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Jansman MMT, Norkute E, Jin W, Kempen PJ, Douka D, Thulstrup PW, Hosta-Rigau L. Nitric oxide-triggering activity of gold-, platinum- and cerium oxide-nanozymes from S-nitrosothiols and diazeniumdiolates. Colloids Surf B Biointerfaces 2024; 244:114161. [PMID: 39191113 DOI: 10.1016/j.colsurfb.2024.114161] [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: 04/29/2024] [Revised: 07/31/2024] [Accepted: 08/11/2024] [Indexed: 08/29/2024]
Abstract
Cardiovascular diseases pose a significant global health challenge, contributing to high mortality rates and impacting overall well-being and quality of life. Nitric oxide (NO) plays a pivotal role as a vasodilator, regulating blood pressure and enhancing blood flow-crucial elements in preventing cardiovascular diseases, making it a prime therapeutic target. Herein, metal-based nanozymes (NZs) designed to induce NO release from both endogenous and exogenous NO-donors are investigated. Successful synthesis of gold, platinum (Pt) and cerium oxide NZs is achieved, with all three NZs demonstrating the ability to catalyze the NO release from various NO sources, namely S-nitrosothiols and diazeniumdiolates. Pt-NZs exhibit the strongest performance among the three NZ types. Further exploration involved investigating encapsulation and coating techniques using poly(lactic-co-glycolic acid) nanoparticles as experimental carriers for Pt-NZs. Both strategies showed efficiency in serving as platforms for Pt-NZs, successfully showing the ability to trigger NO release.
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Affiliation(s)
- Michelle Maria Theresia Jansman
- Department of Health Technology, Center for Nanomedicine and Theranostics, Technical University of Denmark, Nils Koppels Allé, Building 423, Kgs. Lyngby 2800, Denmark
| | - Evita Norkute
- Department of Health Technology, Center for Nanomedicine and Theranostics, Technical University of Denmark, Nils Koppels Allé, Building 423, Kgs. Lyngby 2800, Denmark
| | - Weiguang Jin
- Department of Health Technology, Center for Nanomedicine and Theranostics, Technical University of Denmark, Nils Koppels Allé, Building 423, Kgs. Lyngby 2800, Denmark
| | - Paul Joseph Kempen
- Department of Health Technology, Center for Nanomedicine and Theranostics, Technical University of Denmark, Nils Koppels Allé, Building 423, Kgs. Lyngby 2800, Denmark; DTU Nanolab, National Center for Nano Fabrication and Characterization Technical University of Denmark, Ørsteds Plads, Building 347, Kgs. Lyngby 2800, Denmark
| | - Despoina Douka
- Department of Health Technology, Center for Nanomedicine and Theranostics, Technical University of Denmark, Nils Koppels Allé, Building 423, Kgs. Lyngby 2800, Denmark
| | - Peter Waaben Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, Copenhagen 2100, Denmark
| | - Leticia Hosta-Rigau
- Department of Health Technology, Center for Nanomedicine and Theranostics, Technical University of Denmark, Nils Koppels Allé, Building 423, Kgs. Lyngby 2800, Denmark.
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2
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Li K, Liu P, Zeng Y, Liu M, Ye J, Zhu L. Exploring the bidirectional causal association between Sleep Apnea Syndrome and Depression: A Mendelian randomization study involving gut microbiota, serum metabolites, and inflammatory factors. J Affect Disord 2024; 366:308-316. [PMID: 39216644 DOI: 10.1016/j.jad.2024.08.153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 08/13/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
OBJECTIVE This study aimed to investigate the potential causal association between Sleep Apnea Syndrome (SAS) and Depression, focusing on the roles of gut microbiota, serum metabolites, and inflammatory factors in these conditions. METHODS Mendelian Randomization (MR) analysis was performed using data from genome-wide association studies to assess 211 types of gut microbiota, 1400 serum metabolites, and 91 inflammatory factors as potential contributing factors. Causal inference was conducted using the Inverse Variance Weighted (IVW) method, with additional robustness checks through Cochran's Q test, MR-Egger regression intercept test, MR-PRESSO global test, and leave-one-out analysis. RESULTS The MR analysis indicated a positive correlation between the risk of SAS and Depression (OR = 1.12, 95 % CI: 1.05-1.19, P < 0.001), with a reciprocal analysis showing a similar positive correlation between Depression and the risk of SAS (OR = 1.19, 95 % CI: 1.07-1.31, P = 0.001). Additionally, causal associations were identified between 15 types of gut microbiota, 36 serum metabolites, and 2 inflammatory factors with SAS, and between 11 types of gut microbiota, 23 serum metabolites, and 3 inflammatory factors with Depression (IVW, all P < 0.05). The robustness of these findings was confirmed through the MR-Egger regression intercept test and MR-PRESSO global test. CONCLUSION This study provides epidemiological evidence of a bidirectional causal association between SAS and Depression, emphasizing the potential roles of gut microbiota, serum metabolites, and inflammatory factors in the pathogenesis of these disorders. These findings may inform the development of new therapeutic strategies.
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Affiliation(s)
- Kaiyuan Li
- Graduate School of Dalian Medical University, Dalian Medical University, Dalian, China; Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Peng Liu
- Department of Cardiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuhao Zeng
- Department of Cardiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Miao Liu
- Department of Cardiology, Center Hospital of Shandong First Medical University, Jinan, China.
| | - Jun Ye
- Graduate School of Dalian Medical University, Dalian Medical University, Dalian, China; Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
| | - Li Zhu
- Graduate School of Dalian Medical University, Dalian Medical University, Dalian, China; Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China.
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3
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Myndrul V, Tamashevski A, Lipińska W, Siuzdak K, Iatsunskyi I. Highly sensitive electrochemical multimodal immunosensor for cluster of differentiation 5 (CD5) detection in human blood serum for early stage cancer detection based on laser-processed Ti/Au electrodes. Talanta 2024; 279:126612. [PMID: 39084041 DOI: 10.1016/j.talanta.2024.126612] [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: 04/27/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024]
Abstract
In the rapidly evolving field of medical diagnostics, biomarkers play a pivotal role, particularly in the early detection of cancer. Cluster of differentiation 5 (CD5), a cell surface glycoprotein found on T cells and B-1a lymphocytes, is instrumental in immune regulation and is associated with both autoimmune diseases and malignancies. Despite its significant diagnostic and therapeutic potential, CD5 detection has been limited by modern methods in the pg/ml range. This study presents a novel multimodal electrochemical immunosensor that employs laser-processed Ti/Au electrodes for the ultra-sensitive detection of CD5 in human blood serum. The "multimodal" approach combines different analytical techniques - differential pulse volctammetry (DPV) and electrochemical impedance spectroscopy (EIS) - to ensure comprehensive analysis, enhancing both the accuracy and reliability of the sensor. This novel sensor significantly outperforms existing commercial ELISA kits, achieving a limit of detection (LOD) of 1.1 ± 0.2 fg/mL with DPV and 3.9 ± 0.5 fg/mL with EIS in phosphate-buffered saline (PBS) and 6.6 ± 3.1 fg/mL and 15.6 ± 3.1 fg/mL in human serum (HS), respectively. These results highlight the immunosensor's potential for improving early-stage cancer diagnosis and broader medical applications.
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Affiliation(s)
- Valerii Myndrul
- Sensor Engineering Department, Faculty of Science and Engineering, Maastricht University, P.O. Box 616, 6200 MD, Maastricht, the Netherlands; NanoBioMedical Centre, Adam Mickiewicz University, 3, Wszechnicy Piastowskiej Str., 61-614, Poznan, Poland.
| | - Alexander Tamashevski
- NanoBioMedical Centre, Adam Mickiewicz University, 3, Wszechnicy Piastowskiej Str., 61-614, Poznan, Poland
| | - Wiktoria Lipińska
- Centre for Plasma and Laser Engineering, Institute of Fluid-Flow Machinery, Polish Academy of Sciences, Fiszera 14 St., 80-231, Gdansk, Poland
| | - Katarzyna Siuzdak
- Centre for Plasma and Laser Engineering, Institute of Fluid-Flow Machinery, Polish Academy of Sciences, Fiszera 14 St., 80-231, Gdansk, Poland
| | - Igor Iatsunskyi
- NanoBioMedical Centre, Adam Mickiewicz University, 3, Wszechnicy Piastowskiej Str., 61-614, Poznan, Poland.
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4
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Duo Y, Han L, Yang Y, Wang Z, Wang L, Chen J, Xiang Z, Yoon J, Luo G, Tang BZ. Aggregation-Induced Emission Luminogen: Role in Biopsy for Precision Medicine. Chem Rev 2024. [PMID: 39380213 DOI: 10.1021/acs.chemrev.4c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
Biopsy, including tissue and liquid biopsy, offers comprehensive and real-time physiological and pathological information for disease detection, diagnosis, and monitoring. Fluorescent probes are frequently selected to obtain adequate information on pathological processes in a rapid and minimally invasive manner based on their advantages for biopsy. However, conventional fluorescent probes have been found to show aggregation-caused quenching (ACQ) properties, impeding greater progresses in this area. Since the discovery of aggregation-induced emission luminogen (AIEgen) have promoted rapid advancements in molecular bionanomaterials owing to their unique properties, including high quantum yield (QY) and signal-to-noise ratio (SNR), etc. This review seeks to present the latest advances in AIEgen-based biofluorescent probes for biopsy in real or artificial samples, and also the key properties of these AIE probes. This review is divided into: (i) tissue biopsy based on smart AIEgens, (ii) blood sample biopsy based on smart AIEgens, (iii) urine sample biopsy based on smart AIEgens, (iv) saliva sample biopsy based on smart AIEgens, (v) biopsy of other liquid samples based on smart AIEgens, and (vi) perspectives and conclusion. This review could provide additional guidance to motivate interest and bolster more innovative ideas for further exploring the applications of various smart AIEgens in precision medicine.
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Affiliation(s)
- Yanhong Duo
- Department of Radiation Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong China
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02138, United States
| | - Lei Han
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, 700 Changcheng Road, Qingdao 266109, Shandong China
| | - Yaoqiang Yang
- Department of Radiation Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong China
| | - Zhifeng Wang
- Department of Urology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, 450003, China
| | - Lirong Wang
- State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou 510640, China
| | - Jingyi Chen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02138, United States
| | - Zhongyuan Xiang
- Department of Laboratory Medicine, The Second Xiangya Hospital, Central South University, Changsha 410000, Hunan, China
| | - Juyoung Yoon
- Department of Chemistry and Nanoscience, Ewha Womans University, 52 Ewhayeodae-gil, Seodaemun-gu, Seoul 03760, Korea
| | - Guanghong Luo
- Department of Radiation Oncology, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen 518020, Guangdong China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen 518172, Guangdong China
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5
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Titkare N, Chaturvedi S, Borah S, Sharma N. Advances in mass spectrometry for metabolomics: Strategies, challenges, and innovations in disease biomarker discovery. Biomed Chromatogr 2024:e6019. [PMID: 39370857 DOI: 10.1002/bmc.6019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Revised: 08/25/2024] [Accepted: 09/03/2024] [Indexed: 10/08/2024]
Abstract
Mass spectrometry (MS) plays a crucial role in metabolomics, especially in the discovery of disease biomarkers. This review outlines strategies for identifying metabolites, emphasizing precise and detailed use of MS techniques. It explores various methods for quantification, discusses challenges encountered, and examines recent breakthroughs in biomarker discovery. In the field of diagnostics, MS has revolutionized approaches by enabling a deeper understanding of tissue-specific metabolic changes associated with disease. The reliability of results is ensured through robust experimental design and stringent system suitability criteria. In the past, data quality, standardization, and reproducibility were often overlooked despite their significant impact on MS-based metabolomics. Progress in this field heavily depends on continuous training and education. The review also highlights the emergence of innovative MS technologies and methodologies. MS has the potential to transform our understanding of metabolic landscapes, which is crucial for disease biomarker discovery. This article serves as an invaluable resource for researchers in metabolomics, presenting fresh perspectives and advancements that propels the field forward.
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Affiliation(s)
- Nikhil Titkare
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Sachin Chaturvedi
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Sapan Borah
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
| | - Nitish Sharma
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Gandhinagar, Gujarat, India
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6
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Api AM, Bartlett A, Belsito D, Botelho D, Bruze M, Bryant-Freidrich A, Burton GA, Cancellieri MA, Chon H, Dagli ML, Dekant W, Deodhar C, Farrell K, Fryer AD, Jones L, Joshi K, Lapczynski A, Lavelle M, Lee I, Moustakas H, Muldoon J, Penning TM, Ritacco G, Sadekar N, Schember I, Schultz TW, Siddiqi F, Sipes IG, Sullivan G, Thakkar Y, Tokura Y. Update to RIFM fragrance ingredient safety assessment, linalyl acetate, CAS registry number 115-95-7. Food Chem Toxicol 2024; 192 Suppl 1:114805. [PMID: 38866197 DOI: 10.1016/j.fct.2024.114805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024]
Affiliation(s)
- A M Api
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - A Bartlett
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - D Belsito
- Member Expert Panel for Fragrance Safety, Columbia University Medical Center, Department of Dermatology, 161 Fort Washington Ave., New York, NY, 10032, USA
| | - D Botelho
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - M Bruze
- Member Expert Panel for Fragrance Safety, Malmo University Hospital, Department of Occupational & Environmental Dermatology, Sodra Forstadsgatan 101, Entrance 47, Malmo, SE-20502, Sweden
| | - A Bryant-Freidrich
- Member Expert Panel for Fragrance Safety, Pharmaceutical Sciences, Wayne State University, 42 W. Warren Ave., Detroit, MI, 48202, USA
| | - G A Burton
- Member Expert Panel for Fragrance Safety, School of Natural Resources & Environment, University of Michigan, Dana Building G110, 440 Church St., Ann Arbor, MI, 58109, USA
| | - M A Cancellieri
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - H Chon
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - M L Dagli
- Member Expert Panel for Fragrance Safety, University of Sao Paulo, School of Veterinary Medicine and Animal Science, Department of Pathology, Av. Prof. dr. Orlando Marques de Paiva, 87, Sao Paulo, CEP 05508-900, Brazil
| | - W Dekant
- Member Expert Panel for Fragrance Safety, University of Wuerzburg, Department of Toxicology, Versbacher Str. 9, 97078, Würzburg, Germany
| | - C Deodhar
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - K Farrell
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - A D Fryer
- Member Expert Panel for Fragrance Safety, Oregon Health & Science University, 3181 SW Sam Jackson Park Rd., Portland, OR, 97239, USA
| | - L Jones
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - K Joshi
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - A Lapczynski
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - M Lavelle
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - I Lee
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - H Moustakas
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - J Muldoon
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - T M Penning
- Member of Expert Panel for Fragrance Safety, University of Pennsylvania, Perelman School of Medicine, Center of Excellence in Environmental Toxicology, 1316 Biomedical Research Building (BRB) II/III, 421 Curie Boulevard, Philadelphia, PA, 19104-3083, USA
| | - G Ritacco
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - N Sadekar
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - I Schember
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - T W Schultz
- Member Expert Panel for Fragrance Safety, The University of Tennessee, College of Veterinary Medicine, Department of Comparative Medicine, 2407 River Dr., Knoxville, TN, 37996- 4500, USA
| | - F Siddiqi
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - I G Sipes
- Member Expert Panel for Fragrance Safety, Department of Pharmacology, University of Arizona, College of Medicine, 1501 North Campbell Avenue, P.O. Box 245050, Tucson, AZ, 85724-5050, USA
| | - G Sullivan
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA.
| | - Y Thakkar
- Research Institute for Fragrance Materials, Inc., 50 Tice Boulevard, Woodcliff Lake, NJ, 07677, USA
| | - Y Tokura
- Member Expert Panel for Fragrance Safety, The Journal of Dermatological Science (JDS), Department of Dermatology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
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7
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Wang Z, Zhang B, Zhang J, Xu S, Dai Y, Ding J, Guo J, Qi X, Chang X, Wu C, Zhou Z. Prenatal exposure to per- and polyfluoroalkyl substances and sex-specific associations with offspring adiposity at 10 years of age: Metabolic perturbation plays a role. ENVIRONMENT INTERNATIONAL 2024; 192:109037. [PMID: 39353210 DOI: 10.1016/j.envint.2024.109037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 09/10/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]
Abstract
BACKGROUND Per- and polyfluoroalkyl substances (PFAS) have been suspected as potential environmental obesogens, with several mechanisms being proposed, including the role of metabolomics. However, current epidemiological studies have yielded inconclusive findings. OBJECTIVES We aimed to estimate the associations of prenatal exposure to PFAS with offspring adiposity measures, and to explore the potential metabolic pathways underlying these associations. METHODS A total of 464 mother-child pairs from the Sheyang Mini Birth Cohort Study (SMBCS) were included in this study. Cord serum concentrations of 12 PFAS and urine metabolite profiles at age 10 were obtained from the SMBCS database. Adiposity-related anthropometric measurements and body composition estimates of children aged 10 were used to assess offspring obesity. Multiple linear regression models and quantile g-computation were conducted to estimate the associations of prenatal exposure to individual and multiple PFAS with obesity at 10 years old. Metabolomics analysis was performed to characterize the biological pathways associated with PFAS exposure or obesity, subsequently identifying the overlapping metabolic pathways underlying the PFAS-obesity relationship. RESULTS Prenatal exposure to several PFAS was significantly associated with elevated obesity-related markers in 10-year-old children. After stratification by sex, the effects were more pronounced in girls. Quantile g-computation results indicated that exposure to higher levels of PFAS mixtures during pregnancy was associated with increased odds of obesity in girls, with PFNA emerging as the predominant driving compound. Untargeted metabolomics results showed that several amino acid metabolic pathways were characterized as the overlapping pathways underlying the above associations. CONCLUSIONS Taken together, our findings suggested the potential obesogenic effects of prenatal exposure to PFAS and offered insight into the possible metabolic mechanisms underlying PFAS-related offspring obesity.
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Affiliation(s)
- Zheng Wang
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Boya Zhang
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Jiming Zhang
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China.
| | - Sinan Xu
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Yiming Dai
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Jiayun Ding
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Jianqiu Guo
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Xiaojuan Qi
- Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, Hangzhou 310051, China
| | - Xiuli Chang
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Chunhua Wu
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Zhijun Zhou
- School of Public Health/MOE Key Laboratory of Public Health Safety, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China.
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8
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Fetse J, Olawode EO, Deb S. Personalized Medicine Approach to Proteomics and Metabolomics of Cytochrome P450 Enzymes: A Narrative Review. Eur J Drug Metab Pharmacokinet 2024:10.1007/s13318-024-00912-5. [PMID: 39269556 DOI: 10.1007/s13318-024-00912-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 09/15/2024]
Abstract
Cytochrome P450 enzymes (CYPs) represent a diverse family of heme-thiolate proteins involved in the metabolism of a wide range of endogenous compounds and xenobiotics. In recent years, proteomics and metabolomics have been used to obtain a comprehensive insight into the role of CYPs in health and disease aspects. The objective of the present work is to better understand the status of proteomics and metabolomics in CYP research in optimizing therapeutics and patient safety from a personalized medicine approach. The literature used in this narrative review was procured by electronic search of PubMed, Medline, Embase, and Google Scholar databases. The following keywords were used in combination to identify related literature: "proteomics," "metabolomics," "cytochrome P450," "drug metabolism," "disease conditions," "proteome," "liquid chromatography-mass spectrometry," "integration," "metabolites," "pathological conditions." We reviewed studies that utilized proteomics and metabolomics approaches to explore the multifaceted roles of CYPs in identifying disease markers and determining the contribution of CYP enzymes in developing treatment strategies. The applications of various cutting-edge analytical techniques, including liquid chromatography-mass spectrometry, nuclear magnetic resonance, and bioinformatics analyses in CYP proteomics and metabolomics studies, have been highlighted. The identification of CYP enzymes through metabolomics and/or proteomics in various disease conditions provides key information in the diagnostic and therapeutic landscape. Leveraging both proteomics and metabolomics presents a powerful approach for an exhaustive exploration of the multifaceted roles played by CYP enzymes in personalized medicine. Proteomics and metabolomics have enabled researchers to unravel the complex connection between CYP enzymes and metabolic markers associated with specific diseases. As technology and methodologies evolve, an integrated approach promises to further elucidate the role of CYPs in human health and disease, potentially ushering in a new era of personalized medicine.
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Affiliation(s)
- John Fetse
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, Miami, FL, 33169, USA
| | - Emmanuel Oladayo Olawode
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, Miami, FL, 33169, USA
| | - Subrata Deb
- Department of Pharmaceutical Sciences, College of Pharmacy, Larkin University, Miami, FL, 33169, USA.
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9
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Yang Y, Gao X, Widdicombe B, Zhang X, Zielinski JL, Cheng T, Gunatilaka A, Leung KK, Plaxco KW, Rajasekharan Unnithan R, Stewart AG. Dual-Purpose Aptamer-Based Sensors for Real-Time, Multiplexable Monitoring of Metabolites in Cell Culture Media. ACS NANO 2024; 18. [PMID: 39255458 PMCID: PMC11441400 DOI: 10.1021/acsnano.4c06813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/27/2024] [Accepted: 08/29/2024] [Indexed: 09/12/2024]
Abstract
The availability of high-frequency, real-time measurements of the concentrations of specific metabolites in cell culture systems will enable a deeper understanding of cellular metabolism and facilitate the application of good laboratory practice standards in cell culture protocols. However, currently available approaches to this end either are constrained to single-time-point and single-parameter measurements or are limited in the range of detectable analytes. Electrochemical aptamer-based (EAB) biosensors have demonstrated utility in real-time monitoring of analytes in vivo in blood and tissues. Here, we characterize a pH-sensing capability of EAB sensors that is independent of the specific target analyte of the aptamer sequence. We applied this dual-purpose EAB to the continuous measurement of pH and phenylalanine in several in vitro cell culture settings. The miniature EAB sensor that we developed exhibits rapid response times, good stability, high repeatability, and biologically relevant sensitivity. We also developed and characterized a leak-free reference electrode that mitigates the potential cytotoxic effects of silver ions released from conventional reference electrodes. Using the resulting dual-purpose sensor, we performed hourly measurements of pH and phenylalanine concentrations in the medium superfusing cultured epithelial tumor cell lines (A549, MDA-MB-23) and a human fibroblast cell line (MRC-5) for periods of up to 72 h. Our scalable technology may be multiplexed for high-throughput monitoring of pH and multiple analytes in support of the broad metabolic qualification of microphysiological systems.
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Affiliation(s)
- Yiling Yang
- Department
of Electrical and Electronic Engineering, University of Melbourne, Melbourne, Victoria 3010, Australia
- ARC
Centre for Personalised Therapeutics Technologies, Melbourne, Victoria 3010, Australia
| | - Xumei Gao
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Melbourne, Victoria 3010, Australia
- ARC
Centre for Personalised Therapeutics Technologies, Melbourne, Victoria 3010, Australia
| | - Bryce Widdicombe
- Department
of Electrical and Electronic Engineering, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Xiaodan Zhang
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jana Lorraine Zielinski
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Tianhong Cheng
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Avanka Gunatilaka
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kaylyn K. Leung
- Department
of Chemistry and Biochemistry, University
of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Kevin W. Plaxco
- Department
of Chemistry and Biochemistry, University
of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Ranjith Rajasekharan Unnithan
- Department
of Electrical and Electronic Engineering, University of Melbourne, Melbourne, Victoria 3010, Australia
- ARC
Centre for Personalised Therapeutics Technologies, Melbourne, Victoria 3010, Australia
| | - Alastair G. Stewart
- Department
of Biochemistry and Pharmacology, University
of Melbourne, Melbourne, Victoria 3010, Australia
- ARC
Centre for Personalised Therapeutics Technologies, Melbourne, Victoria 3010, Australia
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10
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Huang G. Advances in metabolomics profiling of pediatric kidney diseases: A review. BIOMOLECULES & BIOMEDICINE 2024; 24:1044-1054. [PMID: 38400839 PMCID: PMC11379015 DOI: 10.17305/bb.2024.10098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 02/26/2024]
Abstract
Pediatric renal diseases encompass a diverse array of pathological conditions, often engendering enduring ramifications. Metabolomics, an emergent branch of omics sciences, endeavors to holistically delineate alterations in metabolite compositions through the amalgamation of sophisticated analytical chemistry techniques and robust statistical methodologies. Recent advancements in metabolomics research within the realm of pediatric nephrology have been substantial, offering promising avenues for the identification of robust biomarkers, the elaboration of novel therapeutic targets, and the intricate elucidation of molecular mechanisms. The present discourse aims to critically review the progress in metabolomics profiling pertinent to pediatric renal disorders over the previous 12 years.
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Affiliation(s)
- Guoping Huang
- Department of Nephrology, Children’s Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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11
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Gobbato R, Fornasaro S, Sergo V, Bonifacio A. Direct comparison of different protocols to obtain surface enhanced Raman spectra of human serum. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124390. [PMID: 38749203 DOI: 10.1016/j.saa.2024.124390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/21/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
Label-free Surface Enhanced Raman Spectroscopy (SERS) is a rapid technique that has been extensively applied in clinical diagnosis and biomedicine for the analysis of biofluids. The purpose of this approach relies on the ability to detect specific "metabolic fingerprints" of complex biological samples, but the full potential of this technique in diagnostics is yet to be exploited, mainly because of the lack of common analytical protocols for sample preparation and analysis. Variation of experimental parameters, such as substrate type, laser wavelength and sample processing can greatly influence spectral patterns, making results from different research groups difficult to compare. This study aims at making a step toward a standardization of the protocols in the analysis of human serum samples with Ag nanoparticles, by directly comparing the SERS spectra obtained from five different methods in which parameters like laser power, nanoparticle concentration, incubation/deproteinization steps and type of substrate used vary. Two protocols are the most used in the literature, and the other three are "in-house" protocols proposed by our group; all of them are employed to analyze the same human serum sample. The experimental results show that all protocols yield spectra that share the same overall spectral pattern, conveying the same biochemical information, but they significantly differ in terms of overall spectral intensity, repeatability, and preparation steps of the sample. A Principal Component Analysis (PCA) was performed revealing that protocol 3 and protocol 1 have the least variability in the dataset, while protocol 2 and 4 are the least repeatable.
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Affiliation(s)
- Roberto Gobbato
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, Via Valerio 6a, 34127 Trieste, TS, Italy.
| | - Stefano Fornasaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgieri 1, 34127 Trieste, TS, Italy.
| | - Valter Sergo
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, Via Valerio 6a, 34127 Trieste, TS, Italy.
| | - Alois Bonifacio
- Raman Spectroscopy Laboratory, Department of Engineering and Architecture, University of Trieste, Via Valerio 6a, 34127 Trieste, TS, Italy.
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12
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Vu N, Maile TM, Gollapudi S, Gaun A, Seitzer P, O'Brien JJ, Hackett SR, Zavala-Solorio J, McAllister FE, Kolumam G, Keyser R, Bennett BD. Automated preparation of plasma lipids, metabolites, and proteins for LC/MS-based analysis of a high-fat diet in mice. J Lipid Res 2024; 65:100607. [PMID: 39067520 PMCID: PMC11399584 DOI: 10.1016/j.jlr.2024.100607] [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: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024] Open
Abstract
Blood plasma is one of the most commonly analyzed and easily accessible biological samples. Here, we describe an automated liquid-liquid extraction platform that generates accurate, precise, and reproducible samples for metabolomic, lipidomic, and proteomic analyses from a single aliquot of plasma while minimizing hands-on time and avoiding contamination from plasticware. We applied mass spectrometry to examine the metabolome, lipidome, and proteome of 90 plasma samples to determine the effects of age, time of day, and a high-fat diet in mice. From 25 μl of mouse plasma, we identified 907 lipid species from 16 different lipid classes and subclasses, 233 polar metabolites, and 344 proteins. We found that the high-fat diet induced only mild changes in the polar metabolome, upregulated apolipoproteins, and induced substantial shifts in the lipidome, including a significant increase in arachidonic acid and a decrease in eicosapentaenoic acid content across all lipid classes.
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Affiliation(s)
- Ngoc Vu
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | | | - Rob Keyser
- Calico Life Sciences LLC, South San Francisco, CA, USA
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13
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Viola G, Trivellato D, Meulli L, Tira R, Lauriola A, Munari F, Montagnana M, Buffelli M, Assfalg M, D'Onofrio M. Stable ubiquitin conjugation for biological interrogation of ubiquitinated tau repeat domain. Bioorg Chem 2024; 150:107549. [PMID: 38896934 DOI: 10.1016/j.bioorg.2024.107549] [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: 04/17/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
Protein semisynthesis approaches are key for gaining insights into the effects of post-translational modifications (PTMs) on the structure and function of modified proteins. Among PTMs, ubiquitination involves the conjugation of a small protein modifier to a substrate amino acid residue and is unique in controlling a variety of cellular processes. Interest has grown in understanding the role of ubiquitination in neurodegenerative conditions, including tauopathies. The latter are characterized by the accumulation of the intrinsically disordered protein tau in the form of neurofibrillary tangles in the brains of patients. The presence of ubiquitinated tau in the pathological aggregates suggests that ubiquitination might play a role in the formation of abnormal protein deposits. In this study, we developed a new strategy, based on dehydroalanine chemistry, to install wild type ubiquitin on a tau repeat domain construct with site-specificity. We optimized a three-step reaction which yielded a good amount of highly pure tau repeat domain ubiquitinated in position 353. The structural features of the conjugate were examined by circular dichroism and NMR spectroscopy. The ubiquitinated tau was challenged in a number of assays: fibrils formation under aggregating conditions in vitro, chemical stability upon exposure to a variety of biological media including cell extracts, and internalization into astrocytes. The results demonstrated the wide applicability of the new semisynthetic strategy for the investigation of ubiquitinated substrates in vitro or in cell, and in particular for studying if ubiquitination has a role in the molecular mechanisms that underlie the aberrant transition of tau into pathological aggregates.
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Affiliation(s)
- Giovanna Viola
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Lorenzo Meulli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Roberto Tira
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Angela Lauriola
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Francesca Munari
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Martina Montagnana
- Department of Engineering for Innovation Medicine, University of Verona, 37134 Verona, Italy
| | - Mario Buffelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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14
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Sampaio J, Pinto J, Pizarro A, Oliveira B, Moreira A, Padrão P, Moreira P, Guedes de Pinho P, Carvalho J, Barros R. Combined mediterranean diet-based sustainable healthy diet and multicomponent training intervention impact on plasma biomarkers and metabolome in older adults. Clin Nutr 2024; 43:2125-2135. [PMID: 39116619 DOI: 10.1016/j.clnu.2024.07.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 07/22/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024]
Abstract
BACKGROUND AND AIMS Healthy dietary patterns and exercise practices have been associated with improved metabolic and inflammatory profiles. However, studies regarding the combined effect of these interventions on plasma biomarkers and metabolome in older adults are sparser. The primary aim of this study was to investigate the impact of a combined Mediterranean Diet-based Sustainable Healthy Diet (SHD) and Multicomponent Training (MT) intervention on the plasma biomarkers and metabolome and how dietary intake and exercise could modulate these effects. METHODS SHD intervention included a weekly supply of Mediterranean Diet-based SHD food and four nutrition sessions involving a Mediterranean-Diet culinary workshop, and the exercise program included 50-min MT group sessions, held three times a week, lasting both 12 weeks. Plasma biomarkers were obtained through standard biochemical analysis. A proton (1H) nuclear magnetic resonance (NMR) spectroscopy-based metabolomics approach was used to study the metabolome in blood plasma. Repeated measures ANOVA were performed and adjusted for confounders. RESULTS SHD + MT intervention significantly decreased HDL-C and calcium. SHD + MT showed some changes in common with the SHD and MT group, namely a significant decrease in citrate levels (p = 0.009 for SHD + MT; p = 0.037 for SHDT) and an increase in pyruvate (p < 0.001 for MT and SHD + MT). The SHD + MT group also revealed specific changes in the levels of some amino acids (decrease in alanine, glutamine and lysine: p = 0.026; p < 0.001; p = 0.038, respectively). Increases in formate (p = 0.025) and unsaturated lipids (p = 0.011) are consistent with changes in energy and lipoprotein metabolism. CONCLUSION Our data show that a combined lifestyle intervention program, including a Mediterranean Diet-based SHD and MT, could modulate biomarker and metabolome and there seems to be a metabolic path associated to these interventions in older adults. Due to its wide-ranging relevance, it is pertinent to assess to what extent combined SHD and MT can contribute to better clinical profiles.
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Affiliation(s)
- Joana Sampaio
- Faculty of Sport (FADEUP), University of Porto, Porto, Portugal; Research Centre in Physical Activity, Health, and Leisure (CIAFEL), University of Porto, Porto, Portugal; Epidemiology Unit (EPIUnit), Public Health Institute (ISPUP), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal.
| | - Joana Pinto
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Andreia Pizarro
- Faculty of Sport (FADEUP), University of Porto, Porto, Portugal; Research Centre in Physical Activity, Health, and Leisure (CIAFEL), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal
| | - Bruno Oliveira
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, Porto, Portugal
| | - André Moreira
- Epidemiology Unit (EPIUnit), Public Health Institute (ISPUP), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal; Faculty of Medicine (FMUP), University of Porto, Porto, Portugal
| | - Patrícia Padrão
- Epidemiology Unit (EPIUnit), Public Health Institute (ISPUP), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal; Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, Porto, Portugal
| | - Pedro Moreira
- Research Centre in Physical Activity, Health, and Leisure (CIAFEL), University of Porto, Porto, Portugal; Epidemiology Unit (EPIUnit), Public Health Institute (ISPUP), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal; Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, University of Porto, Porto, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Joana Carvalho
- Faculty of Sport (FADEUP), University of Porto, Porto, Portugal; Research Centre in Physical Activity, Health, and Leisure (CIAFEL), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal.
| | - Renata Barros
- Epidemiology Unit (EPIUnit), Public Health Institute (ISPUP), University of Porto, Porto, Portugal; Laboratory for Integrative and Translational Research in Population Health (ITR), Porto, Portugal; Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, Porto, Portugal.
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15
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Surrer DB, Schüsser S, König J, Fromm MF, Gessner A. Transport of aromatic amino acids l-tryptophan, l-tyrosine, and l-phenylalanine by the organic anion transporting polypeptide (OATP) 3A1. FEBS J 2024. [PMID: 39206635 DOI: 10.1111/febs.17255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/11/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Amino acids are important for cellular metabolism. Their uptake across the plasma membrane is mediated by transport proteins. Despite the fact that the organic anion transporting polypeptide 4C1 (OATP4C1, Uniprot: Q6ZQN7) mediates transport of l-arginine and l-arginine derivatives, other members of the OATP family have not been characterized as amino acid transporters. The OATP family member OATP3A1 (gene symbol SLCO3A1, Uniprot: Q9UIG8) is ubiquitously expressed in human cells and highly expressed in many cancer tissues and cell lines. However, only a few substrates are known for OATP3A1. Accordingly, knowledge about its biological relevance is restricted. Our aim was to identify new substrates of OATP3A1 to gain insights into its (patho-)physiological function. In an LC-MS-based untargeted metabolomics assay using untreated OATP3A1-overexpressing HEK293 cells and control cells, we identified several amino acids as potential substrates of OATP3A1. Subsequent uptake experiments using exogenously added substrates revealed OATP3A1-mediated transport of l-tryptophan, l-tyrosine, and l-phenylalanine with 194.8 ± 28.7% (P < 0.05), 226.2 ± 18.7% (P < 0.001), and 235.2 ± 13.5% (P < 0.001), respectively, in OATP3A1-overexpressing cells compared to control cells. Furthermore, kinetic transport parameters (Km values) were determined (Trp = 61.5 ± 14.2 μm, Tyr = 220.8 ± 54.5 μm, Phe = 234.7 ± 20.6 μm). In summary, we identified the amino acids l-tryptophan, l-tyrosine, and l-phenylalanine as new substrates of OATP3A1. These findings could be used for a better understanding of (patho-)physiological processes involving increased demand of amino acids, where OATP3A1 should be considered as an important uptake transporter of l-tryptophan, l-tyrosine, and l-phenylalanine.
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Affiliation(s)
- Daniela B Surrer
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Sarah Schüsser
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Jörg König
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Martin F Fromm
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
| | - Arne Gessner
- Institute of Experimental and Clinical Pharmacology and Toxicology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
- FAU NeW - Research Center New Bioactive Compounds, Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany
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16
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Gupta I, Badrzadeh F, Tsentalovich Y, Gaykalova DA. Connecting the dots: investigating the link between environmental, genetic, and epigenetic influences in metabolomic alterations in oral squamous cell carcinoma. J Exp Clin Cancer Res 2024; 43:239. [PMID: 39169426 PMCID: PMC11337877 DOI: 10.1186/s13046-024-03141-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/28/2024] [Indexed: 08/23/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) accounts for around 90% of all oral cancers and is the eighth most common cancer worldwide. Despite progress in managing OSCC, the overall prognosis remains poor, with a survival rate of around 50-60%, largely due to tumor size and recurrence. The challenges of late-stage diagnosis and limitations in current methods emphasize the urgent need for less invasive techniques to enable early detection and treatment, crucial for improving outcomes in this aggressive form of oral cancer. Research is currently aimed at unraveling tumor-specific metabolite profiles to identify candidate biomarkers as well as discover underlying pathways involved in the onset and progression of cancer that could be used as new targets for diagnostic and therapeutic purposes. Metabolomics is an advanced technological approach to identify metabolites in different sample types (biological fluids and tissues). Since OSCC promotes metabolic reprogramming influenced by a combination of genetic predisposition and environmental factors, including tobacco and alcohol consumption, and viral infections, the identification of distinct metabolites through screening may aid in the diagnosis of this condition. Moreover, studies have shown the use of metabolites during the catalysis of epigenetic modification, indicating a link between epigenetics and metabolism. In this review, we will focus on the link between environmental, genetic, and epigenetic influences in metabolomic alterations in OSCC. In addition, we will discuss therapeutic targets of tumor metabolism, which may prevent oral tumor growth, metastasis, and drug resistance.
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Affiliation(s)
- Ishita Gupta
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Fariba Badrzadeh
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA
| | - Yuri Tsentalovich
- International tomography center CB RAS, Institutskaya str. 3a, Novosibirsk, 630090, Russia
| | - Daria A Gaykalova
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
- Department of Otorhinolaryngology-Head and Neck Surgery, Marlene & Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Medical Center, Baltimore, MD, USA.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
- Institute for Genome Sciences, 670 West Baltimore Street, Baltimore, MD, 21201, USA.
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17
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Bussi C, Lai R, Athanasiadi N, Gutierrez MG. Physiologic medium renders human iPSC-derived macrophages permissive for M. tuberculosis by rewiring organelle function and metabolism. mBio 2024; 15:e0035324. [PMID: 38984828 PMCID: PMC11323749 DOI: 10.1128/mbio.00353-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024] Open
Abstract
In vitro studies are crucial for our understanding of the human macrophage immune functions. However, traditional in vitro culture media poorly reflect the metabolic composition of blood, potentially affecting the outcomes of these studies. Here, we analyzed the impact of a physiological medium on human induced pluripotent stem cell (iPSC)-derived macrophages (iPSDM) function. Macrophages cultured in a human plasma-like medium (HPLM) were more permissive to Mycobacterium tuberculosis (Mtb) replication and showed decreased lipid metabolism with increased metabolic polarization. Functionally, we discovered that HPLM-differentiated macrophages showed different metabolic organelle content and activity. Specifically, HPLM-differentiated macrophages displayed reduced lipid droplet and peroxisome content, increased lysosomal proteolytic activity, and increased mitochondrial activity and dynamics. Inhibiting or inducing lipid droplet formation revealed that lipid droplet content is a key factor influencing macrophage permissiveness to Mtb. These findings underscore the importance of using physiologically relevant media in vitro for accurately studying human macrophage function. IMPORTANCE This work compellingly demonstrates that the choice of culture medium significantly influences M. tuberculosis replication outcomes, thus emphasizing the importance of employing physiologically relevant media for accurate in vitro host-pathogen interaction studies. We anticipate that our work will set a precedent for future research with clinical relevance, particularly in evaluating antibiotic efficacy and resistance in cellulo.
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Affiliation(s)
- Claudio Bussi
- The Francis Crick Institute, London, United Kingdom
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Rachel Lai
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
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18
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Pang N, Yang W, Yang G, Yang C, Tong K, Yu R, Jiang F. The utilization of blood serum ATR-FTIR spectroscopy for the identification of gastric cancer. Discov Oncol 2024; 15:350. [PMID: 39143357 PMCID: PMC11324634 DOI: 10.1007/s12672-024-01231-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/12/2024] [Indexed: 08/16/2024] Open
Abstract
Gastric cancer represents a significant public health challenge, necessitating advancements in early diagnostic methodologies. This investigation employed attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy to conduct a multivariate analysis of human serum. The study encompassed the examination of blood samples from 96 individuals diagnosed with gastric cancer and 96 healthy volunteers. Principal component analysis (PCA) was utilized to interpret the infrared spectral data of the serum samples. Specific spectral bands exhibiting intensity variations between the two groups were identified. The infrared spectral ranges of 3500 ~ 3000 cm⁻1, 1700 ~ 1600 cm⁻1, and 1090 ~ 1070 cm⁻1 demonstrated significant diagnostic value for gastric cancer, likely attributable to differences in protein conformation and nucleic acids. By employing machine learning algorithms to differentiate between gastric cancer patients (n = 96) and healthy controls (n = 96), we achieved a sensitivity of up to 89.7% and a specificity of 87.2%. Receiver operating characteristic (ROC) analysis yielded an area under the curve (AUC) of 0.901. These findings underscore the potential of our serum-based ATR-FTIR spectroscopy examination method as a straightforward, minimally invasive, and reliable diagnostic test for the detection of gastric cancer.
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Affiliation(s)
- Nan Pang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Wanli Yang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Guizhe Yang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Chao Yang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Kuiyuan Tong
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, Jiangsu, China
| | - Ruihua Yu
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Feng Jiang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China.
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19
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Allen LH, Fenech M, LeVatte MA, West KP, Wishart DS. Multiomics: Functional Molecular Biomarkers of Micronutrients for Public Health Application. Annu Rev Nutr 2024; 44:125-153. [PMID: 39207879 DOI: 10.1146/annurev-nutr-062322-022751] [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: 09/04/2024]
Abstract
Adequate micronutrient intake and status are global public health goals. Vitamin and mineral deficiencies are widespread and known to impair health and survival across the life stages. However, knowledge of molecular effects, metabolic pathways, biological responses to variation in micronutrient nutriture, and abilities to assess populations for micronutrient deficiencies and their pathology remain lacking. Rapidly evolving methodological capabilities in genomics, epigenomics, proteomics, and metabolomics offer unparalleled opportunities for the nutrition research community to link micronutrient exposure to cellular health; discover new, arguably essential micronutrients of microbial origin; and integrate methods of molecular biology, epidemiology, and intervention trials to develop novel approaches to assess and prevent micronutrient deficiencies in populations. In this review article, we offer new terminology to specify nutritional application of multiomic approaches and encourage collaboration across the basic to public health sciences to advance micronutrient deficiency prevention.
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Affiliation(s)
- Lindsay H Allen
- Western Human Nutrition Research Center, United States Department of Agriculture, Agricultural Research Service, Davis, California, USA
- Department of Nutrition, University of California, Davis, California, USA
| | - Michael Fenech
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
- Genome Health Foundation, North Brighton, South Australia, Australia
| | - Marcia A LeVatte
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Keith P West
- Center for Human Nutrition, Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA;
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
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20
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Sharma G, Gupta DP, Halder A, Banerjee A, Srivastava S. Cysteamine Nanoemulsion Delivery by Inhalation to Attenuate Adverse Effects of Exposure to Cigarette Smoke: A Metabolomics Study in Wistar Rats. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:421-437. [PMID: 38979603 DOI: 10.1089/omi.2024.0127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
There is a pressing need for novel pharmacological interventions and drug delivery innovations to attenuate the cigarette smoke-associated oxidative stress and lung disease. We report here on the attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) and metabolomics of Wistar rats exposed to cigarette smoke for 28 days. The animals were treated for 15 days with plain cysteamine given orally or cysteamine as nanoemulsion given orally or via inhalation. The study design also included two control groups as follows: rats exposed to cigarette smoke but did not receive a treatment (diseased control group) and rats neither exposed to cigarette smoke nor a treatment (normal control group). The targeted metabolomics using Parallel Reaction Monitoring showed that in the diseased control group, ornithine, nicotinamide, xanthine, hypoxanthine, and caprolactam were increased compared with the normal control group. In addition, (±)8(9)-DiHET, which was initially downregulated in the diseased control group, exhibited a reversal of this trend with cysteamine nanoemulsion given via inhalation. The cysteamine nanoemulsion delivered by inhalation highlighted the importance of the route of drug administration for targeting the lungs. To the best of our knowledge, this is the first work to use ATR-FTIR and metabolomics in Wistar rat lung tissues, suggesting how cysteamine nanoemulsion can potentially reduce cigarette smoke-induced oxidative damage. The metabolites reported herein have potential implications for discovery of novel theranostics and, thus, to cultivate diagnostic and therapeutic innovation for early prevention and treatment of cigarette smoke-associated lung diseases.
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Affiliation(s)
- Gautam Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Debarghya Pratim Gupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Ankit Halder
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Arghya Banerjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India
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21
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Metz TO, Chang CH, Gautam V, Anjum A, Tian S, Wang F, Colby SM, Nunez JR, Blumer MR, Edison AS, Fiehn O, Jones DP, Li S, Morgan ET, Patti GJ, Ross DH, Shapiro MR, Williams AJ, Wishart DS. Introducing 'identification probability' for automated and transferable assessment of metabolite identification confidence in metabolomics and related studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605945. [PMID: 39131324 PMCID: PMC11312557 DOI: 10.1101/2024.07.30.605945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Methods for assessing compound identification confidence in metabolomics and related studies have been debated and actively researched for the past two decades. The earliest effort in 2007 focused primarily on mass spectrometry and nuclear magnetic resonance spectroscopy and resulted in four recommended levels of metabolite identification confidence - the Metabolite Standards Initiative (MSI) Levels. In 2014, the original MSI Levels were expanded to five levels (including two sublevels) to facilitate communication of compound identification confidence in high resolution mass spectrometry studies. Further refinement in identification levels have occurred, for example to accommodate use of ion mobility spectrometry in metabolomics workflows, and alternate approaches to communicate compound identification confidence also have been developed based on identification points schema. However, neither qualitative levels of identification confidence nor quantitative scoring systems address the degree of ambiguity in compound identifications in context of the chemical space being considered, are easily automated, or are transferable between analytical platforms. In this perspective, we propose that the metabolomics and related communities consider identification probability as an approach for automated and transferable assessment of compound identification and ambiguity in metabolomics and related studies. Identification probability is defined simply as 1/N, where N is the number of compounds in a reference library or chemical space that match to an experimentally measured molecule within user-defined measurement precision(s), for example mass measurement or retention time accuracy, etc. We demonstrate the utility of identification probability in an in silico analysis of multi-property reference libraries constructed from the Human Metabolome Database and computational property predictions, provide guidance to the community in transparent implementation of the concept, and invite the community to further evaluate this concept in parallel with their current preferred methods for assessing metabolite identification confidence.
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Affiliation(s)
- Thomas O. Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Christine H. Chang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Vasuk Gautam
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Afia Anjum
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Siyang Tian
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Fei Wang
- Department of Computing Science, University of Alberta, Edmonton, AB, Canada
- Alberta Machine Intelligence Institute, Edmonton, AB, Canada
| | - Sean M. Colby
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Jamie R. Nunez
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Madison R. Blumer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Arthur S. Edison
- Department of Biochemistry & Molecular Biology, Complex Carbohydrate Research Center and Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Dean P. Jones
- Clinical Biomarkers Laboratory, Department of Medicine, Emory University, Atlanta, Georgia, USA
| | - Shuzhao Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Edward T. Morgan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Gary J. Patti
- Center for Mass Spectrometry and Metabolic Tracing, Department of Chemistry, Department of Medicine, Washington University, Saint Louis, Missouri, USA
| | - Dylan H. Ross
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Madelyn R. Shapiro
- Artificial Intelligence & Data Analytics Division, Pacific Northwest National Laboratory, Richland, WA USA
| | - Antony J. Williams
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), Research Triangle Park, NC USA
| | - David S. Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
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22
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Kizilaslan M, Arzik Y, Behrem S, Yavuz E, White SN, Cinar MU. Unravelling the Genetic Architecture of Serum Biochemical Indicators in Sheep. Genes (Basel) 2024; 15:990. [PMID: 39202351 PMCID: PMC11353979 DOI: 10.3390/genes15080990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Revised: 07/16/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Serum biochemical indicators serve as vital proxies that reflect the physiological state and functions of different organs. The genetic parameters and molecular mechanisms underlying serum biochemical indicators of sheep (Ovis aries) have not been well understood. Therefore, the aim of the present study was to identify the genetic architecture and genomic loci underlying ten serum biochemical indicators in sheep, including alanine transaminase, aspartate transferase, lactate dehydrogenase, cholesterol, glucose, phosphorus, calcium, creatinine, urea and total protein levels. We implemented genetic parameter estimations and GWASs for each trait in 422 Akkaraman lambs. Overall, low to moderate heritability estimates were found in the range of 0.14-0.55. Additionally, low to high genetic correlations were observed among traits. In total, 23 SNP loci were associated with serum biochemical indicators leading to 19 genes. These were SPTA1, MGST2, CACUL1, IGFBP7, PARD3, PHB1, SLC15A5, TRIM35, RGS6, NUP93, CNTNAP2, SLC7A11, B3GALT5, DPP10, HST2ST1, NRP1, LRP1B, MAP3K9 and ENSOARG00020040484.1, as well as LOC101103187, LOC101117162, LOC105611309 and LOC101118029. To our knowledge, these data provide the first associations between SPTA1 and serum cholesterol and between ENSOARG00020040484.1 and serum glucose. The current findings provide a comprehensive inventory of the relationships between serum biochemical parameters, genetic variants and disease-relevant characteristics. This information may facilitate the identification of therapeutic targets and fluid biomarkers and establish a strong framework for comprehending the pathobiology of complex diseases as well as providing targets for sheep genetic improvement programs.
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Affiliation(s)
- Mehmet Kizilaslan
- Faculty of Agriculture, Department of Animal Science, Erciyes University, Kayseri 38039, Türkiye; (M.K.); (Y.A.)
- International Center for Livestock Research and Training, Ministry of Agriculture and Forestry, Ankara 06852, Türkiye
| | - Yunus Arzik
- Faculty of Agriculture, Department of Animal Science, Erciyes University, Kayseri 38039, Türkiye; (M.K.); (Y.A.)
- International Center for Livestock Research and Training, Ministry of Agriculture and Forestry, Ankara 06852, Türkiye
| | - Sedat Behrem
- Department of Veterinary Sciences, Aksaray University, Aksaray 68100, Türkiye
| | - Esra Yavuz
- International Center for Livestock Research and Training, Ministry of Agriculture and Forestry, Ankara 06852, Türkiye
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA;
| | - Mehmet Ulas Cinar
- Faculty of Agriculture, Department of Animal Science, Erciyes University, Kayseri 38039, Türkiye; (M.K.); (Y.A.)
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA;
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23
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Lai Y, Koelmel JP, Walker DI, Price EJ, Papazian S, Manz KE, Castilla-Fernández D, Bowden JA, Nikiforov V, David A, Bessonneau V, Amer B, Seethapathy S, Hu X, Lin EZ, Jbebli A, McNeil BR, Barupal D, Cerasa M, Xie H, Kalia V, Nandakumar R, Singh R, Tian Z, Gao P, Zhao Y, Froment J, Rostkowski P, Dubey S, Coufalíková K, Seličová H, Hecht H, Liu S, Udhani HH, Restituito S, Tchou-Wong KM, Lu K, Martin JW, Warth B, Godri Pollitt KJ, Klánová J, Fiehn O, Metz TO, Pennell KD, Jones DP, Miller GW. High-Resolution Mass Spectrometry for Human Exposomics: Expanding Chemical Space Coverage. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:12784-12822. [PMID: 38984754 PMCID: PMC11271014 DOI: 10.1021/acs.est.4c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024]
Abstract
In the modern "omics" era, measurement of the human exposome is a critical missing link between genetic drivers and disease outcomes. High-resolution mass spectrometry (HRMS), routinely used in proteomics and metabolomics, has emerged as a leading technology to broadly profile chemical exposure agents and related biomolecules for accurate mass measurement, high sensitivity, rapid data acquisition, and increased resolution of chemical space. Non-targeted approaches are increasingly accessible, supporting a shift from conventional hypothesis-driven, quantitation-centric targeted analyses toward data-driven, hypothesis-generating chemical exposome-wide profiling. However, HRMS-based exposomics encounters unique challenges. New analytical and computational infrastructures are needed to expand the analysis coverage through streamlined, scalable, and harmonized workflows and data pipelines that permit longitudinal chemical exposome tracking, retrospective validation, and multi-omics integration for meaningful health-oriented inferences. In this article, we survey the literature on state-of-the-art HRMS-based technologies, review current analytical workflows and informatic pipelines, and provide an up-to-date reference on exposomic approaches for chemists, toxicologists, epidemiologists, care providers, and stakeholders in health sciences and medicine. We propose efforts to benchmark fit-for-purpose platforms for expanding coverage of chemical space, including gas/liquid chromatography-HRMS (GC-HRMS and LC-HRMS), and discuss opportunities, challenges, and strategies to advance the burgeoning field of the exposome.
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Affiliation(s)
- Yunjia Lai
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Jeremy P. Koelmel
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Douglas I. Walker
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Elliott J. Price
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Stefano Papazian
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Katherine E. Manz
- Department
of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Delia Castilla-Fernández
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1010 Vienna, Austria
| | - John A. Bowden
- Center for
Environmental and Human Toxicology, Department of Physiological Sciences,
College of Veterinary Medicine, University
of Florida, Gainesville, Florida 32611, United States
| | | | - Arthur David
- Univ Rennes,
Inserm, EHESP, Irset (Institut de recherche en santé, environnement
et travail) − UMR_S, 1085 Rennes, France
| | - Vincent Bessonneau
- Univ Rennes,
Inserm, EHESP, Irset (Institut de recherche en santé, environnement
et travail) − UMR_S, 1085 Rennes, France
| | - Bashar Amer
- Thermo
Fisher Scientific, San Jose, California 95134, United States
| | | | - Xin Hu
- Gangarosa
Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia 30322, United States
| | - Elizabeth Z. Lin
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Akrem Jbebli
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Brooklynn R. McNeil
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Dinesh Barupal
- Department
of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Marina Cerasa
- Institute
of Atmospheric Pollution Research, Italian National Research Council, 00015 Monterotondo, Rome, Italy
| | - Hongyu Xie
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Vrinda Kalia
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Renu Nandakumar
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Randolph Singh
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Zhenyu Tian
- Department
of Chemistry and Chemical Biology, Northeastern
University, Boston, Massachusetts 02115, United States
| | - Peng Gao
- Department
of Environmental and Occupational Health, and Department of Civil
and Environmental Engineering, University
of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
- UPMC Hillman
Cancer Center, Pittsburgh, Pennsylvania 15232, United States
| | - Yujia Zhao
- Institute
for Risk Assessment Sciences, Utrecht University, Utrecht 3584CM, The Netherlands
| | | | | | - Saurabh Dubey
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Kateřina Coufalíková
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Hana Seličová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Helge Hecht
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Sheng Liu
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Hanisha H. Udhani
- Biomarkers
Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, New York 10032, United States
| | - Sophie Restituito
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Kam-Meng Tchou-Wong
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
| | - Kun Lu
- Department
of Environmental Sciences and Engineering, Gillings School of Global
Public Health, The University of North Carolina
at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jonathan W. Martin
- Department
of Environmental Science, Science for Life Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
- National
Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Benedikt Warth
- Department
of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, 1010 Vienna, Austria
| | - Krystal J. Godri Pollitt
- Department
of Environmental Health Sciences, Yale School
of Public Health, New Haven, Connecticut 06520, United States
| | - Jana Klánová
- RECETOX,
Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Oliver Fiehn
- West Coast
Metabolomics Center, University of California−Davis, Davis, California 95616, United States
| | - Thomas O. Metz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Kurt D. Pennell
- School
of Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Dean P. Jones
- Department
of Medicine, School of Medicine, Emory University, Atlanta, Georgia 30322, United States
| | - Gary W. Miller
- Department
of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York 10032, United States
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24
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Marigorta UM, Millet O, Lu SC, Mato JM. Dysfunctional VLDL metabolism in MASLD. NPJ METABOLIC HEALTH AND DISEASE 2024; 2:16. [PMID: 39049993 PMCID: PMC11263124 DOI: 10.1038/s44324-024-00018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 06/22/2024] [Indexed: 07/27/2024]
Abstract
Lipidomics has unveiled the intricate human lipidome, emphasizing the extensive diversity within lipid classes in mammalian tissues critical for cellular functions. This diversity poses a challenge in maintaining a delicate balance between adaptability to recurring physiological changes and overall stability. Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD), linked to factors such as obesity and diabetes, stems from a compromise in the structural and functional stability of the liver within the complexities of lipid metabolism. This compromise inaccurately senses an increase in energy status, such as during fasting-feeding cycles or an upsurge in lipogenesis. Serum lipidomic studies have delineated three distinct metabolic phenotypes, or "metabotypes" in MASLD. MASLD-A is characterized by lower very low-density lipoprotein (VLDL) secretion and triglyceride (TG) levels, associated with a reduced risk of cardiovascular disease (CVD). In contrast, MASLD-C exhibits increased VLDL secretion and TG levels, correlating with elevated CVD risk. An intermediate subtype, with a blend of features, is designated as the MASLD-B metabotype. In this perspective, we examine into recent findings that show the multifaceted regulation of VLDL secretion by S-adenosylmethionine, the primary cellular methyl donor. Furthermore, we explore the differential CVD and hepatic cancer risk across MASLD metabotypes and discuss the context and potential paths forward to gear the findings from genetic studies towards a better understanding of the observed heterogeneity in MASLD.
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Affiliation(s)
- Urko M. Marigorta
- Integrative Genomics Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Oscar Millet
- Precision Medicine and Metabolism Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, 48160 Derio, Spain
| | - Shelly C. Lu
- Karsh Division of Gastroenterology and Hepatology, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - José M. Mato
- Precision Medicine and Metabolism Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), CIBERehd, 48160 Derio, Spain
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25
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Li Y, Peters BA, Yu B, Perreira KM, Daviglus M, Chan Q, Knight R, Boerwinkle E, Isasi CR, Burk R, Kaplan R, Wang T, Qi Q. Blood metabolomic shift links diet and gut microbiota to multiple health outcomes among Hispanic/Latino immigrants in the U.S. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.19.24310722. [PMID: 39072018 PMCID: PMC11275661 DOI: 10.1101/2024.07.19.24310722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Immigrants from less industrialized countries who are living in the U.S. often bear an elevated risk of multiple disease due to the adoption of a U.S. lifestyle. Blood metabolome holds valuable information on environmental exposure and the pathogenesis of chronic diseases, offering insights into the link between environmental factors and disease burden. Analyzing 634 serum metabolites from 7,114 Hispanics (1,141 U.S.-born, 5,973 foreign-born) in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), we identified profound blood metabolic shift during acculturation. Machine learning highlighted the prominent role of non-genetic factors, especially food and gut microbiota, in these changes. Immigration-related metabolites correlated with plant-based foods and beneficial gut bacteria for foreign-born Hispanics, and with meat-based or processed food and unfavorable gut bacteria for U.S.-born Hispanics. Cardiometabolic traits, liver, and kidney function exhibited a link with immigration-related metabolic changes, which were also linked to increased risk of diabetes, severe obesity, chronic kidney disease, and asthma. Graphical abstract Highlights A substantial proportion of identified blood metabolites differ between U.S.-born and foreign-born Hispanics/Latinos in the U.S.Food and gut microbiota are the major modifiable contributors to blood metabolomic difference between U.S.-born and foreign-born Hispanics/Latinos.U.S. nativity related metabolites collectively correlate with a spectrum of clinical traits and chronic diseases.
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26
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Wang X, Ostergaard J, Kang J, Sagong G, Twite R, Vargas-Morales A, Gordon PM. Hypoxanthine in the microenvironment can enable thiopurine resistance in acute lymphoblastic leukemia. Front Oncol 2024; 14:1440650. [PMID: 39099696 PMCID: PMC11294174 DOI: 10.3389/fonc.2024.1440650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/03/2024] [Indexed: 08/06/2024] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy, with relapse being a major obstacle to successful treatment. Our understanding of the mechanisms driving chemotherapy resistance and ultimately relapse in leukemia remains incomplete. Herein, we investigate the impact of the tumor microenvironment on leukemia cell drug responses using human plasma-like media (HPLM), designed to mimic physiological conditions more accurately ex vivo. We demonstrate that while most chemotherapeutics maintain an efficacy in HPLM comparable to standard tissue culture media, the thiopurines 6-mercaptopurine (6-MP) and 6-thioguanine (6-TG) exhibit significantly reduced potency and efficacy against both B- and T- leukemia cells in HPLM. By merging our understanding of thiopurines' mechanism of action with the metabolites supplemented in HPLM compared to standard media, we proposed and subsequently validated the hypothesis that hypoxanthine, a purine derivative, is responsible for conferring resistance to the thiopurines. Importantly, the concentration of hypoxanthine required for resistance is comparable to physiological levels found in vivo, supporting clinical relevance. Our findings demonstrate the utility of a more physiologic media in identifying and characterizing mechanisms by which the microenvironment can enable resistance. Understanding such interactions may inform strategies to overcome drug resistance and improve therapeutic outcomes in pediatric leukemia.
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Affiliation(s)
- Xiaohong Wang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Jason Ostergaard
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Jongseok Kang
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Grace Sagong
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Rachel Twite
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Andrea Vargas-Morales
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
| | - Peter M. Gordon
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States
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27
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Abdullah G, Akpan A, Phelan MM, Wright HL. New insights into healthy ageing, inflammageing and frailty using metabolomics. FRONTIERS IN AGING 2024; 5:1426436. [PMID: 39044748 PMCID: PMC11263002 DOI: 10.3389/fragi.2024.1426436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 06/24/2024] [Indexed: 07/25/2024]
Abstract
Human ageing is a normal process and does not necessarily result in the development of frailty. A mix of genetic, environmental, dietary, and lifestyle factors can have an impact on ageing, and whether an individual develops frailty. Frailty is defined as the loss of physiological reserve both at the physical and cellular levels, where systemic processes such as oxidative stress and inflammation contribute to physical decline. The newest "omics" technology and systems biology discipline, metabolomics, enables thorough characterisation of small-molecule metabolites in biological systems at a particular time and condition. In a biological system, metabolites-cellular intermediate products of metabolic reactions-reflect the system's final response to genomic, transcriptomic, proteomic, epigenetic, or environmental alterations. As a relatively newer technique to characterise metabolites and biomarkers in ageing and illness, metabolomics has gained popularity and has a wide range of applications. We will give a comprehensive summary of what is currently known about metabolomics in studies of ageing, with a focus on biomarkers for frailty. Metabolites related to amino acids, lipids, carbohydrates, and redox metabolism may function as biomarkers of ageing and/or frailty development, based on data obtained from human studies. However, there is a complexity that underpins biological ageing, due to both genetic and environmental factors that play a role in orchestrating the ageing process. Therefore, there is a critical need to identify pathways that contribute to functional decline in people with frailty.
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Affiliation(s)
- Genna Abdullah
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Asangaedem Akpan
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
- Division of Internal Medicine, University of Western Australia, Bunbury, WA, Australia
- Faculty of Health Sciences, Curtis University, Bunbury, WA, Australia
- Department of Geriatric Medicine, Bunbury Regional Hospital, Bunbury, WA, Australia
| | - Marie M. Phelan
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- High Field NMR Facility, Liverpool Shared Research Facilities University of Liverpool, Liverpool, United Kingdom
| | - Helen L. Wright
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
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Li D, Wei H, Hong R, Yue X, Dong L, Fan K, Yu J, Yao D, Xu H, Lu J, Wang G. WS 2 nanosheets-based electrochemical biosensor for highly sensitive detection of tumor marker miRNA-4484. Talanta 2024; 274:125965. [PMID: 38552480 DOI: 10.1016/j.talanta.2024.125965] [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: 10/16/2023] [Revised: 03/18/2024] [Accepted: 03/20/2024] [Indexed: 05/04/2024]
Abstract
In this paper, a few-layer WS2 nanosheets-based electrochemical biosensor was fabricated for the highly sensitive detection of breast cancer tumor marker miRNA-4484. Firstly, few-layer WS2 nanosheets were prepared by shear stripping and characterized by SEM, TEM, AFM and UV spectrophotometer. After modification of few-layer WS2 nanosheets on the electrode surface, the miRNA probe was fixed on the few-layer WS2 nanosheets by polycytosine (PolyC). Then short-chain miRNA containing PolyC was used as the blocking agent to close the excess active sites on the surface of WS2 nanosheets to complete the fabrication of the sensor biosensing interface. Finally, the current changes caused by the specific binding of miRNA-4484 to the probe were analyzed by differential pulse voltammetry (DPV). The results showed that the sensor had a good linear relationship for the detection of miRNA-4484 in the concentration range of 1 aM-100 fM, and the detection limit was as low as 1.61 aM. In addition, the electrochemical sensor had excellent selectivity, stability and reproducibility. The artificial sample tests indicated that the developed biosensors have the potential for clinical application in the future.
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Affiliation(s)
- Dujuan Li
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China; School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Huyue Wei
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China; School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Rui Hong
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Xiaojie Yue
- The Children's Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Linxi Dong
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China.
| | - Kai Fan
- School of Automation, Hangzhou Dianzi University, Hangzhou, 310018, China
| | - Jing Yu
- Zhejiang Key Laboratory of Ecological and Environmental Big Data, Hangzhou, 321001, China
| | - Defei Yao
- Zhejiang Key Laboratory of Ecological and Environmental Big Data, Hangzhou, 321001, China
| | - Hong Xu
- Guangdong Technology Research Center for Marine Algal Bioengineering, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Jun Lu
- Auckland Bioengineering Institute, University of Auckland, Auckland, 1142, New Zealand
| | - Gaofeng Wang
- Ministry of Education Engineering Research Center of Smart Microsensors and Microsystems, Hangzhou Dianzi University, Hangzhou, 310018, China; School of Electronics and Information, Hangzhou Dianzi University, Hangzhou, 310018, China.
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29
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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024; 20:296-321. [PMID: 38623720 PMCID: PMC11163948 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/22/2024] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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30
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Yeo WJ, Surapaneni AL, Hasson DC, Schmidt IM, Sekula P, Köttgen A, Eckardt KU, Rebholz CM, Yu B, Waikar SS, Rhee EP, Schrauben SJ, Feldman HI, Vasan RS, Kimmel PL, Coresh J, Grams ME, Schlosser P. Serum and Urine Metabolites and Kidney Function. J Am Soc Nephrol 2024; 35:00001751-990000000-00343. [PMID: 38844075 PMCID: PMC11387034 DOI: 10.1681/asn.0000000000000403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024] Open
Abstract
Key Points
We provide an atlas of cross-sectional and longitudinal serum and urine metabolite associations with eGFR and urine albumin-creatinine ratio in an older community-based cohort.Metabolic profiling in serum and urine provides distinct and complementary insights into disease.
Background
Metabolites represent a read-out of cellular processes underlying states of health and disease.
Methods
We evaluated cross-sectional and longitudinal associations between 1255 serum and 1398 urine known and unknown (denoted with “X” in name) metabolites (Metabolon HD4, 721 detected in both biofluids) and kidney function in 1612 participants of the Atherosclerosis Risk in Communities study. All analyses were adjusted for clinical and demographic covariates, including for baseline eGFR and urine albumin-creatinine ratio (UACR) in longitudinal analyses.
Results
At visit 5 of the Atherosclerosis Risk in Communities study, the mean age of participants was 76 years (SD 6); 56% were women, mean eGFR was 62 ml/min per 1.73 m2 (SD 20), and median UACR level was 13 mg/g (interquartile range, 25). In cross-sectional analysis, 675 serum and 542 urine metabolites were associated with eGFR (Bonferroni-corrected P < 4.0E-5 for serum analyses and P < 3.6E-5 for urine analyses), including 248 metabolites shared across biofluids. Fewer metabolites (75 serum and 91 urine metabolites, including seven metabolites shared across biofluids) were cross-sectionally associated with albuminuria. Guanidinosuccinate; N2,N2-dimethylguanosine; hydroxy-N6,N6,N6-trimethyllysine; X-13844; and X-25422 were significantly associated with both eGFR and albuminuria. Over a mean follow-up of 6.6 years, serum mannose (hazard ratio [HR], 2.3 [1.6–3.2], P = 2.7E-5) and urine X-12117 (HR, 1.7 [1.3–2.2], P = 1.9E-5) were risk factors of UACR doubling, whereas urine sebacate (HR, 0.86 [0.80–0.92], P = 1.9E-5) was inversely associated. Compared with clinical characteristics alone, including the top five endogenous metabolites in serum and urine associated with longitudinal outcomes improved the outcome prediction (area under the receiver operating characteristic curves for eGFR decline: clinical model=0.79, clinical+metabolites model=0.87, P = 8.1E-6; for UACR doubling: clinical model=0.66, clinical+metabolites model=0.73, P = 2.9E-5).
Conclusions
Metabolomic profiling in different biofluids provided distinct and potentially complementary insights into the biology and prognosis of kidney diseases.
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Affiliation(s)
- Wan-Jin Yeo
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, New York
| | - Aditya L Surapaneni
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, New York
| | - Denise C Hasson
- Division of Pediatric Critical Care Medicine, Hassenfeld Children's Hospital, NYU Langone Health, New York, New York
| | - Insa M Schmidt
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Peggy Sekula
- Department of Data Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Anna Köttgen
- Department of Data Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Casey M Rebholz
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Bing Yu
- Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston Medical Center and Boston University Chobanian & Avedisian School of Medicine, Boston, Massachusetts
| | - Eugene P Rhee
- Nephrology Division and Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Sarah J Schrauben
- Renal-Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold I Feldman
- Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ramachandran S Vasan
- School of Public Health, University of Texas Health San Antonio, San Antonio, Texas
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston Medical Center and Boston University Chobanian and Avedisian School of Medicine, Boston, Massachusetts
| | - Paul L Kimmel
- Division of Kidney, Urologic, and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Optimal Aging Institute, Departments of Population Health and Medicine, NYU Langone Health, New York, New York
- Department of Population Health, NYU Langone Medical Center, New York, New York
| | - Morgan E Grams
- Division of Precision Medicine, Department of Medicine, NYU Langone Health, New York, New York
- Department of Population Health, NYU Langone Medical Center, New York, New York
| | - Pascal Schlosser
- Department of Data Driven Medicine, Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany
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31
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Zhang M, Zhao X, Li Y, Ye Q, Wu Y, Niu Q, Zhang Y, Fan G, Chen T, Xia J, Wu Q. Advances in serum-free media for CHO cells: From traditional serum substitutes to microbial-derived substances. Biotechnol J 2024; 19:e2400251. [PMID: 39031790 DOI: 10.1002/biot.202400251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/25/2024] [Accepted: 05/31/2024] [Indexed: 07/22/2024]
Abstract
The Chinese hamster ovary (CHO) cell is an epithelial-like cell that produces proteins with post-translational modifications similar to human glycosylation. It is widely used in the production of recombinant therapeutic proteins and monoclonal antibodies. Culturing CHO cells typically requires the addition of a certain proportion of fetal bovine serum (FBS) to maintain cell proliferation and passaging. However, serum is characterized by its complex composition, batch-to-batch variability, high cost, and potential risk of exogenous contaminants such as mycoplasma and viruses, which impact the purity and safety of the synthesized proteins. Therefore, search for serum alternatives and development of serum-free media for CHO-based protein biomanufacturing are of great significance. This review systematically summarizes the application advantages of CHO cells and strategies for high-density expression. It highlights the developmental trends of serum substitutes from human platelet lysates to animal-free extracts and microbial-derived substances and elucidates the mechanisms by which these substitutes enhance CHO cell culture performance and recombinant protein production, aiming to provide theoretical guidance for exploring novel serum alternatives and developing serum-free media for CHO cells.
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Affiliation(s)
- Mingcan Zhang
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinyu Zhao
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Ying Li
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinghua Ye
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Yuwei Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qinya Niu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhang
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Guanghan Fan
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Tianxiang Chen
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiarui Xia
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Qingping Wu
- National Health Commission Science and Technology Innovation Platform for Nutrition and Safety of Microbial Food, Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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32
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Rathod ML, Aw WY, Huang S, Lu J, Doherty EL, Whithworth CP, Xi G, Roy-Chaudhury P, Polacheck WJ. Donor-Derived Engineered Microvessels for Cardiovascular Risk Stratification of Patients with Kidney Failure. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307901. [PMID: 38185718 PMCID: PMC11168887 DOI: 10.1002/smll.202307901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 11/28/2023] [Indexed: 01/09/2024]
Abstract
Cardiovascular disease is the cause of death in ≈50% of hemodialysis patients. Accumulation of uremic solutes in systemic circulation is thought to be a key driver of the endothelial dysfunction that underlies elevated cardiovascular events. A challenge in understanding the mechanisms relating chronic kidney disease to cardiovascular disease is the lack of in vitro models that allow screening of the effects of the uremic environment on the endothelium. Here, a method is described for microfabrication of human blood vessels from donor cells and perfused with donor serum. The resulting donor-derived microvessels are used to quantify vascular permeability, a hallmark of endothelial dysfunction, in response to serum spiked with pathophysiological levels of indoxyl sulfate, and in response to serum from patients with chronic kidney disease and from uremic pigs. The uremic environment has pronounced effects on microvascular integrity as demonstrated by irregular cell-cell junctions and increased permeability in comparison to cell culture media and healthy serum. Moreover, the engineered microvessels demonstrate an increase in sensitivity compared to traditional 2D assays. Thus, the devices and the methods presented here have the potential to be utilized to risk stratify and to direct personalized treatments for patients with chronic kidney disease.
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Affiliation(s)
- Mitesh L. Rathod
- Joint Department of Biomedical Engineering, University of
North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and
Raleigh, NC, United States of America
| | - Wen Yih Aw
- Joint Department of Biomedical Engineering, University of
North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and
Raleigh, NC, United States of America
| | - Stephanie Huang
- Joint Department of Biomedical Engineering, University of
North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and
Raleigh, NC, United States of America
| | - Jingming Lu
- Joint Department of Biomedical Engineering, University of
North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and
Raleigh, NC, United States of America
| | - Elizabeth L. Doherty
- Joint Department of Biomedical Engineering, University of
North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and
Raleigh, NC, United States of America
| | - Chloe P. Whithworth
- Department of Genetics, University of North Carolina at
Chapel Hill School of Medicine, Chapel Hill, NC, United States of America
| | - Gang Xi
- UNC Kidney Centre, University of North Carolina at Chapel
Hill, NC, United States of America
| | - Prabir Roy-Chaudhury
- UNC Kidney Centre, University of North Carolina at Chapel
Hill, NC, United States of America
- WG (Bill Hefner) Salisbury VA Medical Center, United States
of America
| | - William J. Polacheck
- Joint Department of Biomedical Engineering, University of
North Carolina at Chapel Hill and North Carolina State University, Chapel Hill and
Raleigh, NC, United States of America
- Department of Cell Biology and Physiology, University of
North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- McAllister Heart Institute, University of North Carolina at
Chapel Hill, Chapel Hill, NC, United States of America
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33
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Rawat V, DeLear P, Prashanth P, Ozgurses ME, Tebeje A, Burns PA, Conger KO, Solís C, Hasnain Y, Novikova A, Endress JE, González-Sánchez P, Dong W, Stephanopoulos G, DeNicola GM, Harris IS, Sept D, Mason FM, Coloff JL. Drug screening in human physiologic medium identifies uric acid as an inhibitor of rigosertib efficacy. JCI Insight 2024; 9:e174329. [PMID: 38815134 PMCID: PMC11383364 DOI: 10.1172/jci.insight.174329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 05/29/2024] [Indexed: 06/01/2024] Open
Abstract
The nonphysiological nutrient levels found in traditional culture media have been shown to affect numerous aspects of cancer cell physiology, including how cells respond to certain therapeutic agents. Here, we comprehensively evaluated how physiological nutrient levels affect therapeutic response by performing drug screening in human plasma-like medium. We observed dramatic nutrient-dependent changes in sensitivity to a variety of FDA-approved and clinically trialed compounds, including rigosertib, an experimental cancer therapeutic that recently failed in phase III clinical trials. Mechanistically, we found that the ability of rigosertib to destabilize microtubules is strongly inhibited by the purine metabolism end product uric acid, which is uniquely abundant in humans relative to traditional in vitro and in vivo cancer models. These results demonstrate the broad and dramatic effects nutrient levels can have on drug response and how incorporation of human-specific physiological nutrient medium might help identify compounds whose efficacy could be influenced in humans.
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Affiliation(s)
- Vipin Rawat
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Patrick DeLear
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Prarthana Prashanth
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Mete Emir Ozgurses
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Anteneh Tebeje
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Philippa A Burns
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Kelly O Conger
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Christopher Solís
- Department of Nutrition and Integrative Physiology, Florida State University, Tallahassee, Florida, USA
| | - Yasir Hasnain
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Anna Novikova
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
| | | | | | - Wentao Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Greg Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Gina M DeNicola
- Department of Metabolism and Physiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Isaac S Harris
- Department of Biomedical Genetics, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, New York, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank M Mason
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jonathan L Coloff
- Department of Physiology and Biophysics, University of Illinois College of Medicine, University of Illinois Cancer Center, Chicago, Illinois, USA
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34
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Ovbude ST, Sharmeen S, Kyei I, Olupathage H, Jones J, Bell RJ, Powers R, Hage DS. Applications of chromatographic methods in metabolomics: A review. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1239:124124. [PMID: 38640794 DOI: 10.1016/j.jchromb.2024.124124] [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: 10/03/2023] [Revised: 03/11/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024]
Abstract
Chromatography is a robust and reliable separation method that can use various stationary phases to separate complex mixtures commonly seen in metabolomics. This review examines the types of chromatography and stationary phases that have been used in targeted or untargeted metabolomics with methods such as mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. General considerations for sample pretreatment and separations in metabolomics are considered, along with the various supports and separation formats for chromatography that have been used in such work. The types of liquid chromatography (LC) that have been most extensively used in metabolomics will be examined, such as reversed-phase liquid chromatography and hydrophilic liquid interaction chromatography. In addition, other forms of LC that have been used in more limited applications for metabolomics (e.g., ion-exchange, size-exclusion, and affinity methods) will be discussed to illustrate how these techniques may be utilized for new and future research in this field. Multidimensional LC methods are also discussed, as well as the use of gas chromatography and supercritical fluid chromatography in metabolomics. In addition, the roles of chromatography in NMR- vs. MS-based metabolomics are considered. Applications are given within the field of metabolomics for each type of chromatography, along with potential advantages or limitations of these separation methods.
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Affiliation(s)
- Susan T Ovbude
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Sadia Sharmeen
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Isaac Kyei
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Harshana Olupathage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Jacob Jones
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Richard J Bell
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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35
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Wang X, Wu Y, Zhao P, Wang X, Wu W, Yang J. The causal relationship between serum metabolites and acne vulgaris: a Mendelian randomization study. Sci Rep 2024; 14:11045. [PMID: 38744939 PMCID: PMC11093973 DOI: 10.1038/s41598-024-61850-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
In individuals with acne vulgaris, alterations occur in serum metabolite composition, yet the exact causal link between these metabolites and acne development remains elusive. Using genome-wide association datasets, we performed bidirectional Mendelian randomization (MR) to investigate the potential causal relationship between 309 serum metabolites and acne vulgaris. We performed sensitivity analysis to evaluate the presence of heterogeneity and pleiotropy. Forward MR analysis found 14 serum metabolites significantly associated with acne vulgaris, and reverse MR analysis found no significant association between acne vulgaris and these serum metabolites. Through validation using data from the FinnGen database of acne vulgaris studies, we found a conclusive and significant correlation between stearoylcarnitine and acne vulgaris. This provides new evidence in the search for new targets for the treatment of acne vulgaris.
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Affiliation(s)
- Xiaoyun Wang
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Yujia Wu
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Pengfei Zhao
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Xinren Wang
- School of Basic Medical Sciences, Dali University, Dali, China
| | - Wenjuan Wu
- Department of Dermatology, First Affiliated Hospital of Kunming Medical University, Kunming, China.
| | - Jiankang Yang
- School of Basic Medical Sciences, Dali University, Dali, China.
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Sarkar S, Chakraborty G, Pal H. Surfactant-based supramolecular dye assembly: A highly selective and economically viable platform for quantification of heparin antidote. Colloids Surf B Biointerfaces 2024; 237:113839. [PMID: 38492411 DOI: 10.1016/j.colsurfb.2024.113839] [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: 01/11/2024] [Revised: 02/23/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024]
Abstract
Herein, we have employed a supramolecular assembly of a cationic dye, LDS-698 and a common surfactant sodium dodecyl sulfate (SDS) as a turn-on fluorescent sensor for protamine (Pr) detection. Addition of cationic Pr to the solution of dye-surfactant complex brings negatively charged SDS molecules together through strong electrostatic interaction, assisting aggregation of SDS way before its critical micellar concentration (CMC). These aggregates encapsulate the dye molecules within their hydrophobic region, arresting non-radiative decay channels of the excited dye. Thus, the LDS-698•SDS assembly displays substantial enhancement in fluorescence intensity that follows a nice linear trend with Pr concentration, providing limit of detection (LOD) for Pr as low as 3.84(±0.11) nM in buffer, 124.4(±6.7) nM in 1% human serum and 28.3(±0.5) nM in 100% human urine. Furthermore, high selectivity, low background signal, large stokes shift, and emission in the biologically favorable deep-red region make the studied assembly a promising platform for Pr sensing. As of our knowledge it is the first ever Pr sensory platform, using a very common surfactant (SDS), which is economically affordable and very easily available in the market. This innovative approach can replace the expensive, exotic and specialized chemicals considered for the purpose and thus showcase its potential in practical applications.
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Affiliation(s)
- Soumyadeep Sarkar
- Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Indian Institute of Science Education and Research, Campus Road, Mohanpur, Nadia, Kolkata, West Bengal 741246, India
| | - Goutam Chakraborty
- Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Haridas Pal
- Chemistry Group, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094, India.
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Hemmer S, Manier SK, Wagmann L, Meyer MR. Comparison of reversed-phase, hydrophilic interaction, and porous graphitic carbon chromatography columns for an untargeted toxicometabolomics study in pooled human liver microsomes, rat urine, and rat plasma. Metabolomics 2024; 20:49. [PMID: 38689195 PMCID: PMC11061011 DOI: 10.1007/s11306-024-02115-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/20/2024] [Indexed: 05/02/2024]
Abstract
INTRODUCTION Untargeted metabolomics studies are expected to cover a wide range of compound classes with high chemical diversity and complexity. Thus, optimizing (pre-)analytical parameters such as the analytical liquid chromatography (LC) column is crucial and the selection of the column depends primarily on the study purpose. OBJECTIVES The current investigation aimed to compare six different analytical columns. First, by comparing the chromatographic resolution of selected compounds. Second, on the outcome of an untargeted toxicometabolomics study using pooled human liver microsomes (pHLM), rat plasma, and rat urine as matrices. METHODS Separation and analysis were performed using three different reversed-phase (Phenyl-Hexyl, BEH C18, and Gold C18), two hydrophilic interaction chromatography (HILIC) (ammonium-sulfonic acid and sulfobetaine), and one porous graphitic carbon (PGC) columns coupled to high-resolution mass spectrometry (HRMS). Their impact was evaluated based on the column performance and the size of feature count, amongst others. RESULTS All three reversed-phase columns showed a similar performance, whereas the PGC column was superior to both HILIC columns at least for polar compounds. Comparing the size of feature count across all datasets, most features were detected using the Phenyl-Hexyl or sulfobetaine column. Considering the matrices, most significant features were detected in urine and pHLM after using the sulfobetaine and in plasma after using the ammonium-sulfonic acid column. CONCLUSION The results underline that the outcome of this untargeted toxicometabolomic study LC-HRMS metabolomic study was highly influenced by the analytical column, with the Phenyl-Hexyl or sulfobetaine column being the most suitable. However, column selection may also depend on the investigated compounds as well as on the investigated matrix.
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Affiliation(s)
- Selina Hemmer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Sascha K Manier
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Lea Wagmann
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, Homburg, Germany.
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Urrutia AA, Mesa-Ciller C, Guajardo-Grence A, Alkan HF, Soro-Arnáiz I, Vandekeere A, Ferreira Campos AM, Igelmann S, Fernández-Arroyo L, Rinaldi G, Lorendeau D, De Bock K, Fendt SM, Aragonés J. HIF1α-dependent uncoupling of glycolysis suppresses tumor cell proliferation. Cell Rep 2024; 43:114103. [PMID: 38607920 PMCID: PMC11063627 DOI: 10.1016/j.celrep.2024.114103] [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: 07/28/2022] [Revised: 11/20/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Hypoxia-inducible factor-1α (HIF1α) attenuates mitochondrial activity while promoting glycolysis. However, lower glycolysis is compromised in human clear cell renal cell carcinomas, in which HIF1α acts as a tumor suppressor by inhibiting cell-autonomous proliferation. Here, we find that, unexpectedly, HIF1α suppresses lower glycolysis after the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) step, leading to reduced lactate secretion in different tumor cell types when cells encounter a limited pyruvate supply such as that typically found in the tumor microenvironment in vivo. This is because HIF1α-dependent attenuation of mitochondrial oxygen consumption increases the NADH/NAD+ ratio that suppresses the activity of the NADH-sensitive GAPDH glycolytic enzyme. This is manifested when pyruvate supply is limited, since pyruvate acts as an electron acceptor that prevents the increment of the NADH/NAD+ ratio. Furthermore, this anti-glycolytic function provides a molecular basis to explain how HIF1α can suppress tumor cell proliferation by increasing the NADH/NAD+ ratio.
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Affiliation(s)
- Andrés A Urrutia
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa (IIS IP), Autonomous University of Madrid, 28009 Madrid, Spain
| | - Claudia Mesa-Ciller
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa (IIS IP), Autonomous University of Madrid, 28009 Madrid, Spain
| | - Andrea Guajardo-Grence
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa (IIS IP), Autonomous University of Madrid, 28009 Madrid, Spain
| | - H Furkan Alkan
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Inés Soro-Arnáiz
- Laboratory of Exercise and Health, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Anke Vandekeere
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Ana Margarida Ferreira Campos
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Sebastian Igelmann
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Lucía Fernández-Arroyo
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa (IIS IP), Autonomous University of Madrid, 28009 Madrid, Spain
| | - Gianmarco Rinaldi
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Doriane Lorendeau
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Katrien De Bock
- Laboratory of Exercise and Health, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, VIB, Herestraat 49, 3000 Leuven, Belgium; Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute (LKI), Herestraat 49, 3000 Leuven, Belgium
| | - Julián Aragonés
- Research Unit, Hospital of Santa Cristina, Research Institute Princesa (IIS IP), Autonomous University of Madrid, 28009 Madrid, Spain; CIBER de Enfermedades Cardiovasculares (CIBERCV), Carlos III Health Institute, Madrid, Spain.
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Chen Y, Lin J, Tao M. Association between cheese and fish consumption and the occurrence of depression based on European population: mediating role of metabolites. Front Nutr 2024; 11:1322254. [PMID: 38694223 PMCID: PMC11061354 DOI: 10.3389/fnut.2024.1322254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/28/2024] [Indexed: 05/04/2024] Open
Abstract
Background The consumption of cheese and fish has been linked to the onset of depression. However, the connection between consuming cheese, consuming fish, experiencing depression, and the pathways that mediate this relationship remains unclear. The purpose of this research was to investigate the potential association between the consumption of cheese and fish and the occurrence of depression. Moreover, it is important to identify any metabolites that might be involved and understand their respective roles and functions. Methods A two-step, two-sample Mendelian randomization (MR) study was conducted using genome-wide association study (GWAS) data on cheese, non-oily fish, and oily fish consumption and depression, along with 12 alternate mediators. The study included a total of 451,486 participants in the cheese consumption group, 460,880 in the non-oily fish consumption group, 460,443 in the oily fish consumption group, and 322,580 with a diagnosis of depression. The single nucleotide polymorphism (SNP) estimates were pooled using inverse-variance weighted, weighted median, MR-Egger, simple mode, and weighted mode. Results The data we collected suggested that consuming more cheese correlated with a lower likelihood of experiencing depression (OR: 0.95; 95% CI: 0.92 to 0.98). Neither non-oily fish nor oily fish consumption was directly linked to depression onset (p = 0.08, p = 0.78, respectively). Although there was a direct causal relationship with depression, the mediating relationship of triglycerides (TG), total cholesterol in large HDL, cholesterol to total lipids ratio in large HDL, free cholesterol to total lipids ratio in large HDL, glycine, and phospholipids to total lipids ratio in very large HDL of cheese intake on depression risk were - 0.002 (95% CI: -0.023 - 0.020), -0.002 (95% CI: -0.049 - 0.045), -0.001 (95% CI: -0.033 - 0.031), -0.001 (95% CI: -0.018 - 0.015), 0.001 (95% CI: -0.035 - 0.037), and - 0.001 (95% CI: -0.024 - 0.021), respectively. The mediating relationship of uridine, free cholesterol to total lipids ratio in large HDL, total cholesterol in large HDL, acetoacetate, and 3-hydroxybutyrate (3-HB) between non-oily fish consumption and depression risk were 0.016 (95% CI: -0.008 - 0.040), 0.011 (95% CI: -1.269 - 1.290), 0.010 (95% CI: -1.316 - 1.335), 0.011 (95% CI: -0.089 - 0.110), and 0.008 (95% CI: -0.051 - 0.068), respectively. The mediation effect of uridine and free cholesterol to total lipids ratio in large HDL between intake of oily fish and the risk of depression was found to be 0.006 (95% CI: -0.015 - 0.028) and - 0.002 (95% CI: -0.020 - 0.017), respectively. The correlation between eating cheese and experiencing depression persisted even when adjusting for other variables like Indian snacks, mango consumption, sushi consumption, and unsalted peanuts using multivariable MR. Conclusion The consumption of cheese and fish influenced the likelihood of experiencing depression, and this may be mediated by certain metabolites in the body. Our study provided a new perspective on the clinical treatment of depression.
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Affiliation(s)
- Yan Chen
- Second Clinical Medical School, Zhejiang Chinese Medical University, Hangzhou, China
| | - Jixin Lin
- Second Clinical Medical School, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ming Tao
- Second Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
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Møller-Hansen I, Sáez-Sáez J, van der Hoek SA, Dyekjær JD, Christensen HB, Wright Muelas M, O’Hagan S, Kell DB, Borodina I. Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds. Front Microbiol 2024; 15:1376653. [PMID: 38680917 PMCID: PMC11045925 DOI: 10.3389/fmicb.2024.1376653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).
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Affiliation(s)
- Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jane D. Dyekjær
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Hanne B. Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Steve O’Hagan
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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Li S, Looby N, Chandran V, Kulasingam V. Challenges in the Metabolomics-Based Biomarker Validation Pipeline. Metabolites 2024; 14:200. [PMID: 38668328 PMCID: PMC11051909 DOI: 10.3390/metabo14040200] [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: 03/01/2024] [Revised: 03/27/2024] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
As end-products of the intersection between the genome and environmental influences, metabolites represent a promising approach to the discovery of novel biomarkers for diseases. However, many potential biomarker candidates identified by metabolomics studies fail to progress beyond analytical validation for routine implementation in clinics. Awareness of the challenges present can facilitate the development and advancement of innovative strategies that allow improved and more efficient applications of metabolite-based markers in clinical settings. This minireview provides a comprehensive summary of the pre-analytical factors, required analytical validation studies, and kit development challenges that must be resolved before the successful translation of novel metabolite biomarkers originating from research. We discuss the necessity for strict protocols for sample collection, storage, and the regulatory requirements to be fulfilled for a bioanalytical method to be considered as analytically validated. We focus especially on the blood as a biological matrix and liquid chromatography coupled with tandem mass spectrometry as the analytical platform for biomarker validation. Furthermore, we examine the challenges of developing a commercially viable metabolomics kit for distribution. To bridge the gap between the research lab and clinical implementation and utility of relevant metabolites, the understanding of the translational challenges for a biomarker panel is crucial for more efficient development of metabolomics-based precision medicine.
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Affiliation(s)
- Shenghan Li
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Nikita Looby
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Orthopaedic Surgery, Osteoarthritis Research Program, Schroeder Arthritis Institute, University Health Network, Toronto, ON M5T 0S8, Canada
| | - Vinod Chandran
- Division of Rheumatology, Psoriatic Arthritis Program, Schroeder Arthritis Program, University Health Network, Toronto, ON M5T 0S8, Canada; (S.L.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A1, Canada
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
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Chen H, Han Y, Hearne A, Monarchino A, Wiseman JS. Purinergic ligands induce extracellular acidification and increased ATP turnover in HepG2 cells. Toxicol In Vitro 2024; 96:105788. [PMID: 38320684 DOI: 10.1016/j.tiv.2024.105788] [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: 11/29/2023] [Accepted: 01/31/2024] [Indexed: 02/08/2024]
Abstract
Nucleosides and nucleotides at μM concentrations stimulated a 300% increase in acid secretion in HepG2 cells, which was quantitatively accounted for as increased export of lactate generated by glycogenolysis. Agonist selectivity encompassed nucleosides and nucleotides for all 5 natural nucleobases and, along with antagonist profiles, was inconsistent with a role for purinergic receptors in mediating this activity. Agonist catabolism did not contribute significantly to either low selectivity or lactate production. Lactate production was driven by an increase in ATP turnover of as much as 56%. For some agonists, especially adenosine, ATP turnover decreased precipitously at mM concentrations, correlating with known adenosine-stimulated apoptosis. We propose that nucleoside/nucleotide agonists induce a futile energy cycle via a novel mechanism, which results in increased ATP turnover and initiates a continuum of events that for some agonists culminates in apoptosis.
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Affiliation(s)
- Haotong Chen
- Edison Biotechnology Institute, Bldg. 25, The Ridges, Ohio University, Athens, OH, USA; QPS Holding LLC, 3 Innovation Way, Newark, DE 19711, United States of America.
| | - Yong Han
- Edison Biotechnology Institute, Bldg. 25, The Ridges, Ohio University, Athens, OH, USA.
| | - Abby Hearne
- Edison Biotechnology Institute, Bldg. 25, The Ridges, Ohio University, Athens, OH, USA.
| | - Anna Monarchino
- Edison Biotechnology Institute, Bldg. 25, The Ridges, Ohio University, Athens, OH, USA.
| | - Jeffrey S Wiseman
- Edison Biotechnology Institute, Bldg. 25, The Ridges, Ohio University, Athens, OH, USA.
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Gong X, Fu Y, Zhou L, Wei A, Pan C, Zhu T, Li H. Decoding chronic rhinosinusitis: A metabolomics-based approach. Int Forum Allergy Rhinol 2024; 14:828-840. [PMID: 38343156 DOI: 10.1002/alr.23331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Chronic rhinosinusitis (CRS) is a common and intractable disease in otorhinolaryngology, laying a heavy burden on healthcare systems. The worldwide researchers are making efforts to find solutions to this disease. Metabolomics has recently gained more and more traction, and might become a promising tool to unravel the complexity of CRS. This paper provides an overview of current studies on the metabolomics of various CRS subtypes. METHODS We conducted a comprehensive literature search in PubMed, Web of Science, EMBASE, Google Scholar, and Cochrane Library, up to May 25, 2023. Search strategies incorporated key terms such as "chronic rhinosinusitis" and "metabolomics" with relevant synonyms and MeSH terms. Titles and abstracts of 86 screened articles were assessed for relevance to CRS and metabolomics. Methodological robustness, data reliability, and relevance were considered for shortlisted articles. RESULTS After the refined process, a total of 26 articles were included in this study and sorted out by research themes, methodology and pivotal discoveries. These included studies identified the metabolic pathways and markers related to the pathophysiology in each subtype of CRS. CONCLUSIONS Metabolomics helps to shed light on the complexity of CRS. The mentioned findings highlight the importance of specific metabolic pathways and markers in understanding the pathophysiology of CRS. Despite that, challenges and future directions in metabolomics research for CRS would be worth being further explored.
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Affiliation(s)
- Xinru Gong
- Health and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yijie Fu
- School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan, China
| | - Lei Zhou
- Health and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Aiming Wei
- Health and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Chongsheng Pan
- Health and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Tianmin Zhu
- Health and Rehabilitation College, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Hui Li
- School of Preclinical Medicine, Chengdu University, Chengdu, Sichuan, China
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Lu W, McBride MJ, Lee WD, Xing X, Xu X, Li X, Oschmann AM, Shen Y, Bartman C, Rabinowitz JD. Selected Ion Monitoring for Orbitrap-Based Metabolomics. Metabolites 2024; 14:184. [PMID: 38668312 PMCID: PMC11051813 DOI: 10.3390/metabo14040184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/08/2024] [Accepted: 03/18/2024] [Indexed: 04/28/2024] Open
Abstract
Orbitrap mass spectrometry in full scan mode enables the simultaneous detection of hundreds of metabolites and their isotope-labeled forms. Yet, sensitivity remains limiting for many metabolites, including low-concentration species, poor ionizers, and low-fractional-abundance isotope-labeled forms in isotope-tracing studies. Here, we explore selected ion monitoring (SIM) as a means of sensitivity enhancement. The analytes of interest are enriched in the orbitrap analyzer by using the quadrupole as a mass filter to select particular ions. In tissue extracts, SIM significantly enhances the detection of ions of low intensity, as indicated by improved signal-to-noise (S/N) ratios and measurement precision. In addition, SIM improves the accuracy of isotope-ratio measurements. SIM, however, must be deployed with care, as excessive accumulation in the orbitrap of similar m/z ions can lead, via space-charge effects, to decreased performance (signal loss, mass shift, and ion coalescence). Ion accumulation can be controlled by adjusting settings including injection time and target ion quantity. Overall, we suggest using a full scan to ensure broad metabolic coverage, in tandem with SIM, for the accurate quantitation of targeted low-intensity ions, and provide methods deploying this approach to enhance metabolome coverage.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Matthew J. McBride
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
| | - Won Dong Lee
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
| | - Xi Xing
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Xincheng Xu
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Xi Li
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
| | - Anna M. Oschmann
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Yihui Shen
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Caroline Bartman
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Pharmacology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua D. Rabinowitz
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; (W.L.)
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Princeton University, Princeton, NJ 08544, USA
- Rutgers Cancer Institute of New Jersey (CINJ), Rutgers University, New Brunswick, NJ 08901, USA
- Ludwig Institute for Cancer Research, Princeton University, Princeton, NJ 08544, USA
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45
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Song Y, Chen N, Curk T, Katz HE. A Study of the Drift Phenomena of Gate-Functionalized Biosensors and Dual-Gate-Functionalized Biosensors in Human Serum. Molecules 2024; 29:1459. [PMID: 38611739 PMCID: PMC11013244 DOI: 10.3390/molecules29071459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
In this paper, we study the drift behavior of organic electrochemical transistor (OECT) biosensors in a phosphate-buffered saline (PBS) buffer solution and human serum. Theoretical and experimental methods are illustrated in this paper to understand the origin of the drift phenomenon and the mechanism of ion diffusion in the sensing layer. The drift phenomenon is explained using a first-order kinetic model of ion adsorption into the gate material and shows very good agreement with experimental data on drift in OECTs. We show that the temporal current drift can be largely mitigated using a dual-gate OECT architecture and that dual-gate-based biosensors can increase the accuracy and sensitivity of immuno-biosensors compared to a standard single-gate design. Specific binding can be detected at a relatively low limit of detection, even in human serum.
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Affiliation(s)
| | | | - Tine Curk
- Department of Materials Science and Engineering, Johns Hopkins University, 206 Maryland Hall, 3400 North Charles Street, Baltimore, MD 21218, USA; (Y.S.); (N.C.)
| | - Howard E. Katz
- Department of Materials Science and Engineering, Johns Hopkins University, 206 Maryland Hall, 3400 North Charles Street, Baltimore, MD 21218, USA; (Y.S.); (N.C.)
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46
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Pausova Z, Sliz E. Large-Scale Population-Based Studies of Blood Metabolome and Brain Health. Curr Top Behav Neurosci 2024. [PMID: 38509405 DOI: 10.1007/7854_2024_463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Metabolomics technologies enable the quantification of multiple metabolomic measures simultaneously, which provides novel insights into molecular aspects of human health and disease. In large-scale, population-based studies, blood is often the preferred biospecimen. Circulating metabolome may relate to brain health either by affecting or reflecting brain metabolism. Peripheral metabolites may act at or cross the blood-brain barrier and, subsequently, influence brain metabolism, or they may reflect brain metabolism if similar pathways are engaged. Peripheral metabolites may also include those penetrating the circulation from the brain, indicating, for example, brain damage. Most brain health-related metabolomics studies have been conducted in the context of neurodegenerative disorders and cognition, but some studies have also focused on neuroimaging markers of these disorders. Moreover, several metabolomics studies of neurodevelopmental disorders have been performed. Here, we provide a brief background on the types of blood metabolites commonly assessed, and we review the literature describing the relationships between human blood metabolome (n > 50 metabolites) and brain health reported in large-scale studies (n > 500 individuals).
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Affiliation(s)
- Zdenka Pausova
- The Hospital for Sick Children, Toronto, ON, Canada
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, ON, Canada
| | - Eeva Sliz
- Research Unit of Population Health, Faculty of Medicine, University of Oulu, Oulu, Finland.
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47
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Zhang Y, Wang Y, Liao X, Liu T, Yang F, Yang K, Zhou Z, Fu Y, Fu T, Sysa A, Chen X, Shen Y, Lyu J, Zhao Q. Glutamine prevents high-fat diet-induced hepatic lipid accumulation in mice by modulating lipolysis and oxidative stress. Nutr Metab (Lond) 2024; 21:12. [PMID: 38459503 PMCID: PMC10924388 DOI: 10.1186/s12986-024-00784-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024] Open
Abstract
Metabolic-associated fatty liver disease (MAFLD) is related to metabolic dysfunction and is characterized by excess fat storage in the liver. Several studies have indicated that glutamine could be closely associated with lipid metabolism disturbances because of its important role in intermediary metabolism. However, the effect of glutamine supplementation on MAFLD progression remains unclear. Here, we used a high-fat diet (HFD)-induced MAFLD C57BL/6 mouse model, and glutamine was supplied in the drinking water at different time points for MAFLD prevention and reversal studies. A MAFLD prevention study was performed by feeding mice an HFD concomitant with 4% glutamine treatment for 24 weeks, whereas the MAFLD reversal study was performed based on 4% glutamine treatment for 13 weeks after feeding mice an HFD for 10 weeks. In the prevention study, glutamine treatment ameliorated serum lipid storage, hepatic lipid injury, and oxidative stress in HFD-induced obese mice, although glutamine supplementation did not affect body weight, glucose homeostasis, energy expenditure, and mitochondrial function. In the MAFLD reversal study, there were no noticeable changes in the basic physiological phenotype and hepatic lipid metabolism. In summary, glutamine might prevent, but not reverse, HFD-induced MAFLD in mice, suggesting that a cautious attitude is required regarding its use for MAFLD treatment.
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Affiliation(s)
- Yongjie Zhang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Yangli Wang
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Xin Liao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Tong Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Fengyuan Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Kaiqiang Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Zhuohua Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Yinxu Fu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China
| | - Ting Fu
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
| | - Aliaksei Sysa
- Belarusian State University, ISEI BSU, Minsk, Republic of Belarus
| | - Xiandan Chen
- Belarusian State University, ISEI BSU, Minsk, Republic of Belarus
| | - Yao Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.
| | - Jianxin Lyu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China.
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China.
- Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| | - Qiongya Zhao
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China.
- Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
- School of Public Health, Hangzhou Medical College, Hangzhou, China.
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48
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Tirelli C, Mira S, Belmonte LA, De Filippi F, De Grassi M, Italia M, Maggioni S, Guido G, Mondoni M, Canonica GW, Centanni S. Exploring the Potential Role of Metabolomics in COPD: A Concise Review. Cells 2024; 13:475. [PMID: 38534319 DOI: 10.3390/cells13060475] [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: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a pathological condition of the respiratory system characterized by chronic airflow obstruction, associated with changes in the lung parenchyma (pulmonary emphysema), bronchi (chronic bronchitis) and bronchioles (small airways disease). In the last years, the importance of phenotyping and endotyping COPD patients has strongly emerged. Metabolomics refers to the study of metabolites (both intermediate or final products) and their biological processes in biomatrices. The application of metabolomics to respiratory diseases and, particularly, to COPD started more than one decade ago and since then the number of scientific publications on the topic has constantly grown. In respiratory diseases, metabolomic studies have focused on the detection of metabolites derived from biomatrices such as exhaled breath condensate, bronchoalveolar lavage, and also plasma, serum and urine. Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy are powerful tools in the precise identification of potentially prognostic and treatment response biomarkers. The aim of this article was to comprehensively review the relevant literature regarding the applications of metabolomics in COPD, clarifying the potential clinical utility of the metabolomic profile from several biologic matrices in detecting biomarkers of disease and prognosis for COPD. Meanwhile, a complete description of the technological instruments and techniques currently adopted in the metabolomics research will be described.
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Affiliation(s)
- Claudio Tirelli
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Sabrina Mira
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Luca Alessandro Belmonte
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Federica De Filippi
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Mauro De Grassi
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Marta Italia
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Sara Maggioni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Gabriele Guido
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Michele Mondoni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Giorgio Walter Canonica
- Personalized Medicine, Asthma and Allergy, IRCCS Humanitas Clinical and Research Center, 20089 Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, 20072 Milan, Italy
| | - Stefano Centanni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
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49
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Lim H, Lee S, Jin JS, Kim MS. High-Throughput Quantitative Analysis of Amino Acids in Freeze-Dried Drops Using Time-of-Flight Secondary Ion Mass Spectrometry. Anal Chem 2024; 96:3717-3721. [PMID: 38262943 DOI: 10.1021/acs.analchem.3c04855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a promising analytical tool for molecular profiling in biological applications. However, its ultrahigh vacuum environment and matrix effects hamper the absolute quantitation of solution samples. Herein, we present a rapid high-throughput platform for quantitative ToF-SIMS analysis of amino acids in matrix deposits formed from freeze-dried solution drops through ice sublimation on a parylene film microarray substrate. Droplets of the amino acid solutions, which were mixed with stable isotope-labeled phenylalanine (F*) of high concentration (10 mM), were loaded on wells of the microarray, then frozen and evaporated slowly below the freezing point, forming continuous solid-phase F* matrix deposits. The amino acids (≤500 μM), adequately well dispersed throughout the F* matrix deposits on each well, were quantitatively analyzed by ToF-SIMS in a rapid and high-throughput fashion. The lower limit of quantitation reached below 10 μM.
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Affiliation(s)
- Heejin Lim
- Center for Scientific Instrumentation, Korea Basic Science Institute (KBSI), Cheongju 28119, Republic of Korea
| | - Siheun Lee
- School of Undergraduate Studies, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
| | - Jong Sung Jin
- Busan Center, Korea Basic Science Institute (KBSI), Busan 46742, Republic of Korea
| | - Min-Sik Kim
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- New Biology Research Center, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
- Center for Cell Fate Reprogramming and Control, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988, Republic of Korea
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50
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German N, Popov A, Ramanaviciene A. Reagentless Glucose Biosensor Based on Combination of Platinum Nanostructures and Polypyrrole Layer. BIOSENSORS 2024; 14:134. [PMID: 38534241 DOI: 10.3390/bios14030134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024]
Abstract
Two types of low-cost reagentless electrochemical glucose biosensors based on graphite rod (GR) electrodes were developed. The electrodes modified with electrochemically synthesized platinum nanostructures (PtNS), 1,10-phenanthroline-5,6-dione (PD), glucose oxidase (GOx) without and with a polypyrrole (Ppy) layer-(i) GR/PtNS/PD/GOx and (ii) GR/PtNS/PD/GOx/Ppy, respectively, were prepared and tested. Glucose biosensors based on GR/PtNS/PD/GOx and GR/PtNS/PD/GOx/Ppy electrodes were characterized by the sensitivity of 10.1 and 5.31 μA/(mM cm2), linear range (LR) up to 16.5 and 39.0 mM, limit of detection (LOD) of 0.198 and 0.561 mM, good reproducibility, and storage stability. The developed glucose biosensors based on GR/PtNS/PD/GOx/Ppy electrodes showed exceptional resistance to interfering compounds and proved to be highly efficient for the determination of glucose levels in blood serum.
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Affiliation(s)
- Natalija German
- Department of Immunology and Bioelectrochemistry, State Research Institute Centre for Innovative Medicine, Santariskiu 5, LT-08406 Vilnius, Lithuania
| | - Anton Popov
- Department of Immunology and Bioelectrochemistry, State Research Institute Centre for Innovative Medicine, Santariskiu 5, LT-08406 Vilnius, Lithuania
- NanoTechnas-Center of Nanotechnology and Materials Science, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 243, LT-03225 Vilnius, Lithuania
| | - Almira Ramanaviciene
- Department of Immunology and Bioelectrochemistry, State Research Institute Centre for Innovative Medicine, Santariskiu 5, LT-08406 Vilnius, Lithuania
- NanoTechnas-Center of Nanotechnology and Materials Science, Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko str. 243, LT-03225 Vilnius, Lithuania
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