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Wang X, Shang D, Chen J, Cheng S, Chen D, Zhang Z, Liu C, Yu J, Cao H, Li L, Li L. Serum metabolomics reveals the effectiveness of human placental mesenchymal stem cell therapy for Crohn's disease. Talanta 2024; 277:126442. [PMID: 38897006 DOI: 10.1016/j.talanta.2024.126442] [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: 02/02/2024] [Revised: 06/10/2024] [Accepted: 06/15/2024] [Indexed: 06/21/2024]
Abstract
Mesenchymal stem cell (MSC) therapy offers a promising cure for Crohn's disease (CD), however, its therapeutic effects vary significantly due to individual differences. Therefore, identifying easily detectable biomarkers is essential to assess the efficacy of MSC therapy. In this study, SAMP1/Yit mice were used as a model of CD, which develop spontaneous chronic ileitis, closely resembling the characteristics present in CD patients. Serum metabolic alterations during treatment were analyzed, through the application of differential 12C-/13C-dansylation labeling liquid chromatography-mass spectrometry. Based on the significant differences and time-varying trends of serum amine/phenol-containing metabolites abundance between the control group, the model group, and the treatment group, four serum biomarkers were ultimately screened for evaluating the efficacy of MSC treatment for CD, namely 4-hydroxyphenylpyruvate, 4-hydroxyphenylacetaldehyde, caffeate, and N-acetyltryptamine, whose abundances both increased in the serum of CD model mice and decreased after MSC treatment. These metabolic alterations were associated with tyrosine metabolism, which was validated by the dysregulation of related enzymes. The discovery of biomarkers may help to improve the targeting and effectiveness of treatment and provide innovative prospects for the clinical application of MSC for CD.
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Affiliation(s)
- Xiao Wang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan City 250117, China
| | - Dandan Shang
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan City 250117, China
| | - Junyao Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China
| | - Sheng Cheng
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China
| | - Deying Chen
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China
| | - Zhehua Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China
| | - Chaoxu Liu
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China
| | - Jiong Yu
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan City 250117, China; State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China; Zhejiang Key Laboratory for Diagnosis and Treatment of Physic-chemical and Aging-related Injuries, 79 Qingchun Rd, Hangzhou City 310003, China.
| | - Hongcui Cao
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan City 250117, China; State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China; Zhejiang Key Laboratory for Diagnosis and Treatment of Physic-chemical and Aging-related Injuries, 79 Qingchun Rd, Hangzhou City 310003, China.
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Lanjuan Li
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan City 250117, China; State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd., Hangzhou City 310003, China
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Yuan Y, Wang Y, Zhang Y, Yan H. Development and Application of a Selective Analytical Method for Indole Metabolites in Urine: Dietary Exposure Biomarkers for Broccoli Consumption. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12822-12831. [PMID: 38803050 DOI: 10.1021/acs.jafc.3c08452] [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: 05/29/2024]
Abstract
The identification of dietary exposure biomarkers is crucial for advancing our understanding of the health benefits of specific foods. Broccoli, a vegetable with well-known anticancer properties, contains active ingredients, such as isothiocyanates with indole side chains. Hence, indole metabolites related to broccoli consumption have the potential to serve as biomarkers of dietary exposure. In this work, we developed a new analytical method for indole metabolites in urine using a poly(deep eutectic solvents)-molecularly imprinted polymer/vinyl-functionalized graphene oxide (PDESs-MIP/VGO) in miniaturized centrifugal pipet-tip solid-phase extraction (CPT-SPE) coupled with liquid chromatography. This method integrates the strengths of PDESs-MIP/VGO, including rich adsorption interactions, high adsorption capacity, and excellent selectivity, with the simplicity and cost-effectiveness of CPT-SPE. The proposed method demonstrated low limits of quantification (1.2-2.5 ng mL-1), high accuracy (91.7-104.8%), and good precision (relative standard deviation ≤4.4%). By applying this method to analyze indole metabolites in urine, our results suggested that indole-3-carbinol and indole-3-acetonitrile have the potential to emerge as reliable dietary exposure biomarkers for broccoli intake. Furthermore, highly selective analytical methods based on molecular imprinting technology are advantageous for precise screening and analysis of dietary exposure biomarkers associated with food consumption.
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Affiliation(s)
- Yanan Yuan
- Hebei Key Laboratory of Public Health Safety, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Science, Hebei University, Baoding 071002, China
- Hebei Key Laboratory of Analytical Science and Technology, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Yibo Wang
- Hebei Key Laboratory of Public Health Safety, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Science, Hebei University, Baoding 071002, China
| | - Yanfei Zhang
- Hebei Key Laboratory of Public Health Safety, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Science, Hebei University, Baoding 071002, China
| | - Hongyuan Yan
- Hebei Key Laboratory of Public Health Safety, Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, College of Pharmaceutical Science, Hebei University, Baoding 071002, China
- Hebei Key Laboratory of Analytical Science and Technology, State Key Laboratory of New Pharmaceutical Preparations and Excipients, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
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Ghafari N, Sleno L. Challenges and recent advances in quantitative mass spectrometry-based metabolomics. ANALYTICAL SCIENCE ADVANCES 2024; 5:e2400007. [PMID: 38948317 PMCID: PMC11210748 DOI: 10.1002/ansa.202400007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 06/03/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
The field of metabolomics has gained tremendous interest in recent years. Whether the goal is to discover biomarkers related to certain pathologies or to better understand the impact of a drug or contaminant, numerous studies have demonstrated how crucial it is to understand variations in metabolism. Detailed knowledge of metabolic variabilities can lead to more effective treatments, as well as faster or less invasive diagnostics. Exploratory approaches are often employed in metabolomics, using relative quantitation to look at perturbations between groups of samples. Most metabolomics studies have been based on metabolite profiling using relative quantitation, with very few studies using an approach for absolute quantitation. Using accurate quantitation facilitates the comparison between different studies, as well as enabling longitudinal studies. In this review, we discuss the most widely used techniques for quantitative metabolomics using mass spectrometry (MS). Various aspects will be addressed, such as the use of external and/or internal standards, derivatization techniques, in vivo isotopic labelling, or quantitative MS imaging. The principles, as well as the associated limitations and challenges, will be described for each approach.
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Affiliation(s)
- Nathan Ghafari
- Chemistry Department/CERMO‐FCUniversity of Quebec in Montreal (UQAM)MontrealCanada
| | - Lekha Sleno
- Chemistry Department/CERMO‐FCUniversity of Quebec in Montreal (UQAM)MontrealCanada
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Wieërs MLAJ, Beynon-Cobb B, Visser WJ, Attaye I. Dietary acid load in health and disease. Pflugers Arch 2024; 476:427-443. [PMID: 38282081 PMCID: PMC11006742 DOI: 10.1007/s00424-024-02910-7] [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: 10/27/2023] [Revised: 01/07/2024] [Accepted: 01/09/2024] [Indexed: 01/30/2024]
Abstract
Maintaining an appropriate acid-base equilibrium is crucial for human health. A primary influencer of this equilibrium is diet, as foods are metabolized into non-volatile acids or bases. Dietary acid load (DAL) is a measure of the acid load derived from diet, taking into account both the potential renal acid load (PRAL) from food components like protein, potassium, phosphorus, calcium, and magnesium, and the organic acids from foods, which are metabolized to bicarbonate and thus have an alkalinizing effect. Current Western diets are characterized by a high DAL, due to large amounts of animal protein and processed foods. A chronic low-grade metabolic acidosis can occur following a Western diet and is associated with increased morbidity and mortality. Nutritional advice focusing on DAL, rather than macronutrients, is gaining rapid attention as it provides a more holistic approach to managing health. However, current evidence for the role of DAL is mainly associative, and underlying mechanisms are poorly understood. This review focusses on the role of DAL in multiple conditions such as obesity, cardiovascular health, impaired kidney function, and cancer.
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Affiliation(s)
- Michiel L A J Wieërs
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Beverley Beynon-Cobb
- Department of Nutrition & Dietetics, University Hospitals Coventry & Warwickshire NHS Trust, Coventry, UK
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Wesley J Visser
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Division of Dietetics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Ilias Attaye
- Department of Internal Medicine, Division of Nephrology and Transplantation, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
- Amsterdam Cardiovascular Sciences, Diabetes & Metabolism, Amsterdam, The Netherlands.
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Pal VK, Kannan K. Stability of volatile organic compound metabolites in urine at various storage temperatures and freeze-thaw cycles for 8 months. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 345:123493. [PMID: 38316251 PMCID: PMC10939821 DOI: 10.1016/j.envpol.2024.123493] [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: 11/29/2023] [Revised: 01/15/2024] [Accepted: 02/02/2024] [Indexed: 02/07/2024]
Abstract
The urinary concentrations of mercapturic acid metabolites of volatile organic compounds (VOCs) have been used as biomarkers of human exposure to this class of chemicals. However, long-term stability of these VOC metabolites (VOCMs) in urine at various storage conditions such as temperature, duration, and freeze-thaw cycles is not known. In this study, spot urine samples collected from three volunteers, stored at 22 °C (room temperature: RT), 4 °C (refrigerator) and -20 °C (freezer) for up to 240 days were analyzed at weekly to monthly interval for a total of 19 time points. Samples stored at 4 °C and -20 °C underwent 18 freeze-thaw cycles at RT for 30 min at each of the time points. Among 38 VOCMs analyzed, up to 18 metabolites were detected at concentrations above their respective detection limits on Day 0 (baseline concentration), and the concentrations of several VOCMs declined with the storage duration. Eight to ten VOCMs were lost completely within 240 days of storage at RT, compared to between two and five at 4 °C and between one and seven at -20 °C. The loss rate varied depending on the sample, storage temperature, VOCM, and number of freeze-thaw cycles. Storage of urine at RT led to a rapid loss of VOCMs in comparison to that stored at 4 °C or -20 °C. Among VOCMs measured, CEMA, SBMA, GAMA, DHBMA, AMCC, TCVMA, and HPMMA were lost more rapidly than the other metabolites. CMEMA, a major VOCM found in all three urines at baseline, exhibited a rapid loss in those of two volunteers but not of the other volunteer, suggesting sample to sample variation in lose rates. Freeze-thaw cycles considerably affected VOCM concentrations in urines stored at 4 °C or -20 °C. It is recommended that urine samples are analyzed for VOCMs within a couple of months of collection and stored at temperatures below -20 °C, with minimal or no freeze-thaw cycles. This study highlights the need for appropriate storage conditions to maintain the integrity of samples for biomonitoring studies.
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Affiliation(s)
- Vineet Kumar Pal
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12237, United States; Department of Pediatrics and Environmental Medicine, New York University, New York, 10016, United States
| | - Kurunthachalam Kannan
- Wadsworth Center, New York State Department of Health, Empire State Plaza, Albany, NY, 12237, United States; Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY, 12237, United States; Department of Pediatrics and Environmental Medicine, New York University, New York, 10016, United States.
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Botter SM, Kessler TM. Neuro-Urology and Biobanking: An Integrated Approach for Advancing Research and Improving Patient Care. Int J Mol Sci 2023; 24:14281. [PMID: 37762582 PMCID: PMC10531693 DOI: 10.3390/ijms241814281] [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: 08/14/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Understanding the molecular mechanisms underlying neuro-urological disorders is crucial for the development of targeted therapeutic interventions. Through the establishment of comprehensive biobanks, researchers can collect and store various biological specimens, including urine, blood, tissue, and DNA samples, to study these mechanisms. In the context of neuro-urology, biobanking facilitates the identification of genetic variations, epigenetic modifications, and gene expression patterns associated with neurogenic lower urinary tract dysfunction. These conditions often present as symptoms of neurological diseases such as Alzheimer's disease, multiple sclerosis, Parkinson's disease, spinal cord injury, and many others. Biobanking of tissue specimens from such patients is essential to understand why these diseases cause the respective symptoms and what can be done to alleviate them. The utilization of high-throughput technologies, such as next-generation sequencing and gene expression profiling, enables researchers to explore the molecular landscape of these conditions in an unprecedented manner. The development of specific and reliable biomarkers resulting from these efforts may help in early detection, accurate diagnosis, and effective monitoring of neuro-urological conditions, leading to improved patient care and management. Furthermore, these biomarkers could potentially facilitate the monitoring of novel therapies currently under investigation in neuro-urological clinical trials. This comprehensive review explores the synergistic integration of neuro-urology and biobanking, with particular emphasis on the translation of biobanking approaches in molecular research in neuro-urology. We discuss the advantages of biobanking in neuro-urological studies, the types of specimens collected and their applications in translational research. Furthermore, we highlight the importance of standardization and quality assurance when collecting samples and discuss challenges that may compromise sample quality and impose limitations on their subsequent utilization. Finally, we give recommendations for sampling in multicenter studies, examine sustainability issues associated with biobanking, and provide future directions for this dynamic field.
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Affiliation(s)
- Sander M. Botter
- Swiss Center for Musculoskeletal Biobanking, Balgrist Campus AG, 8008 Zürich, Switzerland
| | - Thomas M. Kessler
- Department of Neuro-Urology, Balgrist University Hospital, University of Zürich, 8008 Zürich, Switzerland;
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Choi E, Yoo WJ, Jang HY, Kim TY, Lee SK, Oh HB. Machine learning liquid chromatography retention time prediction model augments the dansylation strategy for metabolite analysis of urine samples. J Chromatogr A 2023; 1705:464167. [PMID: 37348224 DOI: 10.1016/j.chroma.2023.464167] [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: 04/16/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
Herein, a standalone software equipped with a graphic user interface (GUI) is developed to predict liquid chromatography mass spectrometry (LC-MS) retention times (RTs) of dansylated metabolites. Dansylation metabolomics strategy developed by Li et al. narrows down a vast chemical space of metabolites into the metabolites containing amines and phenolic hydroxyls. Combined with differential isotope labeling, e.g., 12C-reagent labeled individual samples spiked with a 13C-reagent labeled reference or pooled sample, LC-MS analysis of the dansylated samples enables accurate relative quantification of all labeled metabolites. Herein, the LC-RTs for dansylated metabolites are predicted using an artificial neural network (ANN) machine-learning model. For the ANN modeling, 315 dansylated urine metabolites obtained from the DnsID database are used. The ANN LC-RT prediction model was reliable, with a mean absolute deviation of 0.74 min for the 30 min LC run. In the RT model, a deviation of more than 2 min was observed in only 3.2% of the total 315 metabolites, while a deviation of 1.5 min or more was observed in 11% of the metabolites. Furthermore, it was found that the LC-RT prediction was also reliable even for metabolites containing both amine and phenolic functional groups that can undergo dansylation on either one of the two functional groups, resulting in the generation of two isomeric forms. This RT-prediction model is embedded into a user-friendly GUI and can be used for identifying nontargeted dansylated metabolites with unknown RTs, along with accurate mass measurements. Furthermore, it is demonstrated that the developed software can help identify metabolites from a urine sample of an anonymous healthy pregnant woman.
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Affiliation(s)
- Eunwoo Choi
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Won Jun Yoo
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Hwa-Yong Jang
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Tae-Young Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Sung Ki Lee
- Department of Obstetrics and Gynecology, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea.
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
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