs' syndrome and PVIAU. RESULTS Comparisons of metabolic profiles identified 29 differential metabolites between Fuchs' syndrome patients and controls, 36 differential metabolites between PVIAU patients and controls, and 30 differential metabolites between Fuchs' syndrome patients and PVIAU patients. DL-serine was markedly elevated in Fuchs' syndrome, and 1-palmitoyl-sn-glycero-3-phosphocholine in PVIAU. KEGG pathway analysis suggested that the differential metabolites in Fuchs' syndrome compared with control were mostly enriched in central carbon metabolism in cancer, adenosine triphosphate-binding cassette (ABC) transporters, and mineral absorption, while those in PVIAU compared with control were mostly enriched in protein digestion and absorption, biosynthesis of unsaturated fatty acids, and ABC transporters. The metabolic pathways differentially affected in Fuchs' syndrome compared to PVIAU included central carbon metabolism in cancer, protein digestion and absorption, and ascorbate and aldarate metabolism. CONCLUSIONS In Fuchs' syndrome and PVIAU patients, the aqueous humor exhibited specific metabolic profiles and enriched metabolic pathways, which provides a better understanding of the pathogenesis of Fuchs' syndrome and PVIAU in Han Chinese patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Jiadong Ding
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Guannan Su
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Huafei Wang
- Department of Biological Sample Bank, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xin Tian
- Department of Biological Sample Bank, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Xu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Na Li
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiang Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
| | - Peizeng Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Province Eye Hospital, Henan International Joint Research Laboratory for Ocular Immunology and Retinal Injury Repair, Zhengzhou, People's Republic of China; The Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology, Chongqing Eye Institute, Chongqing Branch of National Clinical Research Center for Ocular Diseases, Chongqing, China
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12
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Long-Term Mastication Changed Salivary Metabolomic Profiles. Metabolites 2022; 12:metabo12070660. [PMID: 35888784 PMCID: PMC9322701 DOI: 10.3390/metabo12070660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/08/2022] [Accepted: 07/15/2022] [Indexed: 11/29/2022] Open
Abstract
Saliva is an ideal biofluid for monitoring oral and systemic health. Repeated mastication is a typical physical stimulus that improves salivary flow and oral hygiene. Recent metabolomic studies have shown the potential of salivary metabolomic components for various disease monitoring systems. Here, we evaluated the effect of long-term mastication on salivary metabolomic profiles. Young women with good oral hygiene (20.8 ± 0.3 years, n = 17) participated. They were prohibited from chewing gum during control periods (4 weeks each) and were instructed to chew a piece of gum base seven times a day for 10 min each time during the intervention period. Paired samples of unstimulated whole saliva collected on the last day of the control and intervention period were compared. Liquid chromatography−time-of-flight mass spectrometry successfully quantified 85 metabolites, of which 41 showed significant differences (p < 0.05, Wilcoxon paired test corrected by false discovery rate). Except for a few metabolites, such as citrate, most metabolites showed lower concentrations after the intervention. The pathways related to glycogenic amino acids, such as alanine, arginine, and glutamine, altered considerably. This study suggests that long-term mastication induces unstimulated salivary component-level changes.
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13
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Comprehensive Proteomic Profiling of Vitreous Humor in Ocular Sarcoidosis Compared with Other Vitreoretinal Diseases. J Clin Med 2022; 11:jcm11133606. [PMID: 35806888 PMCID: PMC9267904 DOI: 10.3390/jcm11133606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/04/2022] [Accepted: 06/19/2022] [Indexed: 12/10/2022] Open
Abstract
Ocular sarcoidosis is an inflammatory disease that manifests as uveitis, and is often difficult to distinguish from other forms of uveitis based on nonspecific findings alone. Comprehensive proteomic analyses of vitreous humor using LC-MS/MS were performed in each patient with ocular sarcoidosis, vitreoretinal lymphoma (VRL), and controls with epiretinal membrane or macular hole. Differential expression proteins (DEPs) were identified by comparing with VRL and controls, and functional pathway analysis was performed. The candidate biomarker proteins for ocular sarcoidosis were validated using enzyme-linked immunosorbent assay. A total of 1590 proteins were identified in all samples. Of these, 290 and 174 DEPs were detected in vitreous of ocular sarcoidosis compared with controls and VRL, respectively. Enrichment pathway analysis revealed that pathways related to the immune system were most upregulated. Validation of two candidate biomarkers for ocular sarcoidosis, neutrophil gelatinase-associated lipocalin (NGAL) and junctional adhesion molecules B (JAMB), confirmed upregulated NGAL and JAMB protein expressions in ocular sarcoidosis compared to controls and VRL. The results of this study revealed that altered vitreous protein expression levels may discriminate ocular sarcoidosis from other uveitis diseases. Vitreous NGAL and JAMB are potential biomarkers and may serve as an auxiliary tool for the diagnosis of ocular sarcoidosis.
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14
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Sugimoto M. Editorial of Special Issue "Metabolomic Analysis in Health and Diseases". J Clin Med 2021; 10:jcm10163491. [PMID: 34441787 PMCID: PMC8396909 DOI: 10.3390/jcm10163491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/05/2022] Open
Affiliation(s)
- Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan; or ; Tel.: +81-235-29-0528; Fax: +81-235-29-0574
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan
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15
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Mizuno T, Konno H, Nagata T, Isaka M, Ohde Y. Osteogenic and brain metastases after non-small cell lung cancer resection. Int J Clin Oncol 2021; 26:1840-1846. [PMID: 34165658 DOI: 10.1007/s10147-021-01969-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND A significant number of non-small cell lung cancer (NSCLC) patients develop osteogenic metastases (OMs) and/or brain metastases (BMs) after surgery, however, routine chest computed tomography (CT) sometimes fails to diagnose these recurrences. We investigated the incidence of BMs and OMs after pulmonary resection and aimed to identify candidates who can benefit from brain magnetic resonance imaging (MRI) and 18F-fluorodeoxyglucose-positron emission tomography (FDG-PET) in addition to CT. METHODS We retrospectively reviewed medical records of 1099 NSCLC patients who underwent pulmonary resection between 2002 and 2013. Clinicopathological factors associated with OM and/or BM were investigated using univariate and multivariate analyses. RESULTS Postoperative recurrence occurred in 344 patients (32.6%). OMs were diagnosed in 56 patients (5.6%) with 93% within 3 years. BMs were identified in 72 patients (6.6%) with 91.1% within 3 years. Multivariate analysis revealed that poorly differentiated tumor and the presence of pathological nodal metastases were significantly associated with postoperative BM (p = 0.037, < 0.001), preoperative serum carcinoembryonic antigen (CEA) level of 5 ng/mL or higher and the presence of pathological nodal metastases were significantly associated with OM (p = 0.034, < 0.001). The prevalence of OM and/or BM in 5 years was as high as 25.9% in patients with pathological nodal metastases. CONCLUSIONS We identified significant predictive factors of postoperative BM and OM. Under patient selection, the effectiveness of intensive surveillance for the modes of recurrence should be investigated with respect to earlier detection, maintenance of quality of life, and survival outcomes.
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Affiliation(s)
- Tetsuya Mizuno
- Division of Thoracic Surgery, Shizuoka Cancer Center, Shimonagakubo 1007, Nagaizumi-cho, Shunto-gun, Shizuoka, 411-8777, Japan.
| | - Hayato Konno
- Division of Thoracic Surgery, Shizuoka Cancer Center, Shimonagakubo 1007, Nagaizumi-cho, Shunto-gun, Shizuoka, 411-8777, Japan
| | - Toshiyuki Nagata
- Division of Thoracic Surgery, Shizuoka Cancer Center, Shimonagakubo 1007, Nagaizumi-cho, Shunto-gun, Shizuoka, 411-8777, Japan
| | - Mitsuhiro Isaka
- Division of Thoracic Surgery, Shizuoka Cancer Center, Shimonagakubo 1007, Nagaizumi-cho, Shunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuhisa Ohde
- Division of Thoracic Surgery, Shizuoka Cancer Center, Shimonagakubo 1007, Nagaizumi-cho, Shunto-gun, Shizuoka, 411-8777, Japan
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16
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Kuroiwa M, Hamaoka-Fuse S, Sugimoto M, Kurosawa Y, Aita Y, Tomita A, Anjo M, Tanaka R, Endo T, Kime R, Hamaoka T. Correlation of Plasma Amino Acid and Anthropometric Profiles with Brown Adipose Tissue Density in Humans. J Clin Med 2021; 10:jcm10112339. [PMID: 34071816 PMCID: PMC8199240 DOI: 10.3390/jcm10112339] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 12/14/2022] Open
Abstract
This study examined the relationship between plasma amino acid (AA) concentrations, including branched-chain AAs, and brown adipose tissue density (BAT-d). One hundred and seventy-three subjects (69 men, 104 women) aged 22-68 years were recruited during the winter season. AAs were comprehensively quantified using liquid chromatography-time-of-flight-mass spectrometry. The total hemoglobin concentration in the supraclavicular region ([total-Hb]sup), an indicator of BAT-d, was assessed using near-infrared time-resolved spectroscopy. Anthropometric parameters, including age, percentage of body fat, and visceral fat, were evaluated. Factors associated with higher (≥74 µM) or lower (<74 µM) [total-Hb]sup were investigated by multiple logistic regression models that included AA concentrations alone (model 1) or AA concentrations and anthropometric parameters (model 2) as independent variables. When adjusted for the false discovery rate, [total-Hb]sup was positively correlated with glycine and asparagine levels in men and with the serine level in both men and women and was negatively correlated with the branched-chain AA concentration in men. Models 1 and 2 correlated with higher or lower BAT-d for men (r = 0.73, p = 0.015) and women (r = 0.58, p = 0.079) and for men (r = 0.82, p = 0.0070) and women (r = 0.70, p = 0.020), respectively. A combination of anthropometric parameters and plasma AA concentrations could be a reliable biomarker for higher and lower BAT-d.
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Affiliation(s)
- Miyuki Kuroiwa
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Sayuri Hamaoka-Fuse
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies, Institute of Medical Science, Tokyo Medical University, Tokyo 160-8402, Japan; (M.S.); (Y.A.); (A.T.)
| | - Yuko Kurosawa
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Yasuko Aita
- Research and Development Center for Minimally Invasive Therapies, Institute of Medical Science, Tokyo Medical University, Tokyo 160-8402, Japan; (M.S.); (Y.A.); (A.T.)
| | - Atsumi Tomita
- Research and Development Center for Minimally Invasive Therapies, Institute of Medical Science, Tokyo Medical University, Tokyo 160-8402, Japan; (M.S.); (Y.A.); (A.T.)
| | - Mikiko Anjo
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Riki Tanaka
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Tasuki Endo
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Ryotaro Kime
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
| | - Takafumi Hamaoka
- Department of Sports Medicine for Health Promotion, Tokyo Medical University, Tokyo 160-8402, Japan; (M.K.); (S.H.-F.); (Y.K.); (M.A.); (R.T.); (T.E.); (R.K.)
- Correspondence:
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