1
|
Zhu M, Lamont L, Maas P, Harms AC, Beekman M, Slagboom PE, Dubbelman AC, Hankemeier T. Matrix effect evaluation using multi-component post-column infusion in untargeted hydrophilic interaction liquid chromatography-mass spectrometry plasma metabolomics. J Chromatogr A 2024; 1740:465580. [PMID: 39644743 DOI: 10.1016/j.chroma.2024.465580] [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: 07/26/2024] [Revised: 11/28/2024] [Accepted: 12/02/2024] [Indexed: 12/09/2024]
Abstract
Metabolomics based on hydrophilic interaction liquid chromatography (HILIC) coupled with mass spectrometry (MS) is a powerful tool for polar metabolite identification and quantification to further contribute to biomarker discovery and disease mechanism elucidation. However, matrix effect (ME), which may lead to altered ionization efficiency due to co-eluting compounds, is a significant challenge during biological analysis. Therefore, ME evaluation plays a crucial role during method development. Two approaches to evaluate ME are using stable isotope labelled-internal standards (SIL-IS) and post-column infusion (PCI) of standards. In this study, we developed an untargeted HILIC-MS method by applying four PCI standards for ME evaluation. We found PCI is a compelling approach for ME assessment compared to SIL-IS method due to its advantage in untargeted analysis. Through the ME evaluation and chromatographic performance comparison of 18 SIL standards across three columns and three different mobile phase pH conditions, our findings revealed that the BEH-Z-HILIC column operated at pH 4 with 10 mM ammonium formate exhibited minimal ME and superior performance. The method showed exceptional linearity (R² > 0.98), reliable repeatability (RSD < 15 %), good inter-day precision (RSD < 30 %), and acceptable recovery (>75 %) for all SIL standards. Absolute matrix effect (AME) and relative matrix effect (RME) assessment in three plasma donors revealed a high consistency between PCI and SIL-IS approaches. Finally, this method coupled with the PCI approach was applied to 40 plasma samples. Fifty endogenous compounds were detected and their AME and RME were evaluated. Results showed that many compounds experienced severe ion suppression, though their ME variation between 40 samples is low. In conclusion, PCI method is a robust alternative for monitoring ME and evaluating ME of endogenous compounds during untargeted method optimization and biological analysis.
Collapse
Affiliation(s)
- Mengle Zhu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Lieke Lamont
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Pascal Maas
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Marian Beekman
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - P Eline Slagboom
- Department of Biomedical Data Sciences, Section of Molecular Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne-Charlotte Dubbelman
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands; Institute of Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, the Netherlands.
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands.
| |
Collapse
|
2
|
Cai X, Jin J, Ye H, Xiang X, Luo L, Li J. Altered serum metabolome is associated with disease activity and immune responses in rheumatoid arthritis. Clin Rheumatol 2024; 43:3669-3678. [PMID: 39485556 PMCID: PMC11582171 DOI: 10.1007/s10067-024-07201-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2024] [Revised: 10/10/2024] [Accepted: 10/17/2024] [Indexed: 11/03/2024]
Abstract
Rheumatoid arthritis (RA) is widespread globally, with the emergence of metabolites derived from both the host and microbes playing a pivotal role in its pathogenesis. This study aims to elucidate the relationships between serum metabolites and the immunological and clinical features of RA. Serum samples were collected from 35 RA patients and 37 healthy controls (HC). Metabolite profiling was performed using gas chromatography-mass spectrometry (GC/MS). Principal component analysis revealed a significant distinction between the RA and HC cohorts. Employing univariate statistical analysis, we identified 36 differential metabolites. Among these, 9 metabolites, including galactose and glucose, were found to be enriched, while the remaining metabolites, such as citric acid, fumaric acid, and inosine, were depleted in RA. These diverse metabolites encompassed various metabolic processes, including the biosynthesis of fatty acids, amino acids, and glucose. The enrichment of glucose and galactose in RA exhibited a substantial correlation with elevated IgG levels, as determined through correlation analysis. Conversely, the depletion of citric acid was correlated with elevated levels of C3 and CRP. Methionine, which also declined in RA patients, displayed a negative correlation with ESR. Furthermore, galactose and glucose exhibited significant positive correlations with naïve B cells, while the decreased eicosanoic acid level in RA was significantly associated with an increase in natural killer cells. Our findings suggest that the altered serum metabolite profile in RA is closely linked to disease severity and the dysregulated immune responses observed in RA patients. Key Points • Identified nine metabolites with upregulated expression and twenty-seven metabolites with downregulated expression. • Established a correlation between alterations in serum metabolite levels and inflammatory markers in RA patients. • Discovered a significant association between changes in serum metabolites and immune cell profiles in RA patients.
Collapse
Affiliation(s)
- Xuanlin Cai
- Department of Rheumatology and Immunology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China
| | - Jiayang Jin
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, 100044, China
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
| | - Hua Ye
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, 100044, China
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
| | - Xiaohong Xiang
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, 100044, China
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China
| | - Li Luo
- Department of Rheumatology and Immunology, First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830011, Xinjiang, China.
| | - Jing Li
- Department of Rheumatology and Immunology, Peking University People's Hospital, Beijing, 100044, China.
- Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Beijing, 100044, China.
| |
Collapse
|
3
|
Varzieva VG, Mesonzhnik NV, Ilgisonis IS, Belenkov YN, Kozhevnikova MV, Appolonova SA. Metabolomic biomarkers of multiple myeloma: A systematic review. Biochim Biophys Acta Rev Cancer 2024; 1879:189151. [PMID: 38986721 DOI: 10.1016/j.bbcan.2024.189151] [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: 11/21/2023] [Accepted: 07/03/2024] [Indexed: 07/12/2024]
Abstract
Multiple myeloma (MM) is an incurable malignancy of clonal plasma cells. Various diagnostic methods are used in parallel to accurately determine stage and severity of the disease. Identifying a biomarker or a panel of biomarkers could enhance the quality of medical care that patients receive by adopting a more personalized approach. Metabolomics utilizes high-throughput analytical platforms to examine the levels and quantities of biochemical compounds in biosamples. The aim of this review was to conduct a systematic literature search for potential metabolic biomarkers that may aid in the diagnosis and prognosis of MM. The review was conducted in accordance with PRISMA recommendations and was registered in PROSPERO. The systematic search was performed in PubMed, CINAHL, SciFinder, Scopus, The Cochrane Library and Google Scholar. Studies were limited to those involving people with clinically diagnosed MM and healthy controls as comparators. Articles had to be published in English and had no restrictions on publication date or sample type. The quality of articles was assessed according to QUADOMICS criteria. A total of 709 articles were collected during the literature search. Of these, 436 were excluded based on their abstract, with 26 more removed after a thorough review of the full text. Finally, 16 articles were deemed relevant and were subjected to further analysis of their data. A number of promising candidate biomarkers was discovered. Follow-up studies with large sample sizes are needed to determine their suitability for clinical applications.
Collapse
Affiliation(s)
- Valeria G Varzieva
- Department of Pharmacology, Sechenov First Moscow State Medical University (Sechenov University), Vernadskogo pr., 96, 119571 Moscow, Russia; Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia.
| | - Natalia V Mesonzhnik
- Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia.
| | - Irina S Ilgisonis
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Yuri N Belenkov
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Maria V Kozhevnikova
- Hospital Therapy No. 1 Department, Sechenov First Moscow State Medical University (Sechenov University), Bol'shaya Pirogovskaya st. 6/1, 119435 Moscow, Russia
| | - Svetlana A Appolonova
- Department of Pharmacology, Sechenov First Moscow State Medical University (Sechenov University), Vernadskogo pr., 96, 119571 Moscow, Russia; Centre of Biopharmaceutical Analysis and Metabolomics, Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), Nakhimovsky pr., 45, 117418 Moscow, Russia
| |
Collapse
|
4
|
Sharma V, Khokhar M, Panigrahi P, Gadwal A, Setia P, Purohit P. Advancements, Challenges, and clinical implications of integration of metabolomics technologies in diabetic nephropathy. Clin Chim Acta 2024; 561:119842. [PMID: 38969086 DOI: 10.1016/j.cca.2024.119842] [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: 03/30/2024] [Revised: 06/25/2024] [Accepted: 06/29/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Diabetic nephropathy (DN), a severe complication of diabetes, involves a range of renal abnormalities driven by metabolic derangements. Metabolomics, revealing dynamic metabolic shifts in diseases like DN and offering insights into personalized treatment strategies, emerges as a promising tool for improved diagnostics and therapies. METHODS We conducted an extensive literature review to examine how metabolomics contributes to the study of DN and the challenges associated with its implementation in clinical practice. We identified and assessed relevant studies that utilized metabolomics methods, including nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) to assess their efficacy in diagnosing DN. RESULTS Metabolomics unveils key pathways in DN progression, highlighting glucose metabolism, dyslipidemia, and mitochondrial dysfunction. Biomarkers like glycated albumin and free fatty acids offer insights into DN nuances, guiding potential treatments. Metabolomics detects small-molecule metabolites, revealing disease-specific patterns for personalized care. CONCLUSION Metabolomics offers valuable insights into the molecular mechanisms underlying DN progression and holds promise for personalized medicine approaches. Further research in this field is warranted to elucidate additional metabolic pathways and identify novel biomarkers for early detection and targeted therapeutic interventions in DN.
Collapse
Affiliation(s)
- V Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - M Khokhar
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - P Panigrahi
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - A Gadwal
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - P Setia
- Department of Forensic Medicine and Toxicology, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India
| | - P Purohit
- Department of Biochemistry, All India Institute of Medical Sciences, Jodhpur, Rajasthan 342005, India.
| |
Collapse
|
5
|
Zhu X, Huang Y, Ding J, Liu J, Cui C, Han G. Investigating the Impact of SN-38 on Mouse Brain Metabolism Based on Metabolomics. Drug Des Devel Ther 2024; 18:2435-2447. [PMID: 38915864 PMCID: PMC11195675 DOI: 10.2147/dddt.s457698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
Purpose SN-38 (7-ethyl-10-hydroxycamptothecin), the active metabolite of irinotecan, has been extensively studied in drug delivery systems. However, its impact on neural metabolism remains unclear. This study aims to investigate the toxic effects of SN-38 on mouse brain metabolism. Methods Male mice were divided into an SN-38 group and a control group. The SN-38 group received SN-38 (20 mg/kg/day) via intraperitoneal injection, while the control group was given an equal volume of a blank solvent mixture (DMSO and saline, ratio 1:9). Gas chromatography-mass spectrometry (GC-MS) was employed to analyze differential metabolites in the cortical and hippocampal regions of the SN-38-treated mice. Results SN-38 induced metabolic disturbances in the central nervous system. Eighteen differential metabolites were identified in the hippocampus and twenty-four in the cortex, with six common to both regions. KEGG pathway enrichment analysis revealed statistically significant alterations in six metabolic pathways in the hippocampus and ten in the cortex (P<0.05). Conclusion This study is the first to demonstrate the neurotoxicity of SN-38 in male mice through metabolomics. Differential metabolites in the hippocampal and cortical regions were closely linked to purine metabolism, pyrimidine metabolism, amino acid metabolism, and glyceride metabolism, indicating disruptions in the blood-brain barrier, energy metabolism, and central signaling pathways.
Collapse
Affiliation(s)
- Xiaodong Zhu
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, 272000, People’s Republic of China
| | - Ya Huang
- College of Traditional Chinese Medicine, Shandong Polytechnic College, Jining, 272000, People’s Republic of China
| | - Jia Ding
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, 272000, People’s Republic of China
| | - Jianguo Liu
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, 272000, People’s Republic of China
| | - Changmeng Cui
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, 272000, People’s Republic of China
| | - Guangkui Han
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining, 272000, People’s Republic of China
| |
Collapse
|
6
|
Kang J, Li Y, Lee S, Yu K, Cho J. Pioglitazone-induced alterations of purine metabolism in healthy male subjects. Clin Transl Sci 2024; 17:e13834. [PMID: 38771175 PMCID: PMC11107522 DOI: 10.1111/cts.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Pioglitazone is class of thiazolidinediones that activates peroxisome proliferator-activated receptors (PPARs) in adipocytes to improve glucose metabolism and insulin sensitivity and has been used as a treatment for type 2 diabetes. However, the underlying mechanisms of associated pioglitazone-induced effects remain unclear. Our study aimed to investigate endogenous metabolite alterations associated with pioglitazone administration in healthy male subjects using an untargeted metabolomics approach. All subjects received 30 mg of pioglitazone once daily in the assigned sequence and period. Urine samples were collected before pioglitazone administration and for 24 h after 7 days of administration. A total of 1465 compounds were detected and filtered using a coefficient of variance below 30% and 108 metabolites were significantly altered upon pioglitazone administration via multivariate statistical analysis. Fourteen significant metabolites were identified using authentic standards and public libraries. Additionally, pathway analysis revealed that metabolites from purine and beta-alanine metabolisms were significantly altered after pioglitazone administration. Further analysis of quantification of metabolites from purine metabolism, revealed that the xanthine/hypoxanthine and uric acid/xanthine ratios were significantly decreased at post-dose. Pioglitazone-dependent endogenous metabolites and metabolic ratio indicated the potential effect of pioglitazone on the activation of PPAR and fatty acid synthesis. Additional studies involving patients are required to validate these findings.
Collapse
Affiliation(s)
- Jihyun Kang
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
- Kidney Research Institute, Seoul National University Medical Research CenterSeoulKorea
| | - Yufei Li
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - SeungHwan Lee
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
| | - Kyung‐Sang Yu
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulKorea
| | - Joo‐Youn Cho
- Department of Clinical Pharmacology and TherapeuticsSeoul National University College of Medicine and HospitalSeoulKorea
- Kidney Research Institute, Seoul National University Medical Research CenterSeoulKorea
- Department of Biomedical SciencesSeoul National University College of MedicineSeoulKorea
| |
Collapse
|
7
|
Du Y, Li R, Fu D, Zhang B, Cui A, Shao Y, Lai Z, Chen R, Chen B, Wang Z, Zhang W, Chu L. Multi-omics technologies and molecular biomarkers in brain tumor-related epilepsy. CNS Neurosci Ther 2024; 30:e14717. [PMID: 38641945 PMCID: PMC11031674 DOI: 10.1111/cns.14717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/04/2024] [Accepted: 03/29/2024] [Indexed: 04/21/2024] Open
Abstract
BACKGROUND Brain tumors are one of the leading causes of epilepsy, and brain tumor-related epilepsy (BTRE) is recognized as the major cause of intractable epilepsy, resulting in huge treatment cost and burden to patients, their families, and society. Although optimal treatment regimens are available, the majority of patients with BTRE show poor resolution of symptoms. BTRE has a very complex and multifactorial etiology, which includes several influencing factors such as genetic and molecular biomarkers. Advances in multi-omics technologies have enabled to elucidate the pathophysiological mechanisms and related biomarkers of BTRE. Here, we reviewed multi-omics technology-based research studies on BTRE published in the last few decades and discussed the present status, development, opportunities, challenges, and prospects in treating BTRE. METHODS First, we provided a general review of epilepsy, BTRE, and multi-omics techniques. Next, we described the specific multi-omics (including genomics, transcriptomics, epigenomics, proteomics, and metabolomics) techniques and related molecular biomarkers for BTRE. We then presented the associated pathogenetic mechanisms of BTRE. Finally, we discussed the development and application of novel omics techniques for diagnosing and treating BTRE. RESULTS Genomics studies have shown that the BRAF gene plays a role in BTRE development. Furthermore, the BRAF V600E variant was found to induce epileptogenesis in the neuronal cell lineage and tumorigenesis in the glial cell lineage. Several genomics studies have linked IDH variants with glioma-related epilepsy, and the overproduction of D2HG is considered to play a role in neuronal excitation that leads to seizure occurrence. The high expression level of Forkhead Box O4 (FOXO4) was associated with a reduced risk of epilepsy occurrence. In transcriptomics studies, VLGR1 was noted as a biomarker of epileptic onset in patients. Several miRNAs such as miR-128 and miRNA-196b participate in BTRE development. miR-128 might be negatively associated with the possibility of tumor-related epilepsy development. The lncRNA UBE2R2-AS1 inhibits the growth and invasion of glioma cells and promotes apoptosis. Quantitative proteomics has been used to determine dynamic changes of protein acetylation in epileptic and non-epileptic gliomas. In another proteomics study, a high expression of AQP-4 was detected in the brain of GBM patients with seizures. By using quantitative RT-PCR and immunohistochemistry assay, a study revealed that patients with astrocytomas and oligoastrocytomas showed high BCL2A1 expression and poor seizure control. By performing immunohistochemistry, several studies have reported the relationship between D2HG overproduction and seizure occurrence. Ki-67 overexpression in WHO grade II gliomas was found to be associated with poor postoperative seizure control. According to metabolomics research, the PI3K/AKT/mTOR pathway is associated with the development of glioma-related epileptogenesis. Another metabolomics study found that SV2A, P-gb, and CAD65/67 have the potential to function as biomarkers for BTRE. CONCLUSIONS Based on the synthesized information, this review provided new research perspectives and insights into the early diagnosis, etiological factors, and personalized treatment of BTRE.
Collapse
Affiliation(s)
- Yaoqiang Du
- Laboratory Medicine Center, Department of Transfusion MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Rusong Li
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Danqing Fu
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
| | - Biqin Zhang
- Cancer Center, Department of HematologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Ailin Cui
- Cancer Center, Department of Ultrasound MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Yutian Shao
- Zhejiang BioAsia Life Science InstitutePinghuChina
| | - Zeyu Lai
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Rongrong Chen
- School of Clinical MedicineHangzhou Normal UniversityHangzhouChina
| | - Bingyu Chen
- Laboratory Medicine Center, Department of Transfusion MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Zhen Wang
- Laboratory Medicine Center, Department of Transfusion MedicineZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeHangzhouChina
| | - Wei Zhang
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Lisheng Chu
- School of Basic Medical SciencesZhejiang Chinese Medical UniversityHangzhouChina
- Department of PhysiologyZhejiang Chinese Medical UniversityHangzhouChina
| |
Collapse
|
8
|
Zhu P, Dubbelman AC, Hunter C, Genangeli M, Karu N, Harms A, Hankemeier T. Development of an Untargeted LC-MS Metabolomics Method with Postcolumn Infusion for Matrix Effect Monitoring in Plasma and Feces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:590-602. [PMID: 38379502 PMCID: PMC10921459 DOI: 10.1021/jasms.3c00418] [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: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/22/2024]
Abstract
Untargeted metabolomics based on reverse phase LC-MS (RPLC-MS) plays a crucial role in biomarker discovery across physiological and disease states. Standardizing the development process of untargeted methods requires paying attention to critical factors that are under discussed or easily overlooked, such as injection parameters, performance assessment, and matrix effect evaluation. In this study, we developed an untargeted metabolomics method for plasma and fecal samples with the optimization and evaluation of these factors. Our results showed that optimizing the reconstitution solvent and sample injection amount was critical for achieving the balance between metabolites coverage and signal linearity. Method validation with representative stable isotopically labeled standards (SILs) provided insights into the analytical performance evaluation of our method. To tackle the issue of the matrix effect, we implemented a postcolumn infusion (PCI) approach to monitor the overall absolute matrix effect (AME) and relative matrix effect (RME). The monitoring revealed distinct AME and RME profiles in plasma and feces. Comparing RME data obtained for SILs through postextraction spiking with those monitored using PCI compounds demonstrated the comparability of these two methods for RME assessment. Therefore, we applied the PCI approach to predict the RME of 305 target compounds covered in our in-house library and found that targets detected in the negative polarity were more vulnerable to the RME, regardless of the sample matrix. Given the value of this PCI approach in identifying the strengths and weaknesses of our method in terms of the matrix effect, we recommend implementing a PCI approach during method development and applying it routinely in untargeted metabolomics.
Collapse
Affiliation(s)
- Pingping Zhu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Anne-Charlotte Dubbelman
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht 3584 CM, The Netherlands
| | | | - Michele Genangeli
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Naama Karu
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Amy Harms
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, Netherlands
| |
Collapse
|
9
|
Li W, Hou Y, Wang Y, Liu R, Zhang H, Luo Y, Li Q, Njolibimi M, Hong B, Xu T. Shizao decoction for cirrhotic ascites: assessing potential targets based on network analysis combined with pharmacokinetics and metabolomics. Front Pharmacol 2024; 15:1298818. [PMID: 38323084 PMCID: PMC10844526 DOI: 10.3389/fphar.2024.1298818] [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: 09/22/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
Introduction: Shizao decoction (SZD) is a traditional Chinese medicine decoction that has therapeutic effects on cirrhotic ascites (CAS). Because of the unclear treatment mechanism, in the current study, the anti-CAS activity of SZD and molecular mechanisms were analyzed by network analysis combined with pharmacokinetics and metabolomics. Methods: Firstly, we assessed the anti-CAS efficacy of SZD by hematoxylin-eosin (H&E), liver function tests, NO and ET-1 levels, and portal venous pressure. Secondly, network analysis was applied to dig out the metabolites, targets, and pathways related to SZD and CAS. Then, the pharmacokinetics of the pharmacokinetically relevant metabolites (PRM) were analyzed. Thirdly, the serum and urine metabolic biomarkers of rats with CAS were identified using metabolomics by comparing them with the SZD treatment group. In addition, MetaboAnalyst was utilized to conduct metabolic pathway analysis. Finally, the correlation analysis established a dynamic connection between absorbed PRM from SZD and CAS-associated endogenous metabolites. Results: Pharmacodynamic analysis indicated that SZD effectively mitigated liver injury symptoms by ameliorating inflammatory cell infiltration in CAS rats. The network analysis results indicated that twelve RPM contribute to the therapeutic efficacy of SZD against CAS; the key signaling pathways involved might be hepatitis B and PI3K-Akt. Pharmacokinetics results showed that the 12 RPM were efficiently absorbed into rat plasma, ensuring desirable bioavailability. The metabolomic analysis yielded 21 and 23 significantly distinct metabolites from the serum and urine, respectively. The 12 bioavailable SZD-PRM, such as luteolin, apigenin, and rutin, may be associated with various CAS-altered metabolites related to tryptophan metabolism, alpha-linolenic acid metabolism, glycine metabolism, etc. Discussion: A novel paradigm was provided in this study to identify the potential mechanisms of pharmacological effects derived from a traditional Chinese medicine decoction.
Collapse
Affiliation(s)
- Wenjing Li
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| | - Yujiao Hou
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| | - Yanping Wang
- Comprehensive Support Center, Arongqi Medical Security Bureau, Hulunbuir, China
| | - Ronghong Liu
- Pharmacy Department, Xichong Traditional Chinese Medicine Hospital, Nanchong, China
| | - Han Zhang
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| | - Yanqiong Luo
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| | - Qian Li
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| | | | - Bo Hong
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| | - Tao Xu
- School of Pharmacy, Qiqihar Medical University, Qiqihar, China
| |
Collapse
|
10
|
Wang S, Du X, Yan G, Yang L, Sun H, Zhang X, Kong L, Han Y, Han D, Tang S, Wang X. Huangqi Guizhi Wuwu Decoction Improves Inflammatory Factor Levels in Chemotherapy-induced Peripheral Neuropathy by Regulating the Arachidonic Acid Metabolic Pathway. Curr Pharm Des 2024; 30:2701-2717. [PMID: 39092641 DOI: 10.2174/0113816128308622240709102830] [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: 02/06/2024] [Revised: 06/01/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Chemotherapy-induced Peripheral Neuropathy (CIPN) is a common complication that arises from the use of anticancer drugs. Huangqi Guizhi Wuwu Decoction (HGWWD) is an effective classic prescription for treating CIPN; however, the mechanism of the activity is not entirely understood. OBJECTIVE This study aimed to investigate the remedial effects and mechanisms of HGWWD on CIPN. METHODS Changes in behavioral, biochemical, histopathological, and biomarker indices were used to evaluate the efficacy of HGWWD treatment. Ultra-high-performance liquid chromatography/mass spectrometry combined with the pattern recognition method was used to screen biomarkers and metabolic pathways related to CIPN. The results of pathway analyses were verified by protein blotting experiments. RESULTS A total of 29 potential biomarkers were identified and 13 metabolic pathways were found to be involved in CIPN. In addition HGWWD reversed the levels of 19 biomarkers. Prostaglandin H2 and 17α,21-dihydroxypregnenolone were targeted as core biomarkers. CONCLUSION This study provides scientific evidence to support the finding that HGWWD mainly inhibits the inflammatory response during CIPN by regulating arachidonic acid metabolism.
Collapse
Affiliation(s)
- Shanshan Wang
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiaohui Du
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Guangli Yan
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Le Yang
- State Key Laboratory of Dampness Syndrome, The Second Affiliated Hospital Guangzhou Medical University, Guangzhou, China
| | - Hui Sun
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiwu Zhang
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ling Kong
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Han
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Di Han
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Songyuan Tang
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xijun Wang
- State Key Laboratory of Integration and Innovation of Classical Formula and Modern Chinese Medicine, National TCM Key Laboratory of Serum Pharmacochemistry, Metabolomics Laboratory, Department of Pharmaceutical Analysis, National Chinmedomics Research Center, Heilongjiang University of Chinese Medicine, Harbin, China
| |
Collapse
|
11
|
Kazenwadel J, Berezhnoy G, Cannet C, Schäfer H, Geisler T, Rohlfing AK, Gawaz M, Merle U, Trautwein C. Stratification of hypertension and SARS-CoV-2 infection by quantitative NMR spectroscopy of human blood serum. COMMUNICATIONS MEDICINE 2023; 3:145. [PMID: 37845506 PMCID: PMC11081957 DOI: 10.1038/s43856-023-00365-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023] Open
Abstract
BACKGROUND Diagnostic approaches like the nuclear magnetic resonance spectroscopy (NMR) based quantification of metabolites, lipoproteins, and inflammation markers has helped to identify typical alterations in the blood serum of COVID-19 patients. However, confounders such as sex, and comorbidities, which strongly influence the metabolome, were often not considered. Therefore, the aim of this NMR study was to consider sex, as well as arterial hypertension (AHT), when investigating COVID-19-positive serum samples in a large age-and sex matched cohort. METHODS NMR serum data from 329 COVID-19 patients were compared with 305 healthy controls. 134 COVID-19 patients were affected by AHT. These were analyzed together with NMR data from 58 hypertensives without COVID-19. In addition to metabolite, lipoprotein, and glycoprotein data from NMR, common laboratory parameters were considered. Sex was considered in detail for all comparisons. RESULTS Here, we show that several differences emerge from previous NMR COVID-19 studies when AHT is considered. Especially, the previously described triglyceride-rich lipoprotein profile is no longer observed in COVID-19 patients, nor an increase in ketone bodies. Further alterations are a decrease in glutamine, leucine, isoleucine, and lysine, citric acid, HDL-4 particles, and total cholesterol. Additionally, hypertensive COVID-19 patients show higher inflammatory NMR parameters than normotensive patients. CONCLUSIONS We present a more precise picture of COVID-19 blood serum parameters. Accordingly, considering sex and comorbidities should be included in future metabolomics studies for improved and refined patient stratification. Due to metabolic similarities with other viral infections, these results can be applied to other respiratory diseases in the future.
Collapse
Affiliation(s)
- Jasmin Kazenwadel
- Werner Siemens Imaging Center, Department for Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Georgy Berezhnoy
- Werner Siemens Imaging Center, Department for Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Claire Cannet
- Bruker BioSpin GmbH, Applied Industrial and Clinical Division, Ettlingen, Germany
| | - Hartmut Schäfer
- Bruker BioSpin GmbH, Applied Industrial and Clinical Division, Ettlingen, Germany
| | - Tobias Geisler
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Anne-Katrin Rohlfing
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Meinrad Gawaz
- Department of Internal Medicine III, Cardiology and Angiology, University Hospital Tübingen, Tübingen, Germany
| | - Uta Merle
- Department of Internal Medicine IV, University Hospital Heidelberg, Heidelberg, Germany
| | - Christoph Trautwein
- Werner Siemens Imaging Center, Department for Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Tübingen, Germany.
| |
Collapse
|
12
|
Dantas Machado AC, Ramos SF, Gauglitz JM, Fassler AM, Petras D, Aksenov AA, Kim UB, Lazarowicz M, Barnard Giustini A, Aryafar H, Vodkin I, Warren C, Dorrestein PC, Zarrinpar A, Zarrinpar A. Portosystemic shunt placement reveals blood signatures for the development of hepatic encephalopathy through mass spectrometry. Nat Commun 2023; 14:5303. [PMID: 37652904 PMCID: PMC10471626 DOI: 10.1038/s41467-023-40741-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 08/09/2023] [Indexed: 09/02/2023] Open
Abstract
Elective transjugular intrahepatic portosystemic shunt (TIPS) placement can worsen cognitive dysfunction in hepatic encephalopathy (HE) patients due to toxins, including possible microbial metabolites, entering the systemic circulation. We conducted untargeted metabolomics on a prospective cohort of 22 patients with cirrhosis undergoing elective TIPS placement and followed them up to one year post TIPS for HE development. Here we suggest that pre-existing intrahepatic shunting predicts HE severity post-TIPS. Bile acid levels decrease in the peripheral vein post-TIPS, and the abundances of three specific conjugated di- and tri-hydroxylated bile acids are inversely correlated with HE grade. Bilirubins and glycerophosphocholines undergo chemical modifications pre- to post-TIPS and based on HE grade. Our results suggest that TIPS-induced metabolome changes can impact HE development, and that pre-existing intrahepatic shunting could be used to predict HE severity post-TIPS.
Collapse
Affiliation(s)
| | - Stephany Flores Ramos
- Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Anne-Marie Fassler
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- CMFI Cluster of Excellence, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, USA
| | - Un Bi Kim
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Michael Lazarowicz
- Department of Radiology, Division of Interventional Radiology, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Abbey Barnard Giustini
- Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA
- Division of Gastroenterology, Department of Medicine, Veterans Affairs Puget Sounds Health Care System, Seattle, WA, USA
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hamed Aryafar
- San Diego Imaging, San Diego, CA, USA
- Departments of Radiology, University of California San Diego Medical Center, La Jolla, CA, USA
| | - Irine Vodkin
- Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA
| | - Curtis Warren
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA
| | - Ali Zarrinpar
- Department of Surgery, College of Medicine, University of Florida, Gainesville, FL, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL, USA.
- J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL, USA.
| | - Amir Zarrinpar
- Division of Gastroenterology and Hepatology, University of California, San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
- Jennifer Moreno Department of Veterans Affairs Medical Center, La Jolla, CA, USA.
- Institute of Diabetes and Metabolic Health, University of California, San Diego, La Jolla, CA, USA.
| |
Collapse
|
13
|
Pang H, Hu Z. Metabolomics in drug research and development: The recent advances in technologies and applications. Acta Pharm Sin B 2023; 13:3238-3251. [PMID: 37655318 PMCID: PMC10465962 DOI: 10.1016/j.apsb.2023.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/21/2023] [Accepted: 04/28/2023] [Indexed: 09/02/2023] Open
Abstract
Emerging evidence has demonstrated the vital role of metabolism in various diseases or disorders. Metabolomics provides a comprehensive understanding of metabolism in biological systems. With advanced analytical techniques, metabolomics exhibits unprecedented significant value in basic drug research, including understanding disease mechanisms, identifying drug targets, and elucidating the mode of action of drugs. More importantly, metabolomics greatly accelerates the drug development process by predicting pharmacokinetics, pharmacodynamics, and drug response. In addition, metabolomics facilitates the exploration of drug repurposing and drug-drug interactions, as well as the development of personalized treatment strategies. Here, we briefly review the recent advances in technologies in metabolomics and update our knowledge of the applications of metabolomics in drug research and development.
Collapse
Affiliation(s)
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China
| |
Collapse
|
14
|
Wang RC, Wang Z. Precision Medicine: Disease Subtyping and Tailored Treatment. Cancers (Basel) 2023; 15:3837. [PMID: 37568653 PMCID: PMC10417651 DOI: 10.3390/cancers15153837] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
The genomics-based concept of precision medicine began to emerge following the completion of the Human Genome Project. In contrast to evidence-based medicine, precision medicine will allow doctors and scientists to tailor the treatment of different subpopulations of patients who differ in their susceptibility to specific diseases or responsiveness to specific therapies. The current precision medicine model was proposed to precisely classify patients into subgroups sharing a common biological basis of diseases for more effective tailored treatment to achieve improved outcomes. Precision medicine has become a term that symbolizes the new age of medicine. In this review, we examine the history, development, and future perspective of precision medicine. We also discuss the concepts, principles, tools, and applications of precision medicine and related fields. In our view, for precision medicine to work, two essential objectives need to be achieved. First, diseases need to be classified into various subtypes. Second, targeted therapies must be available for each specific disease subtype. Therefore, we focused this review on the progress in meeting these two objectives.
Collapse
Affiliation(s)
- Richard C. Wang
- Department of Radiology and Radiological Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA;
| | - Zhixiang Wang
- Department of Medical Genetics, Faculty of Medicine and Dentistry, College of Health Sciences, University of Alberta, Edmonton, AB T6J 5H4, Canada
| |
Collapse
|
15
|
Martín-Masot R, Jiménez-Muñoz M, Herrador-López M, Navas-López VM, Obis E, Jové M, Pamplona R, Nestares T. Metabolomic Profiling in Children with Celiac Disease: Beyond the Gluten-Free Diet. Nutrients 2023; 15:2871. [PMID: 37447198 DOI: 10.3390/nu15132871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Celiac disease (CD) is included in the group of complex or multifactorial diseases, i.e., those caused by the interaction of genetic and environmental factors. Despite a growing understanding of the pathophysiological mechanisms of the disease, diagnosis is still often delayed and there are no effective biomarkers for early diagnosis. The only current treatment, a gluten-free diet (GFD), can alleviate symptoms and restore intestinal villi, but its cellular effects remain poorly understood. To gain a comprehensive understanding of CD's progression, it is crucial to advance knowledge across various scientific disciplines and explore what transpires after disease onset. Metabolomics studies hold particular significance in unravelling the complexities of multifactorial and multisystemic disorders, where environmental factors play a significant role in disease manifestation and progression. By analyzing metabolites, we can gain insights into the reasons behind CD's occurrence, as well as better comprehend the impact of treatment initiation on patients. In this review, we present a collection of articles that showcase the latest breakthroughs in the field of metabolomics in pediatric CD, with the aim of trying to identify CD biomarkers for both early diagnosis and treatment monitoring. These advancements shed light on the potential of metabolomic analysis in enhancing our understanding of the disease and improving diagnostic and therapeutic strategies. More studies need to be designed to cover metabolic profiles in subjects at risk of developing the disease, as well as those analyzing biomarkers for follow-up treatment with a GFD.
Collapse
Affiliation(s)
- Rafael Martín-Masot
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
- Institute of Nutrition and Food Technology "José MataixVerdú" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18071 Granada, Spain
| | - María Jiménez-Muñoz
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
| | - Marta Herrador-López
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
| | - Víctor Manuel Navas-López
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Malaga, 29010 Málaga, Spain
| | - Elia Obis
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), 25198 Lleida, Spain
| | - Mariona Jové
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), 25198 Lleida, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, Lleida Biomedical Research Institute (IRBLleida), University of Lleida (UdL), 25198 Lleida, Spain
| | - Teresa Nestares
- Institute of Nutrition and Food Technology "José MataixVerdú" (INYTA), Biomedical Research Centre (CIBM), University of Granada, 18071 Granada, Spain
- Department of Physiology, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
| |
Collapse
|
16
|
Gong G, Kam H, Bai Y, Zhao H, Giesy JP, Lee SMY. 6-Benzylaminopurine causes lipid dyshomeostasis via disruption of glycerophospholipid metabolism in zebrafish. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:163194. [PMID: 37001669 DOI: 10.1016/j.scitotenv.2023.163194] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 03/27/2023] [Indexed: 05/13/2023]
Abstract
6-Benzylaminopurine (6-BA) is ubiquitous in agricultural production and is accessible to humans through diets. The modulation of lipid metabolism by 6-BA has been previously demonstrated in plants and oleaginous microorganisms. Therefore, whether it alters lipid homeostasis in other living organisms requires further investigation. In this study, doses ≥10 mg 6-BA/L caused malformation of the yolk sac, steatosis, and other hepatopathies in zebrafish larvae. Exposure to 25 mg 6-BA/L resulted in increased levels of triglyceride and total cholesterol. Results of transcriptomic analysis indicated that 6-BA alters genes associated with fatty acid and glycerophospholipid metabolism. Among them, the expression levels of hmgcra, elovl7b, and apobb.2 were downregulated, whereas those of lpcat3, bco1l, cyp7al, fabp1b.1, elp6, pde6ha, apoa4b.2_2, sgk1, dgkaa, and mogat2 were upregulated. Correspondingly, a study of the metabolome identified lysophosphatidylcholine (LPC) as the major differentially expressed metabolite in response to 6-BA treatment. Therefore, abnormal accumulation of LPCs and dyshomeostasis of glycerophospholipid metabolism were identified as potential mechanisms causing the toxicity of 6-BA, which should be assessed to understand the risks of 6-BA and the products contaminated by it. ENVIRONMENTAL IMPLICATION: 6-Benzylaminopurine (6-BA), an important residue in "toxic bean sprouts," is ubiquitous in agricultural production and is common in typical diets. Its regulation of lipid metabolism has been demonstrated in plants and oleaginous microorganisms. Whether it alters lipid homeostasis in other organisms and the underlying mechanisms remain largely unknown. The worldwide use of 6-BA and the potential exposure of humans have aroused public attention owing to its hazardous effects; thus, its hazardous effects, particularly those on lipid homeostasis, deserve careful clarification.
Collapse
Affiliation(s)
- Guiyi Gong
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang 524045, China; State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macao.
| | - Hiotong Kam
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macao
| | - Yubin Bai
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang 524045, China
| | - Hongxia Zhao
- Zhanjiang Institute of Clinical Medicine, Central People's Hospital of Zhanjiang, Zhanjiang 524045, China
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B3, Canada; Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada; Department of Environmental Sciences, Baylor University, Waco, TX 76706, United States
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, 999078, Macao; Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, 999078, Macao
| |
Collapse
|
17
|
He J, Wang L, Wang Y, Li Z, Chen F, Liu Z. Metabolomics Combined with Network Pharmacology Uncovers Effective Targets of Tao-Hong-Si-Wu Decoction for Its Protection from Sepsis-Associated Acute Lung Injury. JOURNAL OF ANALYSIS AND TESTING 2023; 7:172-186. [DOI: 10.1007/s41664-023-00248-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/18/2023] [Indexed: 07/14/2024]
|
18
|
Wang XB, Wang ML, Chu YJ, Zhou PP, Zhang XY, Zou J, Zuo LH, Shi YY, Kang J, Li B, Cheng WB, Sun Z, Zhang XJ, Du SZ. Integrated pharmacokinetics and pharmacometabolomics to reveal the synergistic mechanism of a multicomponent Chinese patent medicine, Mailuo Shutong pills against thromboangiitis obliterans. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 112:154709. [PMID: 36774843 DOI: 10.1016/j.phymed.2023.154709] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/23/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Mailuo Shutong Pills (MLST) have displayed pharmacological activity against thromboangiitis obliterans (TAO). However, the active ingredients and therapeutic mechanism of MLST against TAO remained to be further clarified. PURPOSE The aim of this study was to explore the active components of MLST and their synergistic mechanism against TAO by integrating pharmacokinetics (PK) and pharmacometabolomics (PM). METHODS TAO model rats were established by sodium laurate solution. Firstly, the efficacy of MLST was evaluated by gangrene score, blood flow velocity, and hematoxylin-eosin (H&E) staining. Secondly, PK research was conducted on bioavailable components to characterize their dynamic behaviors under TAO. Thirdly, multiple plasma and urine metabolic biomarkers for sodium laurate-induced TAO rats were found by untargeted metabolomics, and then variations in TAO-altered metabolites following MLST treatment were analyzed utilizing multivariate and bioinformatic analysis. Additionally, metabolic pathway analysis was performed using MetaboAnalyst. Finally, the dynamic link between absorbed MLST-compounds and TAO-associated endogenous metabolites was established by correlation analysis. RESULTS MLST significantly alleviated gangrene symptoms by improving the infiltration of inflammatory cells and blood supply in TAO rats. Significant differences in metabolic profiles were found in 17 differential metabolites in plasma and 24 in urine between Sham and TAO rats. The 10 bioavailable MLST-compounds, such as chlorogenic acid and paeoniflorin, showed positive or negative correlations with various TAO-altered metabolites related to glutamate metabolism, histidine metabolism, arachidonic acid metabolism and so on. CONCLUSION This study originally investigated the dynamic interaction between MLST and the biosystem, providing unique insight for disclosing the active components of MLST and their synergistic mechanisms against TAO, which also shed light on new therapeutic targets for TAO and treatment.
Collapse
Affiliation(s)
- Xiao-Bao Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Meng-Li Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Yao-Juan Chu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Pei-Pei Zhou
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Xiang-Yu Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Jing Zou
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Li-Hua Zuo
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Ying-Ying Shi
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Jian Kang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China
| | - Bing Li
- State Key Laboratory of Common Technology of Traditional Chinese Medicine and Pharmaceuticals, Lunan Pharmaceutical Group Co., Ltd., Linyi, China
| | - Wen-Bo Cheng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Zhi Sun
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China.
| | - Xiao-Jian Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China.
| | - Shu-Zhang Du
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, Jianshe East Road 1, Zhengzhou 450052, China; Henan Engineering Research Center of Clinical Mass Spectrometry for Precision Medicine, Zhengzhou Key Laboratory of Clinical Mass Spectrometry, Jianshe East Road 1, Zhengzhou 450052, China.
| |
Collapse
|
19
|
Serag A, Salem MA, Gong S, Wu JL, Farag MA. Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications. Metabolites 2023; 13:424. [PMID: 36984864 PMCID: PMC10055942 DOI: 10.3390/metabo13030424] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.
Collapse
Affiliation(s)
- Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo 11751, Egypt
| | - Mohamed A. Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom 32511, Menoufia, Egypt
| | - Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Mohamed A. Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini St., Cairo 11562, Egypt
| |
Collapse
|
20
|
Dantas Machado AC, Ramos SF, Gauglitz JM, Carpenter AM, Petras D, Aksenov AA, Kim UB, Lazarowicz M, Giustini AB, Aryafar H, Vodkin I, Warren C, Dorrestein PC, Zarrinpar A, Zarrinpar A. Pre- and Post-Portosystemic Shunt Placement Metabolomics Reveal Molecular Signatures for the Development of Hepatic Encephalopathy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.02.22281374. [PMID: 36711444 PMCID: PMC9882439 DOI: 10.1101/2023.01.02.22281374] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Hepatic encephalopathy (HE) is a common complication of advanced liver disease causing brain dysfunction. This is likely due to the accumulation of unfiltered toxins within the bloodstream. A known risk factor for developing or worsening HE is the placement of a transjugular intrahepatic portosystemic shunt (TIPS), which connects the pre-hepatic and post-hepatic circulation allowing some blood to bypass the dysfunctional liver and decreases portal hypertension. To better understand the pathophysiology of post-TIPS HE, we conducted a multi-center prospective cohort study employing metabolomic analyses on hepatic vein and peripheral vein blood samples from participants with cirrhosis undergoing elective TIPS placement, measuring chemical modifications and changes in concentrations of metabolites resulting from TIPS placement. In doing so, we identified numerous alterations in metabolites, including bile acids, glycerophosphocholines, and bilirubins possibly implicated in the development and severity of HE.
Collapse
|
21
|
Zhu H, Wang M, Xiong X, Du Y, Li D, Wang Z, Ge W, Zhu Y. Plasma metabolomic profiling reveals factors associated with dose-adjusted trough concentration of tacrolimus in liver transplant recipients. Front Pharmacol 2022; 13:1045843. [PMID: 36386159 PMCID: PMC9659571 DOI: 10.3389/fphar.2022.1045843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/13/2022] [Indexed: 07/30/2023] Open
Abstract
Inter- and intrapatient variability of tacrolimus exposure is a vital prognostic risk factor for the clinical outcome of liver transplantation. New factors or biomarkers characterizing tacrolimus disposition is essential for optimal dose prediction in recipients of liver transplant. The aim of the study was to identify potential plasma metabolites associated with the dose-adjusted trough concentration of tacrolimus in liver transplant recipients by using a global metabolomic approach. A total of 693 plasma samples were collected from 137 liver transplant recipients receiving tacrolimus and regular therapeutic drug monitoring. Untargeted metabolomic analysis was performed by ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry. Univariate and multivariate analyses with a mixed linear model were conducted, and the results showed that the dose-adjusted tacrolimus trough concentration was associated with 31 endogenous metabolites, including medium- and long-chain acylcarnitines such as stearoylcarnitine (β = 0.222, p = 0.001), microbiota-derived uremic retention solutes such as indolelactic acid (β = 0.194, p = 0.007), bile acids such as taurohyodeoxycholic acid (β = -0.056, p = 0.002), and steroid hormones such as testosterone (β = 0.099, p = 0.001). A multiple linear mixed model including 11 metabolites and clinical information was established with a suitable predictive performance (correlation coefficient based on fixed effects = 0.64 and correlation coefficient based on fixed and random effects = 0.78). These data demonstrated that microbiota-derived uremic retention solutes, bile acids, steroid hormones, and medium- and long-chain acylcarnitines were the main metabolites associated with the dose-adjusted trough concentration of tacrolimus in liver transplant recipients.
Collapse
Affiliation(s)
- Huaijun Zhu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
- Department of Pharmacy, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Nanjing Medical Center for Clinical Pharmacy, Nanjing, China
| | - Min Wang
- Department of Pharmacy, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Nanjing Medical Center for Clinical Pharmacy, Nanjing, China
| | - Xiaofu Xiong
- Department of Pharmacy, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yao Du
- Department of Pharmacy, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Nanjing Medical Center for Clinical Pharmacy, Nanjing, China
| | - Danying Li
- Department of Pharmacy, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Nanjing Medical Center for Clinical Pharmacy, Nanjing, China
| | - Zhou Wang
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, China
| | - Weihong Ge
- Department of Pharmacy, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
- Nanjing Medical Center for Clinical Pharmacy, Nanjing, China
| | - Yizhun Zhu
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, China
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, China
| |
Collapse
|
22
|
Metabolomic and Lipidomic Profiling of Gliomas-A New Direction in Personalized Therapies. Cancers (Basel) 2022; 14:cancers14205041. [PMID: 36291824 PMCID: PMC9599495 DOI: 10.3390/cancers14205041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Gliomas comprise an extremely diverse category of brain tumors that are difficult to diagnose and treat. As a result, scientists continue to search for new treatment solutions, with personalized medicine having emerged as a particularly promising therapeutic approach. Metabolomics and its sub-discipline, lipidomics, are two scientific fields well-suited to support this search. Metabolomics focuses on the physicochemical changes in the metabolome, which include all of the small endogenous and exogenous compounds in a biological system. As such, metabolic analysis can help identify important biochemical pathways which could be the targets for new therapeutic approaches. This review examines the new directions of personalized therapies for gliomas and how metabolomic and lipidomic analysis assists in developing these strategies and monitoring their effectiveness. The discussion of new strategies is preceded by a brief overview of the current “gold standard” treatment for gliomas and the obstacles that new treatment approaches must overcome. Abstract In addition to being the most common primary brain tumor, gliomas are also among the most difficult to diagnose and treat. At present, the “gold standard” in glioma treatment entails the surgical resection of the largest possible portion of the tumor, followed by temozolomide therapy and radiation. However, this approach does not always yield the desired results. Additionally, the ability to cross the blood-brain barrier remains a major challenge for new potential drugs. Thus, researchers continue to search for targeted therapies that can be individualized based on the specific characteristics of each case. Metabolic and lipidomic research may represent two of the best ways to achieve this goal, as they enable detailed insights into the changes in the profile of small molecules in a biological system/specimen. This article reviews the new approaches to glioma therapy based on the analysis of alterations to biochemical pathways, and it provides an overview of the clinical results that may support personalized therapies in the future.
Collapse
|
23
|
Kwon HN, Kurtzeborn K, Iaroshenko V, Jin X, Loh A, Escande-Beillard N, Reversade B, Park S, Kuure S. Omics profiling identifies the regulatory functions of the MAPK/ERK pathway in nephron progenitor metabolism. Development 2022; 149:276992. [PMID: 36189831 PMCID: PMC9641663 DOI: 10.1242/dev.200986] [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: 05/25/2022] [Accepted: 08/25/2022] [Indexed: 11/07/2022]
Abstract
Nephron endowment is defined by fetal kidney growth and crucially dictates renal health in adults. Defects in the molecular regulation of nephron progenitors contribute to only a fraction of reduced nephron mass cases, suggesting alternative causative mechanisms. The importance of MAPK/ERK activation in nephron progenitor maintenance has been previously demonstrated, and here, we characterized the metabolic consequences of MAPK/ERK deficiency. Liquid chromatography/mass spectrometry-based metabolomics profiling identified 42 reduced metabolites, of which 26 were supported by in vivo transcriptional changes in MAPK/ERK-deficient nephron progenitors. Among these, mitochondria, ribosome and amino acid metabolism, together with diminished pyruvate and proline metabolism, were the most affected pathways. In vitro cultures of mouse kidneys demonstrated a dosage-specific function for pyruvate in controlling the shape of the ureteric bud tip, a regulatory niche for nephron progenitors. In vivo disruption of proline metabolism caused premature nephron progenitor exhaustion through their accelerated differentiation in pyrroline-5-carboxylate reductases 1 (Pycr1) and 2 (Pycr2) double-knockout kidneys. Pycr1/Pycr2-deficient progenitors showed normal cell survival, indicating no changes in cellular stress. Our results suggest that MAPK/ERK-dependent metabolism functionally participates in nephron progenitor maintenance by monitoring pyruvate and proline biogenesis in developing kidneys.
Collapse
Affiliation(s)
- Hyuk Nam Kwon
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Kristen Kurtzeborn
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Vladislav Iaroshenko
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Xing Jin
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Abigail Loh
- Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore 138648, Singapore
| | - Nathalie Escande-Beillard
- Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore 138648, Singapore,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland
| | - Bruno Reversade
- Institute of Molecular and Cellular Biology (IMCB), A*STAR, Singapore 138648, Singapore,Medical Genetics Department, School of Medicine, Koç University, Istanbul 34010, Turkey
| | - Sunghyouk Park
- College of Pharmacy, Natural Product Research Institute, Seoul National University, Seoul 08826, Korea
| | - Satu Kuure
- Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, Helsinki, FIN-00014, Finland,GM-unit, Laboratory Animal Center, Helsinki Institute of Life Science, University of Helsinki, Helsinki, FIN-00014, Finland,Author for correspondence ()
| |
Collapse
|
24
|
Holers VM, Kuhn KA, Demoruelle MK, Norris JM, Firestein GS, James EA, Robinson WH, Buckner JH, Deane KD. Mechanism-driven strategies for prevention of rheumatoid arthritis. RHEUMATOLOGY & AUTOIMMUNITY 2022; 2:109-119. [PMID: 36312783 PMCID: PMC9610829 DOI: 10.1002/rai2.12043] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023]
Abstract
In seropositive rheumatoid arthritis (RA), the onset of clinically apparent inflammatory arthritis (IA) is typically preceded by a prolonged period of autoimmunity manifest by the presence of circulating autoantibodies that can include antibodies to citrullinated protein antigens (ACPA) and rheumatoid factor (RF). This period prior to clinical IA can be designated preclinical RA in those individuals who have progressed to a clinical diagnosis of RA, and an 'at-risk' status in those who have not developed IA but exhibit predictive biomarkers of future clinical RA. With the goal of developing RA prevention strategies, studies have characterized immune phenotypes of preclinical RA/at-risk states. From these studies, a model has emerged wherein mucosal inflammation and dysbiosis may lead first to local autoantibody production that should normally be transient, but instead is followed by systemic spread of the autoimmunity as manifest by serum autoantibody elevations, and ultimately drives the development of clinically identified joint inflammation. This model can be envisioned as the progression of disease development through serial 'checkpoints' that in principle should constrain or resolve autoimmunity; however, instead the checkpoints 'fail' and clinical RA develops. Herein we review the immune processes that are likely to be present at each step and the potential therapeutic strategies that could be envisioned to delay, diminish, halt or even reverse the progression to clinical RA. Notably, these prevention strategies could utilize existing therapies approved for clinical RA, therapies approved for other diseases that target relevant pathways in the preclinical/at-risk state, or approaches that target novel pathways.
Collapse
Affiliation(s)
- V. Michael Holers
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kristine A. Kuhn
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - M. Kristen Demoruelle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO 80045, USA
| | - Gary S. Firestein
- Division of Rheumatology, Allergy and Immunology, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - William H. Robinson
- Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA and VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | | | - Kevin D. Deane
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| |
Collapse
|
25
|
Cui C, Zhu L, Wang Q, Liu R, Xie D, Guo Y, Yu D, Wang C, Chen D, Jiang P. A GC-MS-based untargeted metabolomics approach for comprehensive metabolic profiling of vancomycin-induced toxicity in mice. Heliyon 2022; 8:e09869. [PMID: 35855991 PMCID: PMC9287194 DOI: 10.1016/j.heliyon.2022.e09869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 12/31/2022] Open
Abstract
Background Vancomycin is a glycopeptide antibiotic that is commonly used for severe drug-resistant infections treatment. Application of vancomycin frequently leads to severe ototoxicity, hepatotoxicity, and nephrotoxicity; however, the comprehensive metabolic analysis of vancomycin-induced toxicity is lacking. Purpose This study attempted to investigate the metabolic changes after vancomycin administration in mice. Methods Experimental mice (n = 9) received continuous intraperitoneal injection of vancomycin (400 mg/kg) every day for 7 days, and mice in control group (n = 9) were treated with the same amount of normal saline. Pathological changes of the kidney were examined using haematoxylin and eosin (HE) staining. A gas chromatography-mass spectrometry (GC-MS) approach was used to identify discriminant metabolites in serum and various organs including the heart, liver, kidney, spleen, cerebral cortex, hippocampus, inner ear, lung, and intestine. The potential metabolites were identified using orthogonal partial least squares discrimination analysis (OPLS-DA). Subsequently, the MetaboAnalyst 5.0 (http://www.metaboanalyst.ca) and Kyoto Encyclopedia of Genes and Genomes database (KEGG, http://www.kegg.jp) were employed to depict the metabolic pathways. Results Compared with the control group, the vancomycin induced 13, 17, 27, 22, 16, 10, 17, 11, 10, and 7 differential metabolites in the serum, liver, kidney, heart, cerebral cortex, lung, spleen, intestine, hippocampus, and inner ear, respectively. Further pathway analyses identified that amino acids metabolism, fatty acids biosynthesis, energy metabolism, and lipid metabolism were disrupted after VCM exposure. Conclusion Vancomycin affects the metabolism in various organs in mice, which provides new insights for identification of vancomycin-induced toxicity, and facilitate to better understanding of the metabolic pathogenesis of vancomycin.
Collapse
Affiliation(s)
- Changmeng Cui
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining 272000, China
| | - Li Zhu
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| | - Qian Wang
- Department of Clinical Medicine, Jining Medical University, Jining 272000, China
| | - Ruijuan Liu
- Department of Pulmonary and Critical Care Medicine, Jining First People's Hospital, Jining 272000, China
| | - Dadi Xie
- Tengzhou Central People's Hospital, Tengzhou 277500, China
| | - Yujin Guo
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| | - Dingyi Yu
- Jining Life Science Center, Jining 272000, China
| | - Changshui Wang
- Department of Neurosurgery, Affiliated Hospital of Jining Medical University, Jining 272000, China
| | - Dan Chen
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| | - Pei Jiang
- Institute of Clinical Pharmacy and Pharmacology, Jining First People's Hospital, Jining Medical University, Jining 272000, China
| |
Collapse
|
26
|
Metabolites comparison in post-fermentation stage of manual (mechanized) Chinese Huangjiu (yellow rice wine) based on GC–MS metabolomics. Food Chem X 2022; 14:100324. [PMID: 35586029 PMCID: PMC9108467 DOI: 10.1016/j.fochx.2022.100324] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/22/2022] Open
Abstract
The differential metabolites of manual (mechanized) Huangjiu were determined during post-fermentation stage. The metabolic pathways associated with the differential metabolites were identified. The contribution of different metabolites to the flavor of Huangjiu was analyzed.
In order to understand the differences of metabolites and their key metabolic pathways between traditional manual and mechanized Huangjiu, gas chromatography-mass spectrometry (GC–MS) combined with non targeted metabolomics was used to track and monitor Huangjiu in the whole post-fermentation stage. The results showed that 25 metabolites and 14 metabolites were identified as differential metabolites in manual and mechanized Huangjiu, respectively (VIP > 1, P < 0.05); three metabolic pathways had significant effects on differential metabolites (−log (P) > 1, impact > 0.01). Compared with the two kinds of Huangjiu, 21 kinds of metabolites were identified as differential metabolites (VIP > 1, P < 0.05); four metabolic pathways had significant effects on differential metabolites (−log (P) > 1, impact > 0.01). This study is helpful to gain insight into the underlying mechanism of flavor formation during the post-fermentation process of Huangjiu and provide a theoretical basis for the industrial development.
Collapse
|
27
|
Shen S, Chen X, Zhuo Q, Ma Y, Wang J, Wang L, Gong Z, Huo J. Integrating untargeted metabolites and targeted analysis for discrimination of kiwifruits from different cultivars. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
28
|
Resurreccion EP, Fong KW. The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer. Metabolites 2022; 12:metabo12060488. [PMID: 35736421 PMCID: PMC9230859 DOI: 10.3390/metabo12060488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.
Collapse
Affiliation(s)
- Eleazer P. Resurreccion
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
| | - Ka-wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA
- Correspondence: ; Tel.: +1-859-562-3455
| |
Collapse
|
29
|
Heritability of Urinary Amines, Organic Acids, and Steroid Hormones in Children. Metabolites 2022; 12:metabo12060474. [PMID: 35736407 PMCID: PMC9228478 DOI: 10.3390/metabo12060474] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Variation in metabolite levels reflects individual differences in genetic and environmental factors. Here, we investigated the role of these factors in urinary metabolomics data in children. We examined the effects of sex and age on 86 metabolites, as measured on three metabolomics platforms that target amines, organic acids, and steroid hormones. Next, we estimated their heritability in a twin cohort of 1300 twins (age range: 5.7–12.9 years). We observed associations between age and 50 metabolites and between sex and 21 metabolites. The monozygotic (MZ) and dizygotic (DZ) correlations for the urinary metabolites indicated a role for non-additive genetic factors for 50 amines, 13 organic acids, and 6 steroids. The average broad-sense heritability for these amines, organic acids, and steroids was 0.49 (range: 0.25–0.64), 0.50 (range: 0.33–0.62), and 0.64 (range: 0.43–0.81), respectively. For 6 amines, 7 organic acids, and 4 steroids the twin correlations indicated a role for shared environmental factors and the average narrow-sense heritability was 0.50 (range: 0.37–0.68), 0.50 (range; 0.23–0.61), and 0.47 (range: 0.32–0.70) for these amines, organic acids, and steroids. We conclude that urinary metabolites in children have substantial heritability, with similar estimates for amines and organic acids, and higher estimates for steroid hormones.
Collapse
|
30
|
Ampong I, Zimmerman KD, Nathanielsz PW, Cox LA, Olivier M. Optimization of Imputation Strategies for High-Resolution Gas Chromatography-Mass Spectrometry (HR GC-MS) Metabolomics Data. Metabolites 2022; 12:429. [PMID: 35629933 PMCID: PMC9144635 DOI: 10.3390/metabo12050429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/17/2022] Open
Abstract
Gas chromatography-coupled mass spectrometry (GC-MS) has been used in biomedical research to analyze volatile, non-polar, and polar metabolites in a wide array of sample types. Despite advances in technology, missing values are still common in metabolomics datasets and must be properly handled. We evaluated the performance of ten commonly used missing value imputation methods with metabolites analyzed on an HR GC-MS instrument. By introducing missing values into the complete (i.e., data without any missing values) National Institute of Standards and Technology (NIST) plasma dataset, we demonstrate that random forest (RF), glmnet ridge regression (GRR), and Bayesian principal component analysis (BPCA) shared the lowest root mean squared error (RMSE) in technical replicate data. Further examination of these three methods in data from baboon plasma and liver samples demonstrated they all maintained high accuracy. Overall, our analysis suggests that any of the three imputation methods can be applied effectively to untargeted metabolomics datasets with high accuracy. However, it is important to note that imputation will alter the correlation structure of the dataset and bias downstream regression coefficients and p-values.
Collapse
Affiliation(s)
- Isaac Ampong
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
| | - Peter W. Nathanielsz
- Center for the Study of Fetal Programming, University of Wyoming, Laramie, WY 82071, USA;
- Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Laura A. Cox
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
- Southwest National Primate Research Center, San Antonio, TX 78227, USA
| | - Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University, Winston-Salem, NC 27157, USA; (I.A.); (K.D.Z.); (L.A.C.)
| |
Collapse
|
31
|
Wang W, Wang J, Yao K, Wang S, Nie M, Zhao Y, Wang B, Pang H, Xu J, Wu G, Lu M, Tang N, Qi C, Pei H, Luo X, Li D, Yang T, Sun Q, Wei X, Li Y, Jiang D, Li P, Song L, Hu Z. Metabolic characterization of hypertrophic cardiomyopathy in human heart. NATURE CARDIOVASCULAR RESEARCH 2022; 1:445-461. [PMID: 39195941 DOI: 10.1038/s44161-022-00057-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/28/2022] [Indexed: 08/29/2024]
Abstract
Hypertrophic cardiomyopathy (HCM) is a common inherited cardiovascular disease with heterogeneous clinical presentations, governed by multiple molecular mechanisms. Metabolic perturbations underlie most cardiovascular diseases; however, the metabolic alterations and their function in HCM are unknown. Here, we describe the metabolome and lipidome of heart and plasma samples from individuals with and without HCM. Correlation analyses showed strong association between metabolic alterations and cardiac function and prognosis of patients with HCM. Using machine learning we identified metabolite panels as potential HCM diagnostic markers or predictors of survival. Clustering based on metabolome and lipidome of heart enabled stratification of patients with HCM into three subgroups with distinct cardiac function and survival. Integration of metabolomics and proteomics data identified metabolic pathways significantly altered in patients with HCM, with the pentose phosphate pathway and oxidative stress being particularly upregulated. Thus, targeting the pentose phosphate pathway and oxidative stress may serve as potential therapeutic strategies for HCM.
Collapse
Affiliation(s)
- Wenmin Wang
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- Shanghai Qi Zhi Institute, Shanghai, China
| | - Jizheng Wang
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Ke Yao
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- Shanghai Qi Zhi Institute, Shanghai, China
| | - Shuiyun Wang
- Department of Cardiac Surgery, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Meng Nie
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Yizi Zhao
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- Shanghai Qi Zhi Institute, Shanghai, China
| | - Bohong Wang
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | - Huanhuan Pang
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
| | | | - Guixin Wu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Minjie Lu
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Tang
- The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Chunmei Qi
- The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Hengzhi Pei
- School of Computer Science, University of Illinois Urbana Champaign, Champaign, IL, USA
| | - Xufang Luo
- Microsoft Research Asia, Shanghai, China
| | | | - Tianshu Yang
- Shanghai Qi Zhi Institute, Shanghai, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Qing Sun
- Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Xiang Wei
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, Wuhan, China
| | - Yan Li
- Institute of Biophysics, Chinese Academy of Science, Beijing, China
| | - Dingsheng Jiang
- Division of Cardiothoracic and Vascular Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Organ Transplantation, Ministry of Education, Chinese Academy of Medical Sciences, Wuhan, China
| | - Peng Li
- Shanghai Qi Zhi Institute, Shanghai, China
- Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Lei Song
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zeping Hu
- School of Pharmaceutical Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China.
| |
Collapse
|
32
|
Chen J, Zhang J, Zhu L, Qian C, Tian H, Zhao Z, Jin L, Yang D. Antibacterial Activity of the Essential Oil From Litsea cubeba Against Cutibacterium acnes and the Investigations of Its Potential Mechanism by Gas Chromatography-Mass Spectrometry Metabolomics. Front Microbiol 2022; 13:823845. [PMID: 35308342 PMCID: PMC8924494 DOI: 10.3389/fmicb.2022.823845] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 01/28/2022] [Indexed: 01/12/2023] Open
Abstract
Cutibacterium acnes (C. acnes) is an anaerobic Gram-positive bacterium generally considered as a human skin commensal, but is also involved in different infections, such as acne and surgical infections. Although there are a variety of treatments, the side effects and the problem of bacterial drug resistance still limit their clinical usage. In this study, we found that essential oil (EO) distilled from fresh mature Litsea cubeba possessed promising antibacterial activity against C. acnes. In order to elucidate its potential mechanism, bacteriostatic activity test, Live/Dead kit assay, scanning electron microscope (SEM), transmission electron microscope (TEM), and metabolomics were employed. In addition, the content of adenosine triphosphate (ATP) in bacterium and the activities of key enzymes involved in critical metabolic pathways were detected using a variety of biochemical assays. The results showed that EO exhibited significant antibacterial activity against C. acnes at a minimum inhibitory concentration (MIC) of 400 μg/mL and a minimum bactericidal concentration (MBC) of 800 μg/mL, and EO could destroy C. acnes morphology and inhibit its growth. Moreover, results from our study showed that EO had a significant effect on the C. acnes normal metabolism. In total, 86 metabolites were altered, and 34 metabolic pathways related to the carbohydrate metabolism, energy metabolism, amino acid metabolism, as well as cell wall and cell membrane synthesis were perturbed after EO administration. The synthesis of ATP in bacterial cells was also severely inhibited, and the activities of key enzymes of the glycolysis and Wood-Werkman cycle were significantly affected (Pyruvate Carboxylase, Malate Dehydrogenase and Pyruvate kinase activities were decreased, and Hexokinase was increased). Taken together, these results illustrated that the bacteriostatic effect of EO against C. acnes by breaking the bacterial cell morphology and perturbing cell metabolism, including inhibition of key enzyme activity and ATP synthesis. The results from our study may shed new light on the discovery of novel drugs with more robust efficacy.
Collapse
Affiliation(s)
- Jing Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Jianing Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Longping Zhu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Chunguo Qian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Hongru Tian
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Zhimin Zhao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Lu Jin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| | - Depo Yang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China.,Guangdong Technology Research Center for Advanced Chinese Medicine, Guangzhou, China
| |
Collapse
|
33
|
Kong D, Tian Y, Duan K, Guo W, Zhang Q, Zhang P, Yang Z, Qin X, Ren L, Zhang W. Elucidating a Complicated Enantioselective Metabolic Profile: A Study From Rats to Humans Using Optically Pure Doxazosin. Front Pharmacol 2022; 13:834897. [PMID: 35359849 PMCID: PMC8960639 DOI: 10.3389/fphar.2022.834897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/26/2022] [Indexed: 12/01/2022] Open
Abstract
Doxazosin (DOX) is prescribed as a racemic drug for the clinical treatment of benign prostatic hyperplasia and hypertension. Recent studies found that the two enantiomers of DOX exhibit differences in blood concentration and pharmacological effects. However, the stereoselective metabolic characteristics and mechanisms for DOX are not yet clear. Herein, we identified 34 metabolites of DOX in rats based on our comprehensive and effective strategy. The relationship among the metabolites and the most discriminative metabolites between (-)-DOX and (+)-DOX administration was analyzed according to the kinetic parameters using state-of-the-art multivariate statistical methods. To elucidate the enantioselective metabolic profile in vivo and in vitro, we carefully investigated the metabolic characteristics of metabolites after optically pure isomers administration in rat plasma, rat liver microsomes (RLMs) or human liver microsomes (HLMs), and recombinant human cytochrome P450 (CYP) enzymes. As a result, the differences of these metabolites were found based on their exposure and elimination rate, and the metabolic profile of (±)-DOX was more similar to that of (+)-DOX. Though the metabolites identified in RLMs and HLMs were the same, the metabolic profiles of the metabolites from (-)-DOX and (+)-DOX were greatly different. Furthermore, four human CYP enzymes could catalyze DOX to produce metabolites, but their preferences seemed different. For example, CYP3A4 highly specifically and selectively catalyzed the formation of the specific metabolite (M22) from (-)-DOX. In conclusion, we established a comprehensive metabolic system using pure optical isomers from in vivo to in vitro, and the complicated enantioselectivity of the metabolites of DOX was clearly shown. More importantly, the comprehensive metabolic system is also suitable to investigate other chiral drugs.
Collapse
Affiliation(s)
- Dezhi Kong
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Yuan Tian
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
- Department of Pharmacy, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Kunfeng Duan
- Department of Pharmacy, Third Hospital of Hebei Medical University, Shijiazhuang, China
| | - Wenyan Guo
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Qingning Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Panpan Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Zuxiao Yang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Xia Qin
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Leiming Ren
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| | - Wei Zhang
- Department of Pharmacology of Chinese Materia Medica, School of Chinese Integrative Medicine, Hebei Medical University, Shijiazhuang, China
| |
Collapse
|
34
|
Amaro F, Carvalho M, Bastos MDL, Guedes de Pinho P, Pinto J. Pharmacometabolomics Applied to Personalized Medicine in Urological Cancers. Pharmaceuticals (Basel) 2022; 15:295. [PMID: 35337093 PMCID: PMC8952371 DOI: 10.3390/ph15030295] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa), bladder cancer (BCa), and renal cell carcinoma (RCC) are the most common urological cancers, and their incidence has been rising over time. Surgery is the standard treatment for these cancers, but this procedure is only effective when the disease is localized. For metastatic disease, PCa is typically treated with androgen deprivation therapy, while BCa is treated with chemotherapy, and RCC is managed primarily with targeted therapies. However, response rates to these therapeutic options remain unsatisfactory due to the development of resistance and treatment-related toxicity. Thus, the discovery of biomarkers with prognostic and predictive value is needed to stratify patients into different risk groups, minimizing overtreatment and the risk of drug resistance development. Pharmacometabolomics, a branch of metabolomics, is an attractive tool to predict drug response in an individual based on its own metabolic signature, which can be collected before, during, and after drug exposure. Hence, this review focuses on the application of pharmacometabolomic approaches to identify the metabolic responses to hormone therapy, targeted therapy, immunotherapy, and chemotherapy for the most prevalent urological cancers.
Collapse
Affiliation(s)
- Filipa Amaro
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.C.); (M.d.L.B.); (P.G.d.P.)
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Márcia Carvalho
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.C.); (M.d.L.B.); (P.G.d.P.)
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- FP-I3ID, FP-ENAS, CEBIMED, University Fernando Pessoa, 4200-150 Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, 4200-150 Porto, Portugal
| | - Maria de Lourdes Bastos
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.C.); (M.d.L.B.); (P.G.d.P.)
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.C.); (M.d.L.B.); (P.G.d.P.)
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Joana Pinto
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.C.); (M.d.L.B.); (P.G.d.P.)
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Toxicology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| |
Collapse
|
35
|
Yuan Y, Wang C, Wang G, Guo X, Jiang S, Zuo X, Wang X, Hsu ACY, Qi M, Wang F. Airway Microbiome and Serum Metabolomics Analysis Identify Differential Candidate Biomarkers in Allergic Rhinitis. Front Immunol 2022; 12:771136. [PMID: 35069544 PMCID: PMC8766840 DOI: 10.3389/fimmu.2021.771136] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
Allergic rhinitis (AR) is a common heterogeneous chronic disease with a high prevalence and a complex pathogenesis influenced by numerous factors, involving a combination of genetic and environmental factors. To gain insight into the pathogenesis of AR and to identity diagnostic biomarkers, we combined systems biology approach to analyze microbiome and serum composition. We collected inferior turbinate swabs and serum samples to study the microbiome and serum metabolome of 28 patients with allergic rhinitis and 15 healthy individuals. We sequenced the V3 and V4 regions of the 16S rDNA gene from the upper respiratory samples. Metabolomics was used to examine serum samples. Finally, we combined differential microbiota and differential metabolites to find potential biomarkers. We found no significant differences in diversity between the disease and control groups, but changes in the structure of the microbiota. Compared to the HC group, the AR group showed a significantly higher abundance of 1 phylum (Actinobacteria) and 7 genera (Klebsiella, Prevotella and Staphylococcus, etc.) and a significantly lower abundance of 1 genus (Pelomonas). Serum metabolomics revealed 26 different metabolites (Prostaglandin D2, 20-Hydroxy-leukotriene B4 and Linoleic acid, etc.) and 16 disrupted metabolic pathways (Linoleic acid metabolism, Arachidonic acid metabolism and Tryptophan metabolism, etc.). The combined respiratory microbiome and serum metabolomics datasets showed a degree of correlation reflecting the influence of the microbiome on metabolic activity. Our results show that microbiome and metabolomics analyses provide important candidate biomarkers, and in particular, differential genera in the microbiome have also been validated by random forest prediction models. Differential microbes and differential metabolites have the potential to be used as biomarkers for the diagnosis of allergic rhinitis.
Collapse
Affiliation(s)
- Yuze Yuan
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Chao Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Guoqiang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xiaoping Guo
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Shengyu Jiang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xu Zuo
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Xinlei Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Alan Chen-Yu Hsu
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute (HMRI), University of Newcastle, New Lambton Heights, NSW, Australia.,School of Medicine and Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Callaghan, NSW, Australia.,Programme in Emerging Infectious Diseases, Duke - National University of Singapore (NUS) Medical School, Singapore, Singapore
| | - Mingran Qi
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| | - Fang Wang
- Department of Pathogeny Biology, College of Basic Medical Sciences, Jilin University, Changchun, China
| |
Collapse
|
36
|
Salmerón AM, Tristán AI, Abreu AC, Fernández I. Serum Colorectal Cancer Biomarkers Unraveled by NMR Metabolomics: Past, Present, and Future. Anal Chem 2022; 94:417-430. [PMID: 34806875 PMCID: PMC8756394 DOI: 10.1021/acs.analchem.1c04360] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ana M. Salmerón
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| | - Ana I. Tristán
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| | - Ana C. Abreu
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| | - Ignacio Fernández
- Department of Chemistry and
Physics, Research Centre CIAIMBITAL, University
of Almería, Ctra. Sacramento, s/n, 04120 Almería, Spain
| |
Collapse
|
37
|
Neumann E, Schreeck F, Herberg J, Jacqz Aigrain E, Maitland-van der Zee AH, Pérez-Martínez A, Hawcutt DB, Schaeffeler E, Rane A, de Wildt SN, Schwab M. How paediatric drug development and use could benefit from OMICs: a c4c expert group white paper. Br J Clin Pharmacol 2022; 88:5017-5033. [PMID: 34997627 DOI: 10.1111/bcp.15216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/01/2022] Open
Abstract
The safety and efficacy of pharmacotherapy in children, particularly preterms, neonates, and infants, is limited by a paucity of good quality data from prospective clinical drug trials. A specific challenge is the establishment of valid biomarkers. OMICs technologies may support these efforts, by complementary information about targeted and non-targeted molecules through systematic characterization and quantitation of biological samples. OMICs technologies comprise at least genomics, epigenomics, transcriptomics, proteomics, metabolomics, and microbiomics in addition to the patient's phenotype. OMICs technologies are in part hypothesis-generating allowing an in depth understanding of disease pathophysiology and pharmacological mechanisms. Application of OMICs technologies in paediatrics faces major challenges before routine adoption. First, developmental processes need to be considered, including a sub-division into specific age groups as developmental changes clearly impact OMICs data. Second, compared to the adult population, the number of patients is limited as well as type and amount of necessary biomaterial, especially in neonates and preterms. Thus, advanced trial designs and biostatistical methods, non-invasive biomarkers, innovative biobanking concepts including data and samples from healthy children, as well as analytical approaches (e.g. liquid biopsies) should be addressed to overcome these obstacles. The ultimate goal is to link OMICs technologies with innovative analysis tools, like artificial intelligence at an early stage. The use of OMICs data based on a feasible approach will contribute to identify complex phenotypes and subpopulations of patients to improve development of medicines for children with potential economic advantages.
Collapse
Affiliation(s)
- Eva Neumann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Filippa Schreeck
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Jethro Herberg
- Department of Paediatric Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Evelyne Jacqz Aigrain
- Pediatric Pharmacology and Pharmacogenetics, Hopital Universitaire Saint-Louis, Paris, France.,Clinical Investigation Center CIC1426, Hôpital Robert Debre, Paris, France.,Pharmacology, University of Paris, Paris, France
| | | | - Antonio Pérez-Martínez
- Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain.,Pediatric Onco-Hematology Department, La Paz University Hospital, Madrid, Spain.,Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Daniel B Hawcutt
- Department of Women's and Children's Health, University of Liverpool, UK.,NIHR Alder Hey Clinical Research Facility, Alder Hey Children's Hospital, Liverpool, UK
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany
| | - Anders Rane
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital, Karolinska Institutet, Stockholm, Sweden
| | - Saskia N de Wildt
- Department of Pharmacology and Toxicology, Radboud Institute for Health Sciences, Radboud university medical center, Nijmegen, The Netherlands.,Intensive Care and Department of Paediatric Surgery, Erasmus MC-Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University of Tuebingen, Tuebingen, Germany.,Departments of Clinical Pharmacology, and of Biochemistry and Pharmacy, University of Tuebingen, Tuebingen, Germany
| |
Collapse
|
38
|
Zaid A, Khan MS, Yan D, Marriott PJ, Wong YF. Comprehensive two-dimensional gas chromatography with mass spectrometry: an advanced bioanalytical technique for clinical metabolomics studies. Analyst 2022; 147:3974-3992. [DOI: 10.1039/d2an00584k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This review highlights the current state of knowledge in the development of GC × GC-MS for the analysis of clinical metabolites. Selected applications are described as well as our perspectives on current challenges and potential future directions.
Collapse
Affiliation(s)
- Atiqah Zaid
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| | - Mohammad Sharif Khan
- Cargill Research and Development Center, Cargill, 14800 28th Ave N, Plymouth, MN 55447, USA
| | - Dandan Yan
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Philip J. Marriott
- Australian Centre for Research on Separation Science, School of Chemistry, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Yong Foo Wong
- Centre for Research on Multidimensional Separation Science, School of Chemical Sciences, Universiti Sains Malaysia, 11800 Penang, Malaysia
| |
Collapse
|
39
|
Ndolo SM, Zachariah M, Molefi L, Phaladze N, Sichilongo KF. Mass spectrometry based metabolomics for small molecule metabolites mining and confirmation as potential biomarkers for schistosomiasis - case of the Okavango Delta communities in Botswana. Expert Rev Proteomics 2021; 19:61-71. [PMID: 34846232 DOI: 10.1080/14789450.2021.2012454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Metabolomics for identifying schistosomiasis biomarkers in noninvasive samples at various infection stages is being actively explored. The literature on the traditional detection of schistosomiasis in human specimens is well documented. However, state-of-the-art technologies based on mass spectrometry have simplified the use of biomarkers for diagnostics. This review examines methods currently in use for the metabolomics of small molecules using separation science and mass spectrometry. AREA COVERED This article highlights the evolution of traditional diagnostic methods for schistosomiasis based on inter alia microscopy, immunology, and polymerase chain reaction. An exhaustive literature search of metabolite mining, focusing on separation science and mass spectrometry, is presented. A comparative analysis of mass spectrometry methods was undertaken, including a projection for the future. EXPERT COMMENTARY Mass spectrometry metabolomics for schistosomiasis will lead to biomarker discovery for noninvasive human samples. These biomarkers, together with those from other neglected tropical diseases, such as malaria and sleeping sickness, could be incorporated as arrays on a single biosensor chip and inserted into smartphones, in order to improve surveillance, monitoring, and management.
Collapse
Affiliation(s)
- Sedireng M Ndolo
- College of Open Schooling, Botswana Open University, Gaborone Regional Campus, Gaborone, Botswana
| | - Matshediso Zachariah
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Lebotse Molefi
- School of Allied Health Professions, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Nthabiseng Phaladze
- School of Nursing, Faculty of Health Sciences, University of Botswana, Gaborone, Botswana
| | - Kwenga F Sichilongo
- Chemistry Department, Faculty of Science, University of Botswana, Gaborone, Botswana
| |
Collapse
|
40
|
Metabolomics in Autoimmune Diseases: Focus on Rheumatoid Arthritis, Systemic Lupus Erythematous, and Multiple Sclerosis. Metabolites 2021; 11:metabo11120812. [PMID: 34940570 PMCID: PMC8708401 DOI: 10.3390/metabo11120812] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 11/24/2021] [Accepted: 11/24/2021] [Indexed: 12/18/2022] Open
Abstract
The metabolomics approach represents the last downstream phenotype and is widely used in clinical studies and drug discovery. In this paper, we outline recent advances in the metabolomics research of autoimmune diseases (ADs) such as rheumatoid arthritis (RA), multiple sclerosis (MuS), and systemic lupus erythematosus (SLE). The newly discovered biomarkers and the metabolic mechanism studies for these ADs are described here. In addition, studies elucidating the metabolic mechanisms underlying these ADs are presented. Metabolomics has the potential to contribute to pharmacotherapy personalization; thus, we summarize the biomarker studies performed to predict the personalization of medicine and drug response.
Collapse
|
41
|
Dawidowska J, Krzyżanowska M, Markuszewski MJ, Kaliszan M. The Application of Metabolomics in Forensic Science with Focus on Forensic Toxicology and Time-of-Death Estimation. Metabolites 2021; 11:metabo11120801. [PMID: 34940558 PMCID: PMC8708813 DOI: 10.3390/metabo11120801] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 12/21/2022] Open
Abstract
Recently, the diagnostic methods used by scientists in forensic examinations have enormously expanded. Metabolomics provides an important contribution to analytical method development. The main purpose of this review was to investigate and summarize the most recent applications of metabolomics in forensic science. The primary research method was an extensive review of available international literature in PubMed. The keywords “forensic” and “metabolomics” were used as search criteria for the PubMed database scan. Most authors emphasized the analysis of different biological sample types using chromatography methods. The presented review is a summary of recently published implementations of metabolomics in forensic science and types of biological material used and techniques applied. Possible opportunities for valuable metabolomics’ applications are discussed to emphasize the essential necessities resulting in numerous nontargeted metabolomics’ assays.
Collapse
Affiliation(s)
- Joanna Dawidowska
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, 80-210 Gdańsk, Poland; (J.D.); (M.J.M.)
- Department of Forensic Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Marta Krzyżanowska
- Department of Forensic Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
| | - Michał Jan Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, 80-210 Gdańsk, Poland; (J.D.); (M.J.M.)
| | - Michał Kaliszan
- Department of Forensic Medicine, Medical University of Gdańsk, 80-210 Gdańsk, Poland;
- Correspondence: ; Tel.: +48-58-3491255
| |
Collapse
|
42
|
Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
Collapse
Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
| |
Collapse
|
43
|
Metabolomics Signature of Plasma Renin Activity and Linkage with Blood Pressure Response to Beta Blockers and Thiazide Diuretics in Hypertensive European American Patients. Metabolites 2021; 11:metabo11090645. [PMID: 34564461 PMCID: PMC8466669 DOI: 10.3390/metabo11090645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/13/2023] Open
Abstract
Plasma renin activity (PRA) is a predictive biomarker of blood pressure (BP) response to antihypertensives in European–American hypertensive patients. We aimed to identify the metabolic signatures of baseline PRA and the linkages with BP response to β-blockers and thiazides. Using data from the Pharmacogenomic Evaluation of Antihypertensive Responses-2 (PEAR-2) trial, multivariable linear regression adjusting for age, sex and baseline systolic-BP (SBP) was performed on European–American individuals treated with metoprolol (n = 198) and chlorthalidone (n = 181), to test associations between 856 metabolites and baseline PRA. Metabolites with a false discovery rate (FDR) < 0.05 or p < 0.01 were tested for replication in 463 European–American individuals treated with atenolol or hydrochlorothiazide. Replicated metabolites were then tested for validation based on the directionality of association with BP response. Sixty-three metabolites were associated with baseline PRA, of which nine, including six lipids, were replicated. Of those replicated, two metabolites associated with higher baseline PRA were validated: caprate was associated with greater metoprolol SBP response (β = −1.7 ± 0.6, p = 0.006) and sphingosine-1-phosphate was associated with reduced hydrochlorothiazide SBP response (β = 7.6 ± 2.8, p = 0.007). These metabolites are clustered with metabolites involved in sphingolipid, phospholipid, and purine metabolic pathways. The identified metabolic signatures provide insights into the mechanisms underlying BP response.
Collapse
|
44
|
Aung MMK, Mills ML, Bittencourt‐Silvestre J, Keeshan K. Insights into the molecular profiles of adult and paediatric acute myeloid leukaemia. Mol Oncol 2021; 15:2253-2272. [PMID: 33421304 PMCID: PMC8410545 DOI: 10.1002/1878-0261.12899] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/18/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022] Open
Abstract
Acute myeloid leukaemia (AML) is a clinically and molecularly heterogeneous disease characterised by uncontrolled proliferation, block in differentiation and acquired self-renewal of hematopoietic stem and myeloid progenitor cells. This results in the clonal expansion of myeloid blasts within the bone marrow and peripheral blood. The incidence of AML increases with age, and in childhood, AML accounts for 20% of all leukaemias. Whilst there are many clinical and biological similarities between paediatric and adult AML with continuum across the age range, many characteristics of AML are associated with age of disease onset. These include chromosomal aberrations, gene mutations and differentiation lineage. Following chemotherapy, AML cells that survive and result in disease relapse exist in an altered chemoresistant state. Molecular profiling currently represents a powerful avenue of experimentation to study AML cells from adults and children pre- and postchemotherapy as a means of identifying prognostic biomarkers and targetable molecular vulnerabilities that may be age-specific. This review highlights recent advances in our knowledge of the molecular profiles with a focus on transcriptomes and metabolomes, leukaemia stem cells and chemoresistant cells in adult and paediatric AML and focus on areas that hold promise for future therapies.
Collapse
Affiliation(s)
- Myint Myat Khine Aung
- Paul O’Gorman Leukaemia Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
| | - Megan L. Mills
- Paul O’Gorman Leukaemia Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
| | | | - Karen Keeshan
- Paul O’Gorman Leukaemia Research CentreInstitute of Cancer SciencesUniversity of GlasgowUK
| |
Collapse
|
45
|
Huang Q, Cao L, Luo N, Qian H, Wei M, Xue L, Zhou Q, Zou B, Tan L, Chu Y, Ma X, Wang C, Wu H, Zhang L, Sun L, Li D, Fan X, Miao L, Zhou G. Predicting Range of Initial Warfarin Dose Based on Pharmacometabolomic and Genetic Inputs. Clin Pharmacol Ther 2021; 110:1585-1594. [PMID: 34460938 DOI: 10.1002/cpt.2407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/22/2021] [Indexed: 12/29/2022]
Abstract
Anticoagulation response to warfarin during the initial stage of therapy varies among individuals. In this study, we aimed to combine pharmacometabolomic and pharmacogenetic data to predict interindividual variation in warfarin response, and, on this basis, suggest an initial daily dose range. The baseline metabolic profiles, genotypes, and clinical information of 160 patients with heart valve disease served as the variables of the function of the last international normalized ratio measured before a patient's discharge (INRday7 ) to screen for potential biomarkers. The partial least-squares model showed that two baseline metabolites (uridine and guanosine), one single-nucleotide variation (VKORC1), and four clinical parameters (weight, creatinine level, amiodarone usage, and initial daily dose) had good predictive power for INRday7 (R2 = 0.753 for the training set, 0.643 for the test set). With these biomarkers, a machine learning algorithm (two-dimensional linear discriminant analysis-multinomial logit model) was used to predict the subgroups with extremely warfarin-sensitive or less warfarin-sensitive patients with a prediction accuracy of 91% for the training set and 90% for the test set, indicating that individual responses to warfarin could be effectively predicted. Based on this model, we have successfully designed an algorithm,"IniWarD," for predicting an effective dose range in the initial 7-day warfarin therapy. The results indicate that the daily dose range suggested by the IniWarD system is more appropriate than that of the conventional genotype-based method, and the risk of bleeding or thrombus due to warfarin could thus be avoided.
Collapse
Affiliation(s)
- Qing Huang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Ling Cao
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Nan Luo
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Hanyu Qian
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Meng Wei
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Ling Xue
- Department of Clinical Pharmacology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiang Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Li Tan
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China
| | - Changtian Wang
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Haiwei Wu
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Lei Zhang
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Lei Sun
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Demin Li
- Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| | - Xialei Fan
- National Medical Products Administration, Key Laboratory for Impurity Profile of Chemical Drugs, Jiangsu Institute for Food and Drug Control, Nanjing, China
| | - Liyan Miao
- Department of Clinical Pharmacology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, China.,Department of Cardio-Thoracic Surgery, Jinling Hospital, The First School of Clinical Medicine, Southern Medical University, Nanjing, China
| |
Collapse
|
46
|
Loy SL, Zhou J, Cui L, Tan TY, Ee TX, Chern BSM, Chan JKY, Lee YH. Discovery and validation of peritoneal endometriosis biomarkers in peritoneal fluid and serum. Reprod Biomed Online 2021; 43:727-737. [PMID: 34446375 DOI: 10.1016/j.rbmo.2021.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/31/2021] [Accepted: 07/07/2021] [Indexed: 12/19/2022]
Abstract
RESEARCH QUESTION What are the potential biomarkers for peritoneal endometriosis in peritoneal fluid and serum? DESIGN Case-control studies composed of independent discovery and validation sets were conducted. In the discovery set, untargeted liquid chromatography-mass spectrometry (LC-MS/MS) metabolomics, multivariable and univariable analyses were conducted to generate global metabolomic profiles of peritoneal fluid for endometriosis and to identify potential metabolites that could distinguish peritoneal endometriosis (n = 10) from controls (n = 31). The identified metabolites from the discovery set were validated in independent peritoneal fluid (n =19 peritoneal endometriosis and n = 20 controls) and serum samples (n = 16 peritoneal endometriosis and n = 19 controls) using targeted metabolomics. The area under the receiver-operating characteristics curve (AUC) analysis was used to evaluate the diagnostic performance of peritoneal endometriosis metabolites. RESULTS In the discovery set, peritoneal fluid phosphatidylcholine (34:3) and phenylalanyl-isoleucine were significantly increased in peritoneal endometriosis groups compared with control groups, with AUC 0.77 (95% CI 0.61 to 0.92; P = 0.018) and AUC 0.98 (95% CI 0.95 to 1.02; P < 0.001), respectively. In the validation set, phenylalanyl-isoleucine retained discriminatory performance to distinguish peritoneal endometriosis from controls in both peritoneal fluid (AUC 0.77, 95% CI 0.61 to 0.92; P = 0.006) and serum samples (AUC 0.81, 95% CI 0.64 to 0.99; P = 0.004), with notably stronger discrimination between peritoneal endometriosis and controls in proliferative phase. CONCLUSION Our preliminary results propose phenylalanyl-isoleucine as a potential biomarker of peritoneal endometriosis, which may be used as a minimally invasive diagnostic biomarker of peritoneal endometriosis.
Collapse
Affiliation(s)
- See Ling Loy
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899; Obstetrics and Gynaecology-Academic Clinical Program, Duke-NUS Medical School, Singapore 169857
| | - Jieliang Zhou
- KK Research Centre, KK Women's and Children's Hospital, Singapore 229899
| | - Liang Cui
- KK Research Centre, KK Women's and Children's Hospital, Singapore 229899; Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #04-13/14 Enterprise Wing, Singapore 138602
| | - Tse Yeun Tan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899
| | - Tat Xin Ee
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899
| | - Bernard Su Min Chern
- Obstetrics and Gynaecology-Academic Clinical Program, Duke-NUS Medical School, Singapore 169857; Department of Obstetrics and Gynaecology, KK Women's and Children's Hospital, Singapore 229899
| | - Jerry Kok Yen Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore 229899; Obstetrics and Gynaecology-Academic Clinical Program, Duke-NUS Medical School, Singapore 169857
| | - Yie Hou Lee
- Obstetrics and Gynaecology-Academic Clinical Program, Duke-NUS Medical School, Singapore 169857; KK Research Centre, KK Women's and Children's Hospital, Singapore 229899; Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, #04-13/14 Enterprise Wing, Singapore 138602.
| |
Collapse
|
47
|
Magliocco G, Desmeules J, Matthey A, Quirós-Guerrero LM, Bararpour N, Joye T, Marcourt L, F Queiroz E, Wolfender JL, Gloor Y, Thomas A, Daali Y. METABOLOMICS REVEALS BIOMARKERS IN HUMAN URINE AND PLASMA TO PREDICT CYP2D6 ACTIVITY. Br J Pharmacol 2021; 178:4708-4725. [PMID: 34363609 PMCID: PMC9290485 DOI: 10.1111/bph.15651] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 06/30/2021] [Accepted: 08/02/2021] [Indexed: 12/01/2022] Open
Abstract
Background and Purpose Individualized assessment of cytochrome P450 2D6 (CYP2D6) activity is usually performed through phenotyping following administration of a probe drug to measure the enzyme's activity. To avoid any iatrogenic harm (allergic drug reaction, dosing error) related to the probe drug, the development of non‐burdensome tools for real‐time phenotyping of CYP2D6 could significantly contribute to precision medicine. This study focuses on the identification of markers of the CYP2D6 enzyme in human biofluids using an LC‐high‐resolution mass spectrometry‐based metabolomic approach. Experimental Approach Plasma and urine samples from healthy volunteers were analysed before and after intake of a daily dose of paroxetine 20 mg over 7 days. CYP2D6 genotyping and phenotyping, using single oral dose of dextromethorphan 5 mg, were also performed in all participants. Key Results We report four metabolites of solanidine and two unknown compounds as possible novel CYP2D6 markers. Mean relative intensities of these features were significantly reduced during the inhibition session compared with the control session (n = 37). Semi‐quantitative analysis showed that the largest decrease (−85%) was observed for the ion m/z 432.3108 normalized to solanidine (m/z 398.3417). Mean relative intensities of these ions were significantly higher in the CYP2D6 normal–ultrarapid metabolizer group (n = 37) compared with the poor metabolizer group (n = 6). Solanidine intensity was more than 15 times higher in CYP2D6‐deficient individuals compared with other volunteers. Conclusion and Implications The applied untargeted metabolomic strategy identified potential novel markers capable of semi‐quantitatively predicting CYP2D6 activity, a promising discovery for personalized medicine.
Collapse
Affiliation(s)
- Gaëlle Magliocco
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, Geneva, Switzerland.,School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Jules Desmeules
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, Geneva, Switzerland.,School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland.,Clinical Research Center, Geneva University Hospitals, Geneva, Switzerland
| | - Alain Matthey
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, Geneva, Switzerland.,Clinical Research Center, Geneva University Hospitals, Geneva, Switzerland
| | - Luis M Quirós-Guerrero
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Nasim Bararpour
- Forensic Toxicology and Chemistry Unit, CURML, Lausanne University Hospital, Geneva University Hospitals, Lausanne, Geneva, Switzerland.,Faculty Unit of Toxicology, CURML, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Timothée Joye
- Forensic Toxicology and Chemistry Unit, CURML, Lausanne University Hospital, Geneva University Hospitals, Lausanne, Geneva, Switzerland.,Faculty Unit of Toxicology, CURML, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Laurence Marcourt
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Emerson F Queiroz
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Yvonne Gloor
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, Geneva, Switzerland
| | - Aurélien Thomas
- Forensic Toxicology and Chemistry Unit, CURML, Lausanne University Hospital, Geneva University Hospitals, Lausanne, Geneva, Switzerland.,Faculty Unit of Toxicology, CURML, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Youssef Daali
- Division of Clinical Pharmacology and Toxicology, Geneva University Hospitals, Geneva, Switzerland.,School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| |
Collapse
|
48
|
Gupta N, Ramakrishnan S, Wajid S. Emerging role of metabolomics in protein conformational disorders. Expert Rev Proteomics 2021; 18:395-410. [PMID: 34227444 DOI: 10.1080/14789450.2021.1948330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Introduction: Metabolomics focuses on interactions among different metabolites associated with various cellular functions in cells, tissues, and organs. In recent years, metabolomics has emerged as a powerful tool to identify perturbed metabolites, pathways influenced by the environment, for protein conformational diseases (PCDs) and also offers wide clinical application.Area Covered: This review provides a brief overview of recent advances in metabolomics as applied to identify metabolic variations in PCDs, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, prion disease, and cardiac amyloidosis. The 'PubMed' and 'Google Scholar' database search methods have been used to screen the published reports with key search terms: metabolomics, biomarkers, and protein conformational disorders.Expert opinion: Metabolomics is the large-scale study of metabolites and is deemed to overwhelm other omics. It plays a crucial role in finding variations in diseases due to protein conformational changes. However, many PCDs are yet to be identified. Metabolomics is still an emerging field; there is a need for new high-resolution analytical techniques and more studies need to be carried out to generate new information.
Collapse
Affiliation(s)
- Nimisha Gupta
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
| | | | - Saima Wajid
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, India
| |
Collapse
|
49
|
Naithani N, Sinha S, Misra P, Vasudevan B, Sahu R. Precision medicine: Concept and tools. Med J Armed Forces India 2021; 77:249-257. [PMID: 34305276 PMCID: PMC8282508 DOI: 10.1016/j.mjafi.2021.06.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Precision medicine is the new age medicine and refers to tailoring treatments to a subpopulation who have a common susceptibility to a particular disease or similar response to a particular drug. Although the concept existed even during the times of Sir William Osler, it was given a shot in the arm with the Precision Medicine Initiative launched by Barack Obama in 2015. The main tools of precision medicine are Big data, artificial intelligence, the various omics, pharmaco-omics, environmental and social factors and the integration of these with preventive and population medicine. Big data can be acquired from electronic health records of patients and includes various biomarkers (clinical and omics based), laboratory and radiological investigations and these can be analysed through machine learning by various complex flowcharts setting up an algorithm for the management of specific subpopulations. So, there is a move away from the traditional "one size fits all" treatment to precision-based medicine. Research in "omics" has increased in leaps and bounds and advancements have included the fields of genomics, epigenomics, proteomics, transcriptomics, metabolomics and microbiomics. Pharmaco-omics has also come to the forefront with development of new drugs and suiting a particular drug to a particular subpopulation, thus avoiding their prescription to non-responders, preventing unwanted adverse effects and proving economical in the long run. Environmental, social and behavioural factors are as important or in fact more important than genetic factors in most complex diseases and managing these factors form an important part of precision medicine. Finally integrating precision with preventive and public health makes "precision medicine" a complete final product which will change the way medicine will be practised in future.
Collapse
Affiliation(s)
- Nardeep Naithani
- Director & Commandant, Armed Forces Medical College, Pune, India
| | - Sharmila Sinha
- Professor & Head, Department of Pharmacology, Armed Forces Medical College, Pune, India
| | - Pratibha Misra
- Professor & Head, Department of Biochemistry, Armed Forces Medical College, Pune, India
| | - Biju Vasudevan
- Professor & Head, Department of Dermatology, Armed Forces Medical College, Pune, India
| | - Rajesh Sahu
- Associate Professor, Department of Community Medicine, Armed Forces Medical College, Pune, India
| |
Collapse
|
50
|
Inflammation, epigenetics, and metabolism converge to cell senescence and ageing: the regulation and intervention. Signal Transduct Target Ther 2021; 6:245. [PMID: 34176928 PMCID: PMC8236488 DOI: 10.1038/s41392-021-00646-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/09/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Remarkable progress in ageing research has been achieved over the past decades. General perceptions and experimental evidence pinpoint that the decline of physical function often initiates by cell senescence and organ ageing. Epigenetic dynamics and immunometabolic reprogramming link to the alterations of cellular response to intrinsic and extrinsic stimuli, representing current hotspots as they not only (re-)shape the individual cell identity, but also involve in cell fate decision. This review focuses on the present findings and emerging concepts in epigenetic, inflammatory, and metabolic regulations and the consequences of the ageing process. Potential therapeutic interventions targeting cell senescence and regulatory mechanisms, using state-of-the-art techniques are also discussed.
Collapse
|