1
|
Hamed MA, Wasinger V, Wang Q, Graham P, Malouf D, Bucci J, Li Y. Prostate cancer-derived extracellular vesicles metabolic biomarkers: Emerging roles for diagnosis and prognosis. J Control Release 2024; 371:126-145. [PMID: 38768661 DOI: 10.1016/j.jconrel.2024.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 04/23/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Prostate cancer (PCa) is a global health concern, ranking as the most common cancer among men in Western countries. Traditional diagnostic methods are invasive with adverse effects on patients. Due to the heterogeneous nature of PCa and their multifocality, tissue biopsies often yield false-negative results. To address these challenges, researchers are exploring innovative approaches, particularly in the realms of proteomics and metabolomics, to identify more reliable biomarkers and improve PCa diagnosis. Liquid biopsy (LB) has emerged as a promising non-invasive strategy for PCa early detection, biopsy selection, active surveillance for low-risk cases, and post-treatment and progression monitoring. Extracellular vesicles (EVs) are lipid-bilayer nanovesicles released by all cell types and play an important role in intercellular communication. EVs have garnered attention as a valuable biomarker resource in LB for PCa-specific biomarkers, enhancing diagnosis, prognostication, and treatment guidance. Metabolomics provides insight into the body's metabolic response to both internal and external stimuli, offering quantitative measurements of biochemical alterations. It excels at detecting non-genetic influences, aiding in the discovery of more accurate cancer biomarkers for early detection and disease progression monitoring. This review delves into the potential of EVs as a resource for LB in PCa across various clinical applications. It also explores cancer-related metabolic biomarkers, both within and outside EVs in PCa, and summarises previous metabolomic findings in PCa diagnosis and risk assessment. Finally, the article addresses the challenges and future directions in the evolving field of EV-based metabolomic analysis, offering a comprehensive overview of its potential in advancing PCa management.
Collapse
Affiliation(s)
- Mahmoud Assem Hamed
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - Valerie Wasinger
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, UNSW Sydney, Kensington, NSW 2052, Australia
| | - Qi Wang
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - Peter Graham
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - David Malouf
- Department of Urology, St, George Hospital, Kogarah, NSW 2217, Australia
| | - Joseph Bucci
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia
| | - Yong Li
- St George and Sutherland Clinical Campuses, School of Clinical Medicine, UNSW Sydney, Kensington, NSW 2052, Australia; Cancer Care Centre, St George Hospital, Kogarah, NSW 2217, Australia.
| |
Collapse
|
2
|
Taunk K, Jajula S, Bhavsar PP, Choudhari M, Bhanuse S, Tamhankar A, Naiya T, Kalita B, Rapole S. The prowess of metabolomics in cancer research: current trends, challenges and future perspectives. Mol Cell Biochem 2024:10.1007/s11010-024-05041-w. [PMID: 38814423 DOI: 10.1007/s11010-024-05041-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/18/2024] [Indexed: 05/31/2024]
Abstract
Cancer due to its heterogeneous nature and large prevalence has tremendous socioeconomic impacts on populations across the world. Therefore, it is crucial to discover effective panels of biomarkers for diagnosing cancer at an early stage. Cancer leads to alterations in cell growth and differentiation at the molecular level, some of which are very unique. Therefore, comprehending these alterations can aid in a better understanding of the disease pathology and identification of the biomolecules that can serve as effective biomarkers for cancer diagnosis. Metabolites, among other biomolecules of interest, play a key role in the pathophysiology of cancer whose levels are significantly altered while 'reprogramming the energy metabolism', a cellular condition favored in cancer cells which is one of the hallmarks of cancer. Metabolomics, an emerging omics technology has tremendous potential to contribute towards the goal of investigating cancer metabolites or the metabolic alterations during the development of cancer. Diverse metabolites can be screened in a variety of biofluids, and tumor tissues sampled from cancer patients against healthy controls to capture the altered metabolism. In this review, we provide an overview of different metabolomics approaches employed in cancer research and the potential of metabolites as biomarkers for cancer diagnosis. In addition, we discuss the challenges associated with metabolomics-driven cancer research and gaze upon the prospects of this emerging field.
Collapse
Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, NH12 Simhat, Haringhata, Nadia, West Bengal, 741249, India
| | - Saikiran Jajula
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Praneeta Pradip Bhavsar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Mahima Choudhari
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Sadanand Bhanuse
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India
| | - Anup Tamhankar
- Department of Surgical Oncology, Deenanath Mangeshkar Hospital and Research Centre, Erandawne, Pune, Maharashtra, 411004, India
| | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal, NH12 Simhat, Haringhata, Nadia, West Bengal, 741249, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India.
- Amrita School of Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Ponekkara, Kochi, Kerala, 682041, India.
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, 411007, India.
| |
Collapse
|
3
|
Liu Z, Wang H, Zhang J, Chen Q, He W, Zhang Y, Luo Y, Tang H, Wang Y, Wang X. Comparative metabolomics profiling highlights unique color variation and bitter taste formation of Chinese cherry fruits. Food Chem 2024; 439:138072. [PMID: 38043274 DOI: 10.1016/j.foodchem.2023.138072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/24/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023]
Abstract
Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don], native to China, is an economically important fruit crop with attractive colors and delicious flavors. However, the specific metabolites present in cherry fruits have remained unknown. Here, we firstly characterized 1439 metabolite components of Chinese cherry fruits, predominantly including amino acids, flavonoids, and phenolic acids. Moreover, we screened ten biomarkers of Chinese cherry accessions by ROC curve analysis. Among 250 flavonoids, 26 structurally unique anthocyanins collectively determined fruit color, with cyanidins playing a dominant role. Differences in accumulated metabolites between anthocyanin and proanthocyanidin pathways were likely responsible for the variation in fruit color, ranging from yellow to black purple. Meanwhile, we found limocitrin-7-O-glucoside, along with eight other compounds, as underlying contributors to bitter off-taste experienced in fruits. This study provides insights into the regulatory network of metabolites involved in color variation and bitterness formation and genetic improvement of Chinese cherry fruits.
Collapse
Affiliation(s)
- Zhenshan Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Hao Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Jing Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu, Sichuan 611130, China.
| | - Wen He
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu, Sichuan 611130, China
| | - Yong Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Ya Luo
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
| | - Yan Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu, Sichuan 611130, China.
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan 611130, China; Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Chengdu, Sichuan 611130, China.
| |
Collapse
|
4
|
Benedetti E, Chetnik K, Flynn T, Barbieri CE, Scherr DS, Loda M, Krumsiek J. Plasma metabolomics profiling of 580 patients from an Early Detection Research Network prostate cancer cohort. Sci Data 2023; 10:830. [PMID: 38007532 PMCID: PMC10676366 DOI: 10.1038/s41597-023-02750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 11/14/2023] [Indexed: 11/27/2023] Open
Abstract
Prostate cancer is the second most common cancer in men and affects 1 in 9 men in the United States. Early screening for prostate cancer often involves monitoring levels of prostate-specific antigen (PSA) and performing digital rectal exams. However, a prostate biopsy is always required for definitive cancer diagnosis. The Early Detection Research Network (EDRN) is a consortium within the National Cancer Institute aimed at improving screening approaches and early detection of cancers. As part of this effort, the Weill Cornell EDRN Prostate Cancer has collected and biobanked specimens from men undergoing a prostate biopsy between 2008 and 2017. In this report, we describe blood metabolomics measurements for a subset of this population. The dataset includes detailed clinical and prospective records for 580 patients who underwent prostate biopsy, 287 of which were subsequentially diagnosed with prostate cancer, combined with profiling of 1,482 metabolites from plasma samples collected at the time of biopsy. We expect this dataset to provide a valuable resource for scientists investigating prostate cancer metabolism.
Collapse
Affiliation(s)
- Elisa Benedetti
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kelsey Chetnik
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Flynn
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA
| | - Christopher E Barbieri
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA
| | - Douglas S Scherr
- Department of Urology, Weill Cornell Medical College, New York-Presbyterian Hospital, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jan Krumsiek
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| |
Collapse
|
5
|
Alahdal M, Perera RA, Moschovas MC, Patel V, Perera RJ. Current advances of liquid biopsies in prostate cancer: Molecular biomarkers. Mol Ther Oncolytics 2023; 30:27-38. [PMID: 37575217 PMCID: PMC10415624 DOI: 10.1016/j.omto.2023.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023] Open
Abstract
Prostate cancer (PCa) incidence is increasing and endangers men's lives. Early detection of PCa could improve overall survival (OS) by preventing metastasis. The prostate-specific antigen (PSA) test is a popular screening method. Several advisory groups, however, warn against using the PSA test due to its high false positive rate, unsupported outcome, and limited benefit. The number of disease-related biopsies performed annually far outweighs the number of diagnoses. Thus, there is an urgent need to develop accurate diagnostic biomarkers to detect PCa and distinguish between aggressive and indolent cancers. Recently, non-coding RNA (ncRNA), circulating tumor DNA (ctDNA)/ctRNA, exosomes, and metabolomic biomarkers in the liquid biopsies (LBs) of patients with PCa showed significant differences and clinical benefits in diagnosis, prognosis, and monitoring response to therapy. The analysis of urinary exosomal ncRNA presented a substantial correlation among Exos-miR-375 downregulation, clinical T stage, and bone metastases of PCa. Furthermore, the expression of miR-532-5p in urine samples was a vital predictive biomarker of PCa progression. Thus, this review focuses on promising molecular and metabolomic biomarkers in LBs from patients with PCa. We thoroughly addressed the most recent clinical findings of LB biomarker use in diagnosing and monitoring PCa in early and advanced stages.
Collapse
Affiliation(s)
- Murad Alahdal
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
- Department of Oncology, Sydney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, 401 N. Broadway, Baltimore, MD 21287, USA
| | - Roshane A. Perera
- AdventHealth Celebration, 380 Celebration Place, Celebration, FL 34747, USA
| | | | - Vipul Patel
- AdventHealth Celebration, 380 Celebration Place, Celebration, FL 34747, USA
| | - Ranjan J. Perera
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
- Department of Oncology, Sydney Kimmel Cancer Center, School of Medicine, Johns Hopkins University, 401 N. Broadway, Baltimore, MD 21287, USA
| |
Collapse
|
6
|
Shi F, Qi Y, Jiang S, Sun N, Deng C. Hollow Core-Shell Metal Oxide Heterojunctions for the Urinary Metabolic Fingerprint-Based Noninvasive Diagnostic Strategy. Anal Chem 2023; 95:7312-7319. [PMID: 37121232 DOI: 10.1021/acs.analchem.3c00369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Urine is a preferred object for noninvasive diagnostic strategies. Urinary metabolic analysis is speculatively regarded as an ideal tool for screening diseases closely related to the genitourinary system in view of the intimate relationship between metabolomics and phenotype. Herein, we propose a urinary metabolic fingerprint-based noninvasive diagnostic strategy by designing hollow core-shell metal oxide heterojunctions (denoted as MOHs). With outstanding light absorption and electron-hole separation ability, MOHs aid in the extraction of high-performance urine metabolic fingerprints. Coupled with optimized machine learning algorithms, we establish a metabolic marker panel for accurate diagnosis of prostate cancer (PCa), which is the most common malignant tumor of the male genitourinary system, achieving accuracies of 84.72 and 83.33% in the discovery and validation sets, respectively. Furthermore, metabolite variations and related pathway analyses confirm the credibility and change correlation of key metabolic features in PCa. This work tends to advance the noninvasive diagnostic strategy toward clinical realities.
Collapse
Affiliation(s)
- Fangying Shi
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| | - Yu Qi
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Shuai Jiang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Urology, Zhongshan Hospital Wusong Branch, Fudan University, Shanghai 200940, China
| | - Nianrong Sun
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chunhui Deng
- Department of Chemistry, Department of Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai 200433, China
| |
Collapse
|
7
|
Krishnan S, Kanthaje S, Punchappady DR, Mujeeburahiman M, Ratnacaram CK. Circulating metabolite biomarkers: a game changer in the human prostate cancer diagnosis. J Cancer Res Clin Oncol 2023; 149:951-967. [PMID: 35764700 DOI: 10.1007/s00432-022-04113-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE Prostate cancer (PCa) is the second most commonly diagnosed cancer in men in Western and Asian countries. Serum prostate-specific antigen (PSA) test has been the routine diagnostic method despite the tremendous research in diagnostic markers for early detection of PCa. A shift towards a promising and potential biomarker for PCa detection is through metabolomic profiling of biofluids, particularly the blood and urine samples. Finding reliable, routinely usable circulating metabolite biomarkers may not be a distant reality. METHODS We performed a PubMed-based literature search of metabolite biomarkers in blood and urine for the early detection of prostate cancer. The timeline of these searches was limited between 2007 and 2022 and the following keywords were used: 'metabolomics', 'liquid biopsy', 'circulating metabolites', 'serum metabolite', 'plasma metabolite', and 'urine metabolite' with respect to 'prostate cancer'. We focussed only on diagnosis-based studies with only the subject-relevant articles published in the English language and excluded all of the other irrelevant publications that included prostate tissue biomarkers and cell line biomarkers. RESULTS We have consolidated all the blood and urine-based potential metabolite candidates in individual as well as panels, including lipid classes, fatty acids, amino acids, and volatile organic compounds which may become useful for PCa diagnosis. CONCLUSION All these metabolome findings unveil the impact of different dimensions of PCa development, giving a promising strategy to diagnose the disease since suspected individuals can be subjected to repeated and largescale blood and urine testing.
Collapse
Affiliation(s)
- Sabareeswaran Krishnan
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India
- Department of Urology, Yenepoya Medical College Hospital, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Shruthi Kanthaje
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - Devasya Rekha Punchappady
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India
| | - M Mujeeburahiman
- Department of Urology, Yenepoya Medical College Hospital, Deralakatte, Mangaluru, 575018, Karnataka, India.
| | - Chandrahas Koumar Ratnacaram
- Yenepoya Research Centre, Yenepoya (Deemed to Be University), University Road, Deralakatte, Mangaluru, 575018, Karnataka, India.
| |
Collapse
|
8
|
Liang P, Ma Y, Yang L, Mao L, Sun Q, Sun C, Liu Z, Mazhar M, Yang S, Ren W. Uncovering the Mechanisms of Active Components from Toad Venom against Hepatocellular Carcinoma Using Untargeted Metabolomics. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227758. [PMID: 36431859 PMCID: PMC9694973 DOI: 10.3390/molecules27227758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022]
Abstract
Toad venom, a dried product of secretion from Bufo bufo gargarizans Cantor or Bufo melanostictus Schneider, has had the therapeutic effects of hepatocellular carcinoma confirmed. Bufalin and cinobufagin were considered as the two most representative antitumor active components in toad venom. However, the underlying mechanisms of this antitumor effect have not been fully implemented, especially the changes in endogenous small molecules after treatment. Therefore, this study was designed to explore the intrinsic mechanism on hepatocellular carcinoma after the cotreatment of bufalin and cinobufagin based on untargeted tumor metabolomics. Ultraperformance liquid chromatography with tandem mass spectrometry (UHPLC-MS/MS) was performed to identify the absorbed components of toad venom in rat plasma. In vitro experiments were determined to evaluate the therapeutic effects of bufalin and cinobufagin and screen the optimal ratio between them. An in vivo HepG2 tumor-bearing nude mice model was established, and a series of pharmacodynamic indicators were determined, including the body weight of mice, tumor volume, tumor weight, and histopathological examination of tumor. Further, the entire metabolic alterations in tumor after treating with bufalin and cinobufagin were also profiled by UHPLC-MS/MS. Twenty-seven active components from toad venom were absorbed in rat plasma. We found that the cotreatment of bufalin and cinobufagin exerted significant antitumor effects both in vitro and in vivo, which were reflected in inhibiting proliferation and inducing apoptosis of HepG2 cells and thereby causing cell necrosis. After cotherapy of bufalin and cinobufagin for twenty days, compared with the normal group, fifty-six endogenous metabolites were obviously changed on HepG2 tumor-bearing nude mice. Meanwhile, the abundance of α-linolenic acid and phenethylamine after the bufalin and cinobufagin intervention was significantly upregulated, which involved phenylalanine metabolism and α-linolenic acid metabolism. Furthermore, we noticed that amino acid metabolites were also altered in HepG2 tumor after drug intervention, such as norvaline and Leu-Ala. Taken together, the cotreatment of bufalin and cinobufagin has significant antitumor effects on HepG2 tumor-bearing nude mice. Our work demonstrated that the in-depth mechanism of antitumor activity was mainly through the regulation of phenylalanine metabolism and α-Linolenic acid metabolism.
Collapse
Affiliation(s)
- Pan Liang
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- State Key Laboratories for Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau 853, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Yining Ma
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Luyin Yang
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Linshen Mao
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Qin Sun
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Changzhen Sun
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Zengjin Liu
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Maryam Mazhar
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
| | - Sijin Yang
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- State Key Laboratories for Quality Research in Chinese Medicines, Faculty of Chinese Medicine, Macau University of Science and Technology, Macau 853, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
- Correspondence: (S.Y.); (W.R.)
| | - Wei Ren
- National Traditional Chinese Medicine Clinical Research Base, Drug Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
- Institute of Integrated Chinese and Western Medicine, Southwest Medical University, Luzhou 646000, China
- Correspondence: (S.Y.); (W.R.)
| |
Collapse
|
9
|
Targeted profiling of polar metabolites in cancer metabolic reprogramming by hydrophilic interaction liquid chromatography-tandem mass spectrometry. J Chromatogr A 2022; 1686:463654. [DOI: 10.1016/j.chroma.2022.463654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/09/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
|
10
|
Krstic N, Multani K, Wishart DS, Blydt-Hansen T, Cohen Freue GV. The impact of methodological choices when developing predictive models using urinary metabolite data. Stat Med 2022; 41:3511-3526. [PMID: 35567357 DOI: 10.1002/sim.9431] [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: 07/18/2020] [Revised: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 11/08/2022]
Abstract
The continuous evolution of metabolomics over the past two decades has stimulated the search for metabolic biomarkers of many diseases. Metabolomic data measured from urinary samples can provide rich information of the biological events triggered by organ rejection in pediatric kidney transplant recipients. With additional validation, metabolic markers can be used to build clinically useful diagnostic tools. However, there are many methodological steps ranging from data processing to modeling that can influence the performance of the resulting metabolomic classifiers. In this study we focus on the comparison of various classification methods that can handle the complex structure of metabolomic data, including regularized classifiers, partial least squares discriminant analysis, and nonlinear classification models. We also examine the effectiveness of a physiological normalization technique widely used in the clinical and biochemical literature but not extensively analyzed and compared in urine metabolomic studies. While the main objective of this work is to interrogate metabolomic data of pediatric kidney transplant recipients to improve the diagnosis of T cell-mediated rejection (TCMR), we also analyze three independent datasets from other disease conditions to investigate the generalizability of our findings.
Collapse
Affiliation(s)
- Nikolas Krstic
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Multani
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Physics, Stanford University, Stanford, California, USA
| | - David S Wishart
- Departments of Computing Science and Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tom Blydt-Hansen
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabriela V Cohen Freue
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
11
|
Liu Z, Li Y, Li C, Lei G, Zhou L, Chen X, Jia X, Lu Y. Intestinal Candida albicans Promotes Hepatocarcinogenesis by Up-Regulating NLRP6. Front Microbiol 2022; 13:812771. [PMID: 35369462 PMCID: PMC8964356 DOI: 10.3389/fmicb.2022.812771] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/19/2022] [Indexed: 12/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC), a primary liver cancer, is closely associated with the gut microbiota. However, the role of gut fungi in the development of HCC remains unclear. The aim of this study was to explore the influence of intestinal Candida albicans on HCC. Here, We found that patients with HCC showed significantly decreased diversity of the gut mycobiome and increased abundance of C. albicans, compared to the patients with liver cirrhosis. The gavage of C. albicans in the WT models increased the tumor size and weight and influenced the plasma metabolome, which was indicated by alterations in 117 metabolites, such as L-carnitine and L-acetylcarnitine, and several KEGG enriched pathways, such as phenylalanine metabolism and citrate cycle. Moreover, the expression of nucleotide oligomerization domain-like receptor family pyrin domain containing 6 (NLRP6) in the intestinal tissues and primary intestinal epithelial cells of the WT mice interacted with C. albicans increased. Notably, the colonization of C. albicans had no effect on tumor growth in Nlrp6–/– mice. In conclusion, the abnormal colonization of C. albicans reprogrammed HCC metabolism and contributed to the progression of HCC dependent on NLRP6, which provided new targets for the treatment of HCC.
Collapse
Affiliation(s)
- Zherui Liu
- Peking University 302 Clinical Medical School, Beijing, China.,Senior Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yinyin Li
- Senior Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Chen Li
- Senior Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Guanglin Lei
- Senior Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lin Zhou
- Senior Department of Oncology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiangling Chen
- Senior Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xiaodong Jia
- Senior Department of Oncology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yinying Lu
- Peking University 302 Clinical Medical School, Beijing, China.,Senior Department of Hepatology, Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
12
|
Shi Z, Zou S, Shen Z, Luan F, Yan J. High-throughput metabolomics using UPLC/Q-TOF-MS coupled with multivariate data analysis reveals the effect and mechanism of syringin against ovariectomized osteoporosis. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1183:122957. [PMID: 34666892 DOI: 10.1016/j.jchromb.2021.122957] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/28/2021] [Accepted: 09/25/2021] [Indexed: 12/15/2022]
Abstract
Osteoporosis is an increasing public health problem in the worldwide and has caused socioeconomic burden. Natural products as candidates have the potential to promote bone formation and suppress bone resorption for osteoporosis treatment. Previously, syringin has showed the potent anti-osteoporosis activity, however the detailed mechanism of syringin against osteoporosis is still unclear. This study aimed to reveal the pharmacological effect and mechanism of syringin through the high-throughput metabolomics. In this study, metabolomics techniques were used to explore the metabolic biomarkers and profiles provides deep insights into the pharmacological effects and mechanism of syringin against osteoporosis. The metabolite biomarkers were monitored based on the high-resolution mass spectrometry. By the integration analysis of metabolomics technology, a total of 23 metabolic biomarkers were discovered and we found the highly relevant pathway involved in glycine and serine metabolism, butyrate metabolism, methionine metabolism, catecholamine biosynthesis, tyrosine metabolism, etc. Interestingly, synthesis and degradation of ketone bodies, phenylalanine, tyrosine and tryptophan biosynthesis, arachidonic acid metabolism, tyrosine metabolism, glycine, serine and threonine metabolism, butanoate metabolism, was related with efficacy of syringin. The present work showed that the metabolomics technology can provide novel strategies for revealing insights into the metabolic effects and action mechanism of drug.
Collapse
Affiliation(s)
- Zhenxing Shi
- Orthopedics and Oncology Department, Second Affiliated Hospital of Medical University of Heilongjiang Province, Harbin 150086, China
| | - Shifeng Zou
- Intensive Care Unit Department, First Affiliated Hospital of Medical University of Heilongjiang Province, Harbin, China
| | - Zilong Shen
- Intensive Care Unit Department, First Affiliated Hospital of Medical University of Heilongjiang Province, Harbin, China
| | - Feiyu Luan
- Orthopedics and Oncology Department, Second Affiliated Hospital of Medical University of Heilongjiang Province, Harbin 150086, China
| | - Jianglong Yan
- Orthopedics and Oncology Department, Second Affiliated Hospital of Medical University of Heilongjiang Province, Harbin 150086, China.
| |
Collapse
|
13
|
Lichtenberg S, Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Metabolomic Laboratory-Developed Tests: Current Status and Perspectives. Metabolites 2021; 11:423. [PMID: 34206934 PMCID: PMC8305461 DOI: 10.3390/metabo11070423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Laboratory-developed tests (LDTs) are a subset of in vitro diagnostic devices, which the US Food and Drug Administration defines as "tests that are manufactured by and used within a single laboratory". The review describes the emergence and history of LDTs. The current state and development prospects of LDTs based on metabolomics are analyzed. By comparing LDTs with the scientific metabolomics study of human bio samples, the characteristic features of metabolomic LDT are shown, revealing its essence, strengths, and limitations. The possibilities for further developments and scaling of metabolomic LDTs and their potential significance for healthcare are discussed. The legal aspects of LDT regulation in the United States, European Union, and Singapore, demonstrating different approaches to this issue, are also provided. Based on the data presented in the review, recommendations were made on the feasibility and ways of further introducing metabolomic LDTs into practice.
Collapse
Affiliation(s)
- Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| |
Collapse
|
14
|
Ren L, Guo HN, Yang J, Guo XY, Wei YS, Yang Z. Dissecting Efficacy and Metabolic Characteristic Mechanism of Taxifolin on Renal Fibrosis by Multivariate Approach and Ultra-Performance Liquid Chromatography Coupled With Mass Spectrometry-Based Metabolomics Strategy. Front Pharmacol 2021; 11:608511. [PMID: 33519473 PMCID: PMC7841412 DOI: 10.3389/fphar.2020.608511] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 11/26/2020] [Indexed: 12/15/2022] Open
Abstract
Taxifolin (TFN) is an important natural compound with antifibrotic activity; however, its pharmacological mechanism is not clear. In this study, our aim is to gain insight into the effects of TFN and its potential mechanisms in unilateral ureteral obstruction (UUO) animal model using metabolomics approach to identify the metabolic biomarkers and perturbed pathways. Serum metabolomics analysis by UPLC-Q-TOF/MS was carried out to discover the changes in the metabolic profile. It showed that TFN has a significant protective effect on UUO-induced renal fibrosis and a total of 32 potential biomarkers were identified and related to RF progression. Of note, 27 biomarkers were regulated by TFN treatment, which participate in eight metabolic pathways, including phenylalanine, tyrosine and tryptophan biosynthesis, and phenylalanine metabolism. It also showed that metabolomics was a promising strategy to better dissect metabolic characteristics and pharmacological mechanisms of natural compounds by multivariate approach and ultra-performance liquid chromatography coupled with mass spectrometry.
Collapse
Affiliation(s)
- Lei Ren
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guangxi, China
| | - Hao-Nan Guo
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guangxi, China
| | - Jun Yang
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guangxi, China
| | - Xiao-Ying Guo
- Department of Clinical Laboratory, Daqing Oilfield General Hospital, Daqing, China
| | - Ye-Sheng Wei
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guangxi, China
| | - Zhao Yang
- Department of Clinical Laboratory, Affiliated Hospital of Guilin Medical University, Guangxi, China
| |
Collapse
|
15
|
UPLC-MS metabolomics method provides valuable insights into the effect and underlying mechanisms of Rhizoma Drynariae protecting osteoporosis. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1152:122262. [PMID: 32682315 DOI: 10.1016/j.jchromb.2020.122262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/26/2020] [Accepted: 07/05/2020] [Indexed: 01/29/2023]
Abstract
Osteoporosis (OP) is a metabolic bone disease in which that volume of bone tissue per unit volume decrease, which is a common disease disturbing the elderly or postmenopausal women. Rhizoma Drynariae (RD) is a kind of herb widely used in thousands of years of clinical practice in China to tonify kidney and prevent osteoporosis, with reliable curative effect. However, the mechanism of its anti-osteoporosis action is still unclear. This study is dedicated to exploration the therapeutic effect of RD on retinoic acid solution-induced OP model rats based on high-throughput metabolomics technology platform, and reveal its influence on metabolomics level, so as to find effective potential biomarkers and therapeutic targets for diagnosing OP. OP model was established by intragastric administration of retinoic acid solution for 21 days, and then the treatment group was treated by intragastric administration of RD solution for 60 days. Blood samples of all groups were collected and analyzed based on UPLC-MS metabolomics and combined with EZinfo 3.0 data analysis, 32 potential biomarkers were identified, including 22 in ESI+ and 10 in ESI-, these biomarkers are related to 9 metabolic pathways. After treatment with RD solution, 21 biomarkers were obviously regulated, these mainly affected linoleic acid metabolic, glycerophospholipid metabolism and arachidonic acid metabolism pathway. The results show that RD can reduce the risk of OP disease, which may be related to the metabolic pathway mentioned above, and provides the foundation for the administer prophylaxis and treatment of OP with natural products.
Collapse
|
16
|
Wang XX, Yu PC, Li J. High-Throughput Metabolomics for Identification of Metabolic Pathways and Deciphering the Effect Mechanism of Dioscin on Rectal Cancer From Cell Metabolic Profiles Coupled With Chemometrics Analysis. Front Pharmacol 2020; 11:68. [PMID: 32180713 PMCID: PMC7059176 DOI: 10.3389/fphar.2020.00068] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/24/2020] [Indexed: 01/05/2023] Open
Abstract
High-throughput liquid chromatography-mass spectrometry (LC-MS)-based metabolomics can provide the holistic analysis of the low molecular weight endogenous metabolites in cells and reflect the changes of cellular regulation and metabolic pathways. Our study designed to reveal the potentially pharmacological effects of dioscin on SW480 rectal cancer cells using nontargeted metabolomics method to probe into small molecular metabolites and pathway changes. After the cell assay of proliferation, apoptosis, migration, and invasion, the dioscin-treated cell samples were prepared for nontargeted metabolomics analysis based on LC-MS tool to describe the metabolic profiles. Dioscin has prevented cell proliferation and accelerated cell apoptosis, and it also inhibited the SW480 rectal cancer cells' migration and invasion. A total of 22 metabolites were selected as promising biomarkers of pharmacological reaction of dioscin to rectal cancer, and eight highly correlated pathways including D-glutamine and D-glutamate metabolism, pyruvate metabolism, arachidonic acid metabolism, phenylalanine metabolism, tryptophan metabolism, glycolysis or gluconeogenesis, citrate cycle (TCA cycle), and butanoate metabolism were identified. It showed that strategies based on cell metabolomics are helpful tools to discover the small molecular metabolites to elucidate the action mechanism of drug.
Collapse
Affiliation(s)
- Xin-Xin Wang
- Heilongjiang Province Land Reclamation Headquarters General Hospital, Heilongjiang Agriculture and Reclamation Bureau, Harbin, China
| | - Peng-cheng Yu
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Jun Li
- Department of Orthopedics, The Affiliated First Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| |
Collapse
|
17
|
Jiang YC, Li YF, Zhou L, Zhang DP. Comparative metabolomics unveils molecular changes and metabolic networks of syringin against hepatitis B mice by untargeted mass spectrometry. RSC Adv 2020; 10:461-473. [PMID: 35492557 PMCID: PMC9048208 DOI: 10.1039/c9ra06332c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022] Open
Abstract
Untargeted metabolomics technology was used to discover the metabolic pathways and biomarkers for revealing the potential biological mechanism of syringin on hepatitis B virus. Serum samples were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS)-based comparative metabolomics coupled with pattern recognition methods and network pathway. In addition, the histopathology, HBV DNA detection of liver tissue, and biochemical indicators of liver function change were also explored for investigating the antiviral effect of syringin. In comparison to the model group, the metabolic profiles of the turbulence in transgenic mice tended to recover to the same as the control group after syringin therapy. A total of 33 potential biomarkers were determined to explore the metabolic disorders in the hepatitis B animal model, of which 25 were regulated by syringin, and 8 metabolic pathways, such as phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arachidonic acid metabolism, glyoxylate and dicarboxylate metabolism, were involved. Syringin markedly reduced the liver pathology change, inhibited HBV DNA replication, and improved liver function. Amino acid metabolism is a potential target for the treatment of hepatitis B. The hepatoprotective effect of syringin may contribute to ameliorating oxidative stress and preventing protein and DNA replication. Comparative metabolomics is a promising tool for discovering metabolic pathways and biomarkers of the hepatitis B animal model as targets to reveal the effects and mechanism of syringin, which benefits the development of natural products and advances the treatment of diseases. Untargeted metabolomics technology was used to discover the metabolic pathways and biomarkers for revealing the potential biological mechanism of syringin on hepatitis B virus.![]()
Collapse
Affiliation(s)
- Yi-chang Jiang
- Third Department of Orthopedics
- First Affiliated Hospital
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Yuan-feng Li
- Third Department of Orthopedics
- First Affiliated Hospital
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Ling Zhou
- First Affiliated Hospital
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Da-peng Zhang
- Third Department of Orthopedics
- First Affiliated Hospital
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| |
Collapse
|
18
|
Li WX, Zhang AH, Zhou XH, Nan Y, Liu Q, Sun H, Fang H, Wang XJ. High-throughput liquid chromatography mass-spectrometry-driven lipidomics discover metabolic biomarkers and pathways as promising targets to reveal the therapeutic effects of the Shenqi pill. RSC Adv 2020; 10:2347-2358. [PMID: 35494613 PMCID: PMC9048437 DOI: 10.1039/c9ra07621b] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/30/2019] [Indexed: 11/21/2022] Open
Abstract
Lipidomics, a branch of metabonomics, could provide a powerful technique for discovery of lipid molecules to reveal disease status and drug efficacy.
Collapse
Affiliation(s)
- Wen-xiu Li
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Ai-hua Zhang
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Xiao-hang Zhou
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Yang Nan
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Qi Liu
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Hui Sun
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Heng Fang
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| | - Xi-jun Wang
- Engineering Research Center of Efficacy Evaluation and Industrial Development of TCM Classic Formulae of the Ministry of Education
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
| |
Collapse
|
19
|
Sun YC, Han SC, Yao MZ, Liu HB, Wang YM. Exploring the metabolic biomarkers and pathway changes in crucian under carbonate alkalinity exposure using high-throughput metabolomics analysis based on UPLC-ESI-QTOF-MS. RSC Adv 2020; 10:1552-1571. [PMID: 35494719 PMCID: PMC9047290 DOI: 10.1039/c9ra08090b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
The aims of this study is to explore the metabolomic biomarker and pathway changes in crucian under carbonate alkalinity exposures using high-throughput metabolomics analysis based on ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-tandem mass spectrometry (UPLC-ESI-QTOF-MS) for carrying out adaptive evolution of fish in environmental exposures and understanding molecular physiological mechanisms of saline–alkali tolerance in fishes. Under 60 day exposure management, the UPLC-ESI-QTOF-MS technology, coupled with a pattern recognition approach and metabolic pathway analysis, was utilized to give insight into the metabolic biomarker and pathway changes. In addition, biochemical parameters in response to carbonate alkalinity in fish were detected for chronic impairment evaluation. A total of twenty-seven endogenous metabolites were identified to distinguish the biochemical changes in fish in clean water under exposure to different concentrations of carbonate alkalinity (CA); these mainly involved amino acid synthesis and metabolism, arachidonic acid metabolism, glyoxylate and dicarboxylate metabolism, pyruvate metabolism and the citrate cycle (TCA cycle). Compared with the control group, CA exposure increased the level of blood ammonia; TP; ALB; Gln in the liver and gills; GS; urea in blood, the liver and gills; CREA; CPS; Glu and LDH; and decreased the level of weight gain rate, oxygen consumption, discharge rate of ammonia, SOD, CAT, ALT, AST and Na+/K+-ATPase. At low concentrations, CA can change the normal metabolism of fish in terms of changing the osmotic pressure regulation capacity, antioxidant capacity, ammonia metabolism and liver and kidney function to adapt to the CA exposure environment. As the concentration of CA increases, various metabolic processes in crucian are inhibited, causing chronic damage to the body. The results show that the metabolomic strategy is a potentially powerful tool for identifying the mechanisms in response to different environmental exposomes and offers precious information about the chronic response of fish to CA. We explore the metabolic biomarker and pathway changes accompanying the adaptive evolution of crucian subjected to carbonate alkalinity exposure, using UPLC-ESI-QTOF-MS, in order to understand the molecular physiological mechanisms of saline–alkali tolerance.![]()
Collapse
Affiliation(s)
- Yan-chun Sun
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products
- Ministry of Agriculture and Rural Areas
- Harbin 150070
- P. R. China
| | - Shi-cheng Han
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products
- Ministry of Agriculture and Rural Areas
- Harbin 150070
- P. R. China
| | - Ming-zhu Yao
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products
- Ministry of Agriculture and Rural Areas
- Harbin 150070
- P. R. China
| | - Hong-bai Liu
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products
- Ministry of Agriculture and Rural Areas
- Harbin 150070
- P. R. China
| | - Yu-mei Wang
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences
- Laboratory of Quality & Safety Risk Assessment for Aquatic Products
- Ministry of Agriculture and Rural Areas
- Harbin 150070
- P. R. China
| |
Collapse
|
20
|
Yao H, Yu PC, Jiang CM. Metabolomics-driven identification of perturbations in amino acid and sphingolipid metabolism as therapeutic targets in a rat model of anorexia nervosa disease using chemometric analysis and a multivariate analysis platform. RSC Adv 2020; 10:4928-4941. [PMID: 35498285 PMCID: PMC9049018 DOI: 10.1039/c9ra05187b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 11/25/2019] [Indexed: 12/03/2022] Open
Abstract
It is important to explore novel therapeutic targets and develop an effective strategy for the treatment of anorexia nervosa. In this work, serum samples were analyzed using ultra-performance liquid chromatography coupled with quadrupole time-of flight mass spectrometry (UPLC/Q-TOF MS) coupled with chemometric analysis and multivariate analysis to obtain the metabolites and their corresponding pathways. In addition, knock-in and knock-down of the key enzyme in vivo was performed to verify the reliability of the obtained metabolic pathway, which is closely associated with the anorexia nervosa pathomechanism and the potential targets. There were significant differences in the biochemical parameters between the model group and the control group. A total of 26 potential biomarkers were identified to resolve the difference between the control and model rats, which were closely related to amino acid metabolism, sphingolipid metabolism, arachidonic acid metabolism, the citrate cycle, and so forth. According to the ingenuity pathway analysis, we further elucidated the relationship between the gene, protein, and metabolite alteration in anorexia nervosa, which are involved in cellular compromise, lipid metabolism, small molecule biochemistry, cell signaling, molecular transport, nucleic acid metabolism, cell morphology, cellular function and maintenance. Arginosuccinate synthetase (ASS) deficiency was accompanied by a significant downregulation of the β-endorphin and ghrelin in the animal models. The metabolites and pathways obtained using the metabolomics strategy may provide valuable information for the early treatment for anorexia nervosa. It is important to explore novel therapeutic targets and develop an effective strategy for the treatment of anorexia nervosa.![]()
Collapse
Affiliation(s)
- Hong Yao
- Neonatology Department
- First Affiliated Hospital of Harbin Medical University
- Harbin 150001
- China
| | - Peng-Cheng Yu
- College of Traditional Chinese Medicine
- Jilin Agricultural University
- Changchun 130118
- China
| | - Chun-Ming Jiang
- Neonatology Department
- First Affiliated Hospital of Harbin Medical University
- Harbin 150001
- China
| |
Collapse
|
21
|
Qiu S, Zhang AH, Guan Y, Sun H, Zhang TL, Han Y, Yan GL, Wang XJ. Functional metabolomics using UPLC-Q/TOF-MS combined with ingenuity pathway analysis as a promising strategy for evaluating the efficacy and discovering amino acid metabolism as a potential therapeutic mechanism-related target for geniposide against alcoholic liver disease. RSC Adv 2020; 10:2677-2690. [PMID: 35496090 PMCID: PMC9048633 DOI: 10.1039/c9ra09305b] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/03/2019] [Indexed: 12/13/2022] Open
Abstract
Metabolomics has been used as a strategy to evaluate the efficacy of and potential targets for natural products.
Collapse
Affiliation(s)
- Shi Qiu
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Ai-hua Zhang
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Yu Guan
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Hui Sun
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Tian-lei Zhang
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Ying Han
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Guang-li Yan
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| | - Xi-jun Wang
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
- National TCM Key Laboratory of Serum Pharmacochemistry
- Metabolomics Laboratory
- Department of Pharmaceutical Analysis
| |
Collapse
|
22
|
Xu J, Jiang ZH, Liu XB, Ma Y, Ma W, Ma L. Ultra-performance liquid chromatography-mass spectrometry-based metabolomics reveals Huangqiliuyi decoction attenuates abnormal metabolism as a novel therapeutic opportunity for type 2 diabetes. RSC Adv 2019; 9:39858-39870. [PMID: 35541427 PMCID: PMC9076227 DOI: 10.1039/c9ra09386a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 11/15/2019] [Indexed: 11/21/2022] Open
Abstract
Background: As a typical chronic metabolic disease, type 2 diabetes mellitus causes a heavy health-care burden to society. In this study, we applied the metabolomics strategy to explore the potential molecular mechanism of the Huangqiliuyi decoction (HQLYD) for type-2 diabetes (T2D). Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) combined with pattern recognition methods was utilized to select specific metabolites closely associated with HQLYD. Biomarker pathway analysis and biological network were utilized to uncover the therapeutic effect and action mechanism related to HQLYD. A total of twenty-five biomarkers were identified in the animal model, in which sixteen biomarkers are associated with HQLYD treatment for T2D. They attenuated the abnormalities of metabolic pathways such as phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and the citrate cycle. HQLYD also significantly elevated the serum FINS and SOD, GSP-x level in the liver and kidney, and reduced the serum TC, TG, HDL, LDL, urea, Scr, AST, ALT, FBG, IRS, MDA, and CAT level. We found that the therapeutic mechanism of HQLYD against T2D affected amino acid metabolism, glucose metabolism and lipid metabolism. Metabolomics revealed that the Huangqiliuyi decoction attenuates abnormal metabolism as a novel therapeutic opportunity for type 2 diabetes.
Collapse
Affiliation(s)
- Jiao Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin 150040 China
- College of Pharmacy, Heilongjiang University of Chinese Medicine Harbin 150040 China
| | - Zhe-Hui Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin 150040 China
| | - Xiu-Bo Liu
- College of Pharmacy, Heilongjiang University of Chinese Medicine Harbin 150040 China
| | - Yan Ma
- School of Business Administration, Harbin University of Commerce Harbin 150040 China
| | - Wei Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin 150040 China
- College of Pharmacy, Heilongjiang University of Chinese Medicine Harbin 150040 China
| | - Ling Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University Harbin 150040 China
| |
Collapse
|
23
|
Zhao FJ, Zhang ZB, Ma N, Teng X, Cai ZC, Liu MX. Untargeted metabolomics using liquid chromatography coupled with mass spectrometry for rapid discovery of metabolite biomarkers to reveal therapeutic effects of Psoralea corylifolia seeds against osteoporosis. RSC Adv 2019; 9:35429-35442. [PMID: 35528068 PMCID: PMC9074708 DOI: 10.1039/c9ra07382e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/23/2019] [Indexed: 11/24/2022] Open
Abstract
Liquid chromatography coupled with mass spectrometry has been used as metabolomics profiling tool to discover and identify the metabolites in metabolic diseases. Osteoporosis (OP) syndrome is a chronic metabolic disease characterized by bone mass reduction and changes in bone microstructure. Psoralea corylifolia Linn. seeds (PCS) have a therapeutic effect on osteoporosis, but their action mechanism and therapeutic target are still unclear. This study aims to explore the metabolic changes of the urine profile in glucocorticoid-induced OP model rats and the therapeutic effect of PCS. High-throughput metabolomics based on the liquid chromatography coupled with mass spectrometry quadrupole time-of-flight mass spectrometry and multivariate data analysis were used to analyze the urine metabolites. The results showed that has an obvious separation between model and control groups. OPLS-DA was used to further analyze and discover substances that contributed to the separation. 42 potential biomarkers and 12 related metabolic pathways were identified in combination with network databases. After the intervention of PCS, 24 biomarkers were significantly regulated, mainly with glycone, serine and threonine metabolism, glutathione metabolism and purine metabolism and other metabolic pathways are related and discovered. This study has proved that PCS has therapeutic effect against OP by regulating that metabolic pathways disturbed in the OP. It provided a basis for the research and future development of new drugs for OP treatment. Liquid chromatography coupled with mass spectrometry has been used as metabolomics profiling tool to discover and identify the metabolites in metabolic diseases.![]()
Collapse
Affiliation(s)
- Fu-Jiang Zhao
- Department of Orthopaedics, Taizhou Central Hospital, Taizhou University Hospital Taizhou 318000 China +86-18767620975 +86-18767620975
| | - Zhao-Bo Zhang
- Department of Orthopaedics, Taizhou Central Hospital, Taizhou University Hospital Taizhou 318000 China +86-18767620975 +86-18767620975
| | - Ning Ma
- Department of Orthopaedics, Taizhou Central Hospital, Taizhou University Hospital Taizhou 318000 China +86-18767620975 +86-18767620975
| | - Xiao Teng
- Department of Orthopaedics, Taizhou Central Hospital, Taizhou University Hospital Taizhou 318000 China +86-18767620975 +86-18767620975
| | - Zhen-Cheng Cai
- Department of Orthopaedics, Taizhou Central Hospital, Taizhou University Hospital Taizhou 318000 China +86-18767620975 +86-18767620975
| | - Ming-Xi Liu
- Department of Orthopaedics, Taizhou Central Hospital, Taizhou University Hospital Taizhou 318000 China +86-18767620975 +86-18767620975
| |
Collapse
|
24
|
1H-NMR-based metabolomics to investigate the effects of Phoenix dactylifera seed extracts in LPS-IFN-γ-induced RAW 264.7 cells. Food Res Int 2019; 125:108565. [PMID: 31554083 DOI: 10.1016/j.foodres.2019.108565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/24/2019] [Accepted: 07/14/2019] [Indexed: 12/13/2022]
Abstract
Inflammation has been revealed to play a central role in the onset and progression of many illnesses. Nuclear magnetic resonance (NMR) based metabolomics method was adopted to evaluate the effects of Phoenix dactylifera seeds, in particular the Algerian date variety of Deglet on the metabolome of the LPS-IFN-γ-induced RAW 264.7 cells. Variations in the extracellular and intracellular profiles emphasized the differences in the presence of tyrosine, phenylalanine, alanine, proline, asparagine, isocitrate, inosine and lysine. Principal component analysis (PCA) revealed noticeable clustering patterns between the treated and induced RAW cells based on the metabolic profile of the extracellular metabolites. However, the effects of treatment on the intracellular metabolites appears to be less distinct as suggested by the PCA and heatmap analyses. A clear group segregation was observed for the intracellular metabolites from the treated and induced cells based on the orthogonal partial least squares-discriminant analysis (OPLS-DA) score plot. Likewise, 11 of the metabolites in the treated cells were significantly different from those in the induced groups, including amino acids and succinate. The enrichment analysis demonstrated that treatment with Deglet seed extracts interfered with the energy and of amino acids metabolism. Overall, the obtained data reinforced the possible application of Deglet seeds as a functional food with anti-inflammatory properties.
Collapse
|
25
|
NMR metabolomics for evaluating passage number and harvesting effects on mammalian cell metabolome. Anal Biochem 2019; 576:20-32. [DOI: 10.1016/j.ab.2019.04.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 04/01/2019] [Accepted: 04/01/2019] [Indexed: 12/18/2022]
|
26
|
Gómez-Cebrián N, Rojas-Benedicto A, Albors-Vaquer A, López-Guerrero JA, Pineda-Lucena A, Puchades-Carrasco L. Metabolomics Contributions to the Discovery of Prostate Cancer Biomarkers. Metabolites 2019; 9:metabo9030048. [PMID: 30857149 PMCID: PMC6468766 DOI: 10.3390/metabo9030048] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/01/2019] [Accepted: 03/04/2019] [Indexed: 02/06/2023] Open
Abstract
Prostate cancer (PCa) is one of the most frequently diagnosed cancers and a leading cause of death among men worldwide. Despite extensive efforts in biomarker discovery during the last years, currently used clinical biomarkers are still lacking enough specificity and sensitivity for PCa early detection, patient prognosis, and monitoring. Therefore, more precise biomarkers are required to improve the clinical management of PCa patients. In this context, metabolomics has shown to be a promising and powerful tool to identify novel PCa biomarkers in biofluids. Thus, changes in polyamines, tricarboxylic acid (TCA) cycle, amino acids, and fatty acids metabolism have been reported in different studies analyzing PCa patients' biofluids. The review provides an up-to-date summary of the main metabolic alterations that have been described in biofluid-based studies of PCa patients, as well as a discussion regarding their potential to improve clinical PCa diagnosis and prognosis. Furthermore, a summary of the most significant findings reported in these studies and the connections and interactions between the different metabolic changes described has also been included, aiming to better describe the specific metabolic signature associated to PCa.
Collapse
Affiliation(s)
- Nuria Gómez-Cebrián
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain.
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe/Instituto de Investigación Sanitaria La Fe, Valencia 46012, Spain.
- Laboratory of Molecular Biology, Fundación Instituto Valenciano de Oncología, Valencia 46009, Spain.
| | - Ayelén Rojas-Benedicto
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain.
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe/Instituto de Investigación Sanitaria La Fe, Valencia 46012, Spain.
| | - Arturo Albors-Vaquer
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain.
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe/Instituto de Investigación Sanitaria La Fe, Valencia 46012, Spain.
| | | | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain.
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe/Instituto de Investigación Sanitaria La Fe, Valencia 46012, Spain.
| | - Leonor Puchades-Carrasco
- Joint Research Unit in Clinical Metabolomics, Centro de Investigación Príncipe Felipe/Instituto de Investigación Sanitaria La Fe, Valencia 46012, Spain.
| |
Collapse
|
27
|
Yang Q, Zhang AH, Miao JH, Sun H, Han Y, Yan GL, Wu FF, Wang XJ. Metabolomics biotechnology, applications, and future trends: a systematic review. RSC Adv 2019; 9:37245-37257. [PMID: 35542267 PMCID: PMC9075731 DOI: 10.1039/c9ra06697g] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022] Open
Abstract
Given the highly increased incidence of human diseases, a better understanding of the related mechanisms regarding endogenous metabolism is urgently needed. Mass spectrometry-based metabolomics has been used in a variety of disease research areas. However, the deep research of metabolites remains a difficult and lengthy process. Fortunately, mass spectrometry is considered to be a universal tool with high specificity and sensitivity and is widely used around the world. Mass spectrometry technology has been applied to various basic disciplines, providing technical support for the discovery and identification of endogenous substances in living organisms. The combination of metabolomics and mass spectrometry is of great significance for the discovery and identification of metabolite biomarkers. The mass spectrometry tool could further improve and develop the exploratory research of the life sciences. This mini review discusses metabolomics biotechnology with a focus on recent applications of metabolomics as a powerful tool to elucidate metabolic disturbances and the related mechanisms of diseases. Given the highly increased incidence of human diseases, a better understanding of the related mechanisms regarding endogenous metabolism is urgently needed.![]()
Collapse
Affiliation(s)
- Qiang Yang
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Ai-hua Zhang
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Jian-hua Miao
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Hui Sun
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Ying Han
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Guang-li Yan
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Fang-fang Wu
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Xi-jun Wang
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| |
Collapse
|
28
|
Lu F, Zhang N, Yu D, Zhao H, Pang M, Fan Y, Liu S. An integrated metabolomics and 16S rRNA gene sequencing approach exploring the molecular pathways and potential targets behind the effects of Radix Scrophulariae. RSC Adv 2019; 9:33354-33367. [PMID: 35529111 PMCID: PMC9073378 DOI: 10.1039/c9ra03912k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
To assess the impact of the caecal microbiota on faecal metabolic phenotypes in the presence of Radix Scrophulariae (Chinese name: Xuanshen), an integrated approach involving 16S rRNA gene sequencing combined with ultrahigh-performance liquid chromatography/time-of-flight mass spectrometry (UHPLC/TOF-MS)-based faecal metabolomics was applied to Radix Scrophulariae-treated rats. Interestingly, Radix Scrophulariae led to significant gut microbiota changes at the phylum and genus levels in treated rats compared to control rats. Additionally, distinct changes in faecal metabolites, including linoleic acid (LA), guanosine, inosine, hypoxanthine, xanthine, 4-hydroxycinnamic acid, cholic acid, N-acetyl-d-glucosamine, l-urobilinogen and uridine, were observed in Radix Scrophulariae-treated rats. Of these, seven metabolites were up-regulated, and the remaining three metabolites were down-regulated. Moreover, there were substantial associations between altered levels of gut microbiota genera and discrepant levels of faecal metabolites, particularly for compounds involved in LA and purine metabolism. These results demonstrated that the gut microbiota is altered in association with faecal metabolism following treatment with Radix Scrophulariae. Our findings suggest that further application of this 16S rRNA gene sequencing and UHPLC/TOF-MS-based metabolomics approach will facilitate the assessment of the pharmacological action of Radix Scrophulariae and thus expand the scope of this herb. An integrated approach to assess impact of caecal microbiota on faecal metabolic phenotypes in the presence of Radix Scrophulariae involving 16S rRNA gene sequencing combined with UHPLC/TOF-MS-based faecal metabolomics was applied to Radix Scrophulariae-treated rats.![]()
Collapse
Affiliation(s)
- Fang Lu
- Institute of Traditional Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- PR China
| | - Ning Zhang
- Fist Affiliated Hospital of Guizhou University of Traditional Chinese Medicine
- Guiyang 550001
- PR China
| | - Donghua Yu
- Institute of Traditional Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- PR China
| | - Hongwei Zhao
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- PR China
| | - Mu Pang
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- PR China
| | - Yue Fan
- Research Department of Academic Theory
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- PR China
| | - Shumin Liu
- Institute of Traditional Chinese Medicine
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- PR China
| |
Collapse
|
29
|
Luo W, Zhang JW, Zhang LJ, Zhang W. High-throughput untargeted metabolomics and chemometrics reveals pharmacological action and molecular mechanism of chuanxiong by ultra performance liquid chromatography combined with quadrupole-time-of-flight-mass spectrometry. RSC Adv 2019; 9:39025-39036. [PMID: 35540684 PMCID: PMC9075942 DOI: 10.1039/c9ra06267j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 11/17/2019] [Indexed: 01/05/2023] Open
Abstract
Metabolomics methods can be used to explore the effect mechanisms underlying treatments with traditional medicine. Lung cancer (LC) causes the highest morbidity and mortality among tumors disease, and has become a serious public health problem. Chuanxiong (CX) is a dried rhizome of Ligusticum Chuanxiong Hort., often used in traditional Chinese medicine and has been widely used in the treatment for tumors. However, the pharmacological effect of CX on the metabolism process of LC mice is still unclear. This study used high-throughput untargeted metabolomics aims to discover biomarkers and metabolic pathways of LC as a potential target to provide insight into the pharmacological action and effective mechanism of CX against LC. The precise structural identification of the LC biomarker has been established using ultra performance liquid chromatography (UPLC) combined with quadrupole-time-of-flight-mass spectrometry (Q-TOF-MS) technology. UPLC-Q-TOF-MS and chemometrics methods were used to analyze the blood metabolism of LC model mice, and revealed the intervention effect of CX on LC model mice and potential therapeutic targets. The results showed that the metabolic profile clustering among the groups was obvious, and 31 potential biomarkers were finally locked, involving 7 related metabolic pathways. After treatment with CX, we found that 22 kinds of biomarkers were recalled to the main metabolic pathway which are associated with lipid metabolism. This study provides an effective biomarker reference for early clinical diagnosis of LC, and also provides a foundation for the expansion of new drugs for CX treatment of LC. Metabolomics methods can be used to explore the effect mechanisms underlying treatments with traditional medicine.![]()
Collapse
Affiliation(s)
- Wen Luo
- Department of Respiratory and Critical Care
- First Affiliated Hospital
- Harbin Medical University
- Harbin 150081
- China
| | - Jia-Wen Zhang
- Department of Respiratory and Critical Care
- First Affiliated Hospital
- Harbin Medical University
- Harbin 150081
- China
| | - Li-Juan Zhang
- Department of Respiratory and Critical Care
- First Affiliated Hospital
- Harbin Medical University
- Harbin 150081
- China
| | - Wei Zhang
- Department of Respiratory and Critical Care
- First Affiliated Hospital
- Harbin Medical University
- Harbin 150081
- China
| |
Collapse
|
30
|
Liang Q, Liu H, Li X, Hairong P, Sun P, Yang Y, Du C. High-throughput metabolic profiling, combined with chemometrics and bioinformatic analysis reveals functional alterations in myocardial dysfunction. RSC Adv 2019; 9:3351-3358. [PMID: 35548688 PMCID: PMC9087870 DOI: 10.1039/c8ra07572g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 01/15/2019] [Indexed: 12/13/2022] Open
Abstract
High-throughput metabolic profiling technology has been used for biomarker discovery and to reveal underlying metabolic mechanisms.
Collapse
Affiliation(s)
- Qun Liang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Han Liu
- Simon Fraser University (SFU)
- Burnaby
- Canada
| | - Xiuli Li
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Panguo Hairong
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Peiyang Sun
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Yang Yang
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| | - Chunpeng Du
- ICU Center
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
| |
Collapse
|
31
|
Li YF, Qiu S, Gao LJ, Zhang AH. Metabolomic estimation of the diagnosis of hepatocellular carcinoma based on ultrahigh performance liquid chromatography coupled with time-of-flight mass spectrometry. RSC Adv 2018; 8:9375-9382. [PMID: 35541871 PMCID: PMC9078651 DOI: 10.1039/c7ra13616a] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 02/23/2018] [Indexed: 01/01/2023] Open
Abstract
Metabolomics has been shown to be an effective tool for biomarker screening and pathway characterization and disease diagnosis. Metabolic characteristics of hepatocellular carcinoma (HCC) may enable the discovery of novel biomarkers for its diagnosis. In this work, metabolomics was used to investigate metabolic alterations of HCC patients. Plasma samples from HCC patients and age-matched healthy controls were investigated using high resolution ultrahigh performance liquid chromatography-mass spectrometry and metabolic differences were analyzed using pattern recognition methods. 23 distinguishable metabolites were identified. The altered metabolic pathways were associated with arginine and proline metabolism, glycine, serine and threonine metabolism, steroid hormone biosynthesis, starch and sucrose metabolism, etc. To demonstrate the utility of plasma biomarkers for the diagnosis of HCC, five metabolites comprising deoxycholic acid 3-glucuronide, 6-hydroxymelatonin glucuronide, 4-methoxycinnamic acid, 11b-hydroxyprogesterone and 4-hydroxyretinoic acid were selected as candidate biomarkers. These metabolites that contributed to the combined model could significantly increase the diagnostic performance of HCC. It has proved to be a powerful tool in the discovery of new biomarkers for disease detection and suggest that panels of metabolites may be valuable to translate our findings to clinically useful diagnostic tests. Metabolomics has been shown to be an effective tool for biomarker screening and pathway characterization and disease diagnosis.![]()
Collapse
Affiliation(s)
- Yuan-Feng Li
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Shi Qiu
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Li-Juan Gao
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| | - Ai-Hua Zhang
- First Affiliated Hospital
- School of Pharmacy
- Heilongjiang University of Chinese Medicine
- Harbin 150040
- China
| |
Collapse
|