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Niazi SK, Mariam Z. Computer-Aided Drug Design and Drug Discovery: A Prospective Analysis. Pharmaceuticals (Basel) 2023; 17:22. [PMID: 38256856 PMCID: PMC10819513 DOI: 10.3390/ph17010022] [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: 11/10/2023] [Revised: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
In the dynamic landscape of drug discovery, Computer-Aided Drug Design (CADD) emerges as a transformative force, bridging the realms of biology and technology. This paper overviews CADDs historical evolution, categorization into structure-based and ligand-based approaches, and its crucial role in rationalizing and expediting drug discovery. As CADD advances, incorporating diverse biological data and ensuring data privacy become paramount. Challenges persist, demanding the optimization of algorithms and robust ethical frameworks. Integrating Machine Learning and Artificial Intelligence amplifies CADDs predictive capabilities, yet ethical considerations and scalability challenges linger. Collaborative efforts and global initiatives, exemplified by platforms like Open-Source Malaria, underscore the democratization of drug discovery. The convergence of CADD with personalized medicine offers tailored therapeutic solutions, though ethical dilemmas and accessibility concerns must be navigated. Emerging technologies like quantum computing, immersive technologies, and green chemistry promise to redefine the future of CADD. The trajectory of CADD, marked by rapid advancements, anticipates challenges in ensuring accuracy, addressing biases in AI, and incorporating sustainability metrics. This paper concludes by highlighting the need for proactive measures in navigating the ethical, technological, and educational frontiers of CADD to shape a healthier, brighter future in drug discovery.
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Affiliation(s)
| | - Zamara Mariam
- Centre for Health and Life Sciences, Coventry University, Coventry City CV1 5FB, UK
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Langbøl M, Rovelt J, Saruhanian A, Saruhanian S, Tiedemann D, Baskaran T, Bocca C, Vohra R, Cvenkel B, Lenaers G, Kolko M. Distinct Metabolic Profiles of Ocular Hypertensives in Response to Hypoxia. Int J Mol Sci 2023; 25:195. [PMID: 38203366 PMCID: PMC10779258 DOI: 10.3390/ijms25010195] [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: 11/26/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Glaucoma is a neurodegenerative disease that affects the retinal ganglion cells (RGCs). The main risk factor is elevated intraocular pressure (IOP), but the actual cause of the disease remains unknown. Emerging evidence indicates that metabolic dysfunction plays a central role. The aim of the current study was to determine and compare the effect of universal hypoxia on the metabolomic signature in plasma samples from healthy controls (n = 10), patients with normal-tension glaucoma (NTG, n = 10), and ocular hypertension (OHT, n = 10). By subjecting humans to universal hypoxia, we aim to mimic a state in which the mitochondria in the body are universally stressed. Participants were exposed to normobaric hypoxia for two hours, followed by a 30 min recovery period in normobaric normoxia. Blood samples were collected at baseline, during hypoxia, and in recovery. Plasma samples were analyzed using a non-targeted metabolomics approach based on liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS). Multivariate analyses were conducted using principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA), and univariate analysis using the Wilcoxon signed-rank test and false discovery rate (FDR) correction. Unique metabolites involved in fatty acid biosynthesis and ketone body metabolism were upregulated, while metabolites of the kynurenine pathway were downregulated in OHT patients exposed to universal hypoxia. Differential affection of metabolic pathways may explain why patients with OHT initially do not suffer or are more resilient from optic nerve degeneration. The metabolomes of NTG and OHT patients are regulated differently from control subjects and show dysregulation of metabolites important for energy production. These dysregulated processes may potentially contribute to the elevation of IOP and, ultimately, cell death of the RGCs.
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Affiliation(s)
- Mia Langbøl
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
| | - Jens Rovelt
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark
| | - Arevak Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
| | - Sarkis Saruhanian
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
- Department of Veterinary & Animal Sciences, University of Copenhagen, 2000 Frederiksberg, Denmark
| | - Daniel Tiedemann
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark
| | - Thisayini Baskaran
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
| | - Cinzia Bocca
- Faculté de Santé, Institut MITOVASC, UMR CNRS 6015, INSERM U1083, Université d’Angers, 49933 Angers, France; (C.B.); (G.L.)
- Département de Biochimie et Biologie Moléculaire, Centre Hospitalier Universitaire (CHU), 49933 Angers, France
| | - Rupali Vohra
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark
| | - Barbara Cvenkel
- Department of Ophthalmology, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia;
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Guy Lenaers
- Faculté de Santé, Institut MITOVASC, UMR CNRS 6015, INSERM U1083, Université d’Angers, 49933 Angers, France; (C.B.); (G.L.)
| | - Miriam Kolko
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen, Denmark; (M.L.); (J.R.); (A.S.); (S.S.); (D.T.); (T.B.); (R.V.)
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark
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Cai H, Yang X, Yang Y, Feng Y, Wen A, Yang Y, Wen M, Ou D. Untargeted metabolomics of the intestinal tract of DEV-infected ducks. Virol J 2023; 20:305. [PMID: 38115106 PMCID: PMC10731684 DOI: 10.1186/s12985-023-02266-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023] Open
Abstract
INTRODUCTION Duck enteritis virus (DEV) mainly causes infectious diseases characterized by intestinal haemorrhage, inflammation and parenchymal organ degeneration in ducks and other poultry. However, the mechanism by which it causes intestinal damage in ducks is not well understood. Metabolomics can provide an in-depth understanding of the full complexity of the disease. METHODS In this study, 24 clinically healthy green-shell ducks (weight 1.5 kg ± 20 g) were randomly divided into 2 groups (experimental group, 18; control group, 6). The experimental group was intramuscularly injected with 0.2 mL of DEV virus in solution (TCID50 3.16 × 108 PFU/mL), and the control group was injected with 0.2 mL of sterile normal saline. Duck duodenum and ileum tissue samples were collected at 66 h, 90 h and 114 h post-injection (12 h of fasting before killing), and metabolomics analysis of duck duodenum and ileum tissues at the three time points (66, 90, 114 h) was performed by liquid chromatography-mass spectrometry (LC-MS) to screen for and analyse the potential differentiated metabolites and related signalling pathways. RESULTS Screening was performed in the positive/negative mode (Pos: Positive ion mode; the ionization of substances at the ion source with positive ions such as H+, NH4+, Na+ and K+; Neg: Negative ion mode; the ionization of substances at the ion source with negative ions such as Cl-, OAc-), and compound abundance was compared to that in the control group. The total number of differentially abundant compounds in the duodenum at 66 h, 90 h and 114 h of DEV infection gradually increased, and metabolites such as cytidine, 2'-deoxyriboside and 4-guanidinobutyric acid were differentially abundant metabolites common to all three time periods. The metabolic pathways related to inflammatory response and immune response were tryptophan acid metabolism, cysteine-methionine metabolism, histidine metabolism and other amino acid metabolism and fat metabolism. Among them, the metabolic pathways with more differentially abundant metabolites were amino acid biosynthesis, cysteine and methionine metabolism, tryptophan metabolism, unsaturated fatty acid biosynthesis and purine metabolism, and the metabolic pathways with more enrichment factors were the IgA-related intestinal immune network pathway and lysosome pathway. Compared with the control group, there were 16 differentially abundant metabolites in the ileum tissue of DEV-infected ducks at 66 h of infection, 52 at 90 h of infection, and 40 at 14 h of infection with TD114. The metabolic pathways with more enriched differentially abundant metabolites were pyrimidine metabolism, tyrosine metabolism, phenylalanine metabolism and tryptophan biosynthesis. The metabolic pathways with the most enrichment factors were the mTOR signalling pathway, ferroptosis pathway, tryptophan metabolism pathway and caffeine metabolism pathway. CONCLUSION Comparative analysis showed that the number of differentially abundant metabolites in the duodenum and ileum differed to some extent after DEV infection, with significantly more differentially abundant metabolites in duodenal tissues and fewer in ileal tissues; after DEV infection, the highest number of differentially abundant metabolites was obtained at 114 h of DEV infection, followed by the second highest at 90 h of infection and the lowest at 66 h of infection. The common differentially abundant metabolites in duodenal and ileal tissues were prostaglandins, arachidonic acid, and arachidonic ethanolamine. The main metabolic pathways in the duodenum were the IgA-associated intestinal immune network pathway and the lysosomal pathway, and the metabolic pathways with more enriched factors in the ileum were the mTOR signalling pathway, the ferroptosis pathway, and the tryptophan metabolism pathway.
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Affiliation(s)
- Haiqing Cai
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
| | - Xia Yang
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
| | - Yunyun Yang
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
| | - Yi Feng
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
| | - Anlin Wen
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
| | - Ying Yang
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
| | - Ming Wen
- School of Animal Science, Guizhou University, Guiyang, China.
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China.
| | - Deyuan Ou
- School of Animal Science, Guizhou University, Guiyang, China
- Guizhou Provincial Animal Biological Products Engineering Technology Research Center, Guiyang, China
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Yang H, Chen D, Wu Y, Zhou H, Diao W, Liu G, Li Q. A feedback loop of PPP and PI3K/AKT signal pathway drives regorafenib-resistance in HCC. Cancer Metab 2023; 11:27. [PMID: 38111012 PMCID: PMC10726576 DOI: 10.1186/s40170-023-00311-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/29/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a principal type of liver cancer with high incidence and mortality rates. Regorafenib is a novel oral multikinase inhibitor for second-line therapy for advanced HCC. However, resistance to regorafenib is gradually becoming a dilemma for HCC and the mechanism remains unclear. In this study, we aimed to reveal the metabolic profiles of regorafenib-resistant cells and the key role and mechanism of the most relevant metabolic pathway in regorafenib resistance. METHODS Metabolomics was performed to detect the metabolic alteration between drug-sensitive and regorafenib-resistant cells. Colony formation assay, CCK-8 assay and flow cytometry were applied to observe cell colony formation, cell proliferation and apoptosis, respectively. The protein and mRNA levels were detected by western blot and RT-qPCR. Cell lines of Glucose-6-phosphate dehydrogenase(G6PD) knockdown in regorafenib-resistant cells or G6PD overexpression in HCC cell lines were stably established by lentivirus infection technique. G6PD activity, NADPH level, NADPH/NADP+ ratio, the ratio of ROS positive cells, GSH level, and GSH/GSSG ratio were detected to evaluate the anti-oxidative stress ability of cells. Phosphorylation levels of NADK were evaluated by immunoprecipitation. RESULTS Metabonomics analysis revealed that pentose phosphate pathway (PPP) was the most relevant metabolic pathway in regorafenib resistance in HCC. Compared with drug-sensitive cells, G6PD enzyme activity, NADPH level and NADPH/NADP+ ratio were increased in regorafenib-resistant cells, but the ratio of ROS positive cells and the apoptosis rate under the conditions of oxidative stress were decreased. Furthermore, G6PD suppression using shRNA or an inhibitor, sensitized regorafenib-resistant cells to regorafenib. In contrast, G6PD overexpression blunted the effects of regorafenib to drug-sensitive cells. Mechanistically, G6PD, the rate-limiting enzyme of PPP, regulated the PI3K/AKT activation. Furthermore, PI3K/AKT inhibition decreased G6PD protein expression, G6PD enzymatic activity and the capacity of PPP to anti-oxidative stress possibly by inhibited the expression and phosphorylation of NADK. CONCLUSION Taken together, a feedback loop of PPP and PI3K/AKT signal pathway drives regorafenib-resistance in HCC and targeting the feedback loop could be a promising approach to overcome drug resistance.
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Affiliation(s)
- Huihua Yang
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Pharmacy, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dahong Chen
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yafei Wu
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Heming Zhou
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjing Diao
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gaolin Liu
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Qin Li
- Department of Clinical Pharmacy, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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105
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Uthailak N, Adisakwattana P, Chienwichai P, Tipthara P, Tarning J, Thawornkuno C, Thiangtrongjit T, Reamtong O. Metabolite profiling of Trichinella spiralis adult worms and muscle larvae identifies their excretory and secretory products. Front Cell Infect Microbiol 2023; 13:1306567. [PMID: 38145042 PMCID: PMC10749202 DOI: 10.3389/fcimb.2023.1306567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 11/20/2023] [Indexed: 12/26/2023] Open
Abstract
Human trichinellosis is a parasitic infection caused by roundworms belonging to the genus Trichinella, especially Trichinella spiralis. Early and accurate clinical diagnoses of trichinellosis are required for efficacious prognosis and treatment. Current drug therapies are limited by antiparasitic resistance, poor absorption, and an inability to kill the encapsulating muscle-stage larvae. Therefore, reliable biomarkers and drug targets for novel diagnostic approaches and anthelmintic drugs are required. In this study, metabolite profiles of T. spiralis adult worms and muscle larvae were obtained using mass spectrometry-based metabolomics. In addition, metabolite-based biomarkers of T. spiralis excretory-secretory products and their related metabolic pathways were characterized. The metabolic profiling identified major, related metabolic pathways involving adenosine monophosphate (AMP)-dependent synthetase/ligase and glycolysis/gluconeogenesis in T. spiralis adult worms and muscle larvae, respectively. These pathways are potential drug targets for the treatment of the intestinal and muscular phases of infection. The metabolome of larva excretory-secretory products was characterized, with amino acid permease and carbohydrate kinase being identified as key metabolic pathways. Among six metabolites, decanoyl-l-carnitine and 2,3-dinor-6-keto prostaglandin F1α-d9 were identified as potential metabolite-based biomarkers that might be related to the host inflammatory processes. In summary, this study compared the relationships between the metabolic profiles of two T. spiralis growth stages. Importantly, the main metabolites and metabolic pathways identified may aid the development of novel clinical diagnostics and therapeutics for human trichinellosis and other related helminthic infections.
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Affiliation(s)
- Naphatsamon Uthailak
- Department of Social and Environmental Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Poom Adisakwattana
- Department of Helminthology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Peerut Chienwichai
- Princess Srisavangavadhana College of Medicine, Chulabhorn Royal Academy, Bangkok, Thailand
| | - Phornpimon Tipthara
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Joel Tarning
- Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Charin Thawornkuno
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tipparat Thiangtrongjit
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Deng K, Gupta DK, Shu XO, Lipworth L, Zheng W, Thomas VE, Cai H, Cai Q, Wang TJ, Yu D. Metabolite Signature of Life's Essential 8 and Risk of Coronary Heart Disease Among Low-Income Black and White Americans. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2023; 16:e004230. [PMID: 38014580 PMCID: PMC10843634 DOI: 10.1161/circgen.123.004230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/26/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Life's essential 8 (LE8) is a comprehensive construct of cardiovascular health. Yet, little is known about the LE8 score, its metabolic correlates, and their predictive implications among Black Americans and low-income individuals. METHODS In a nested case-control study of coronary heart disease (CHD) among 299 pairs of Black and 298 pairs of White low-income Americans from the Southern Community Cohort Study, we estimated LE8 score and applied untargeted plasma metabolomics and elastic net with leave-one-out cross-validation to identify metabolite signature (MetaSig) of LE8. Associations of LE8 score and MetaSig with incident CHD were examined using conditional logistic regression. The mediation effect of MetaSig on the LE8-CHD association was also examined. The external validity of MetaSig was evaluated in another nested CHD case-control study among 299 pairs of Chinese adults. RESULTS Higher LE8 score was associated with lower CHD risk (standardized odds ratio, 0.61 [95% CI, 0.53-0.69]). The MetaSig, consisting of 133 metabolites, showed significant correlation with LE8 score (r=0.61) and inverse association with CHD (odds ratio, 0.57 [0.49-0.65]), robust to adjustment for LE8 score and across participants with different sociodemographic and health status ([odds ratios, 0.42-0.69]; all P<0.05). MetaSig mediated a large portion of the LE8-CHD association: 53% (32%-80%). Significant associations of MetaSig with LE8 score and CHD risk were found in validation cohort (r=0.49; odds ratio, 0.57 [0.46-0.69]). CONCLUSIONS Higher LE8 score and its MetaSig were associated with lower CHD risk among low-income Black and White Americans. Metabolomics may offer an objective measure of LE8 and its metabolic phenotype relevant to CHD prevention among diverse populations.
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Affiliation(s)
- Kui Deng
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Deepak K. Gupta
- Vanderbilt Translational & Clinical Cardiovascular Research Center & Division of Cardiovascular Medicine, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Xiao-Ou Shu
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Loren Lipworth
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Wei Zheng
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Victoria E. Thomas
- Vanderbilt Translational & Clinical Cardiovascular Research Center & Division of Cardiovascular Medicine, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Hui Cai
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Qiuyin Cai
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Thomas J. Wang
- Dept of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Danxia Yu
- Vanderbilt Epidemiology Center and Division of Epidemiology, Dept of Medicine, Vanderbilt University Medical Center, Nashville, TN
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Xiang Y, Zhou X, Zhou H, Li D, Zhong M, Hong X, Song D, Long Y, Zeng X, Chen Y, Zhou J, Liang D, Fu H. Limonin ameliorates cisplatin-induced acute liver injury by inhibiting 11β-hydroxysteroid dehydrogenase type 1. Biomed Pharmacother 2023; 168:115680. [PMID: 37832403 DOI: 10.1016/j.biopha.2023.115680] [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: 07/14/2023] [Revised: 09/28/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Acute liver injury (ALI) is a common side effect of cisplatin treatment in the clinic and can lead to liver failure if not treated promptly. Previous studies have revealed that Limonin, a critical bioactive substance in citrus fruits, can protect multiple organs from various medical conditions. However, whether Limonin could ameliorate cisplatin-induced ALI remains unclear. METHODS In vivo and in vitro models were induced by cisplatin in the present study. Non-targeted metabolomics was employed to analyze the metabolic changes in the liver after ALI. In addition, molecular docking was utilized to predict the potential targets of Limonin. RESULTS Limonin attenuated hepatic histopathological injury by reducing hepatocyte apoptosis, lipid peroxidation, and inflammation in cisplatin-challenged mice. Employing metabolomics, we revealed that Limonin mediated the balance of various disturbed metabolic pathways in the liver after cisplatin-induced ALI. Integrating public data mining, molecular docking studies, and in vitro experiments demonstrated that Limonin suppressed the expression and activity of its direct target, 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), in the liver, thus reducing the production of corticosterone (CORT), a key metabolite promoted hepatocyte apoptosis. CONCLUSIONS Limonin improves the liver metabolic microenvironment by inhibiting 11β-HSD1 to protect against cisplatin-induced ALI.
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Affiliation(s)
- Yadie Xiang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xianke Zhou
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Hong Zhou
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dier Li
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Menghua Zhong
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xue Hong
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongyan Song
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yinyi Long
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xi Zeng
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yudan Chen
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiayi Zhou
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongning Liang
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haiyan Fu
- State Key Laboratory of Organ Failure Research, National Clinical Research Center of Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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Kozioł A, Pupek M, Lewandowski Ł. Application of metabolomics in diagnostics and differentiation of meningitis: A narrative review with a critical approach to the literature. Biomed Pharmacother 2023; 168:115685. [PMID: 37837878 DOI: 10.1016/j.biopha.2023.115685] [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: 08/08/2023] [Revised: 09/28/2023] [Accepted: 10/08/2023] [Indexed: 10/16/2023] Open
Abstract
Due to its high mortality rate associated with various life-threatening sequelae, meningitis poses a vital problem in contemporary medicine. Numerous algorithms, many of which were derived with the aid of artificial intelligence, were brought up in a strive for perfection in predicting the status of sepsis-related survival or exacerbation. This review aims to provide key insights on the contextual utilization of metabolomics. The aim of this the metabolomic approach set of methods can be used to investigate both bacterial and host metabolite sets from both the host and its microbes in several types of specimens - even in one's breath, mainly with use of two methods - Mass Spectrometry (MS) and Nuclear Magnetic Resonance (NMR). Metabolomics, and has been used to elucidate the mechanisms underlying disease development and metabolic identification changes in a wide range of metabolite contents, leading to improved methods of diagnosis, treatment, and prognosis of meningitis. Mass spectrometry (MS) and Nuclear Magnetic Resonance (NMR) are the main analytical platforms used in metabolomics. Its high sensitivity accounts for the usefulness of metabolomics in studies into meningitis, its sequelae, and concomitant comorbidities. Metabolomics approaches are a double-edged sword, due to not only their flexibility, but also - high complexity, as even minor changes in the multi-step methods can have a massive impact on the results. Information on the differential diagnosis of meningitis act as a background in presenting the merits and drawbacks of the use of metabolomics in context of meningeal infections.
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Affiliation(s)
- Agata Kozioł
- Department of Immunochemistry and Chemistry, Wrocław Medical University, M. Skłodowskiej-Curie Street 48/50, 50-369 Wrocław, Poland
| | - Małgorzata Pupek
- Department of Immunochemistry and Chemistry, Wrocław Medical University, M. Skłodowskiej-Curie Street 48/50, 50-369 Wrocław, Poland.
| | - Łukasz Lewandowski
- Department of Medical Biochemistry, Wrocław Medical University, T. Chałubińskiego Street 10, 50-368 Wrocław, Poland
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Tian Y, Wan N, Zhang H, Shao C, Ding M, Bao Q, Hu H, Sun H, Liu C, Zhou K, Chen S, Wang G, Ye H, Hao H. Chemoproteomic mapping of the glycolytic targetome in cancer cells. Nat Chem Biol 2023; 19:1480-1491. [PMID: 37322158 DOI: 10.1038/s41589-023-01355-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely elusive. Here, we introduce a target-responsive accessibility profiling (TRAP) approach that measures changes in ligand binding-induced accessibility for target identification by globally labeling reactive proteinaceous lysines. With TRAP, we mapped 913 responsive target candidates and 2,487 interactions for 10 major glycolytic metabolites in a model cancer cell line. The wide targetome depicted by TRAP unveils diverse regulatory modalities of glycolytic metabolites, and these modalities involve direct perturbation of enzymes in carbohydrate metabolism, intervention of an orphan transcriptional protein's activity and modulation of targetome-level acetylation. These results further our knowledge of how glycolysis orchestrates signaling pathways in cancer cells to support their survival, and inspire exploitation of the glycolytic targetome for cancer therapy.
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Affiliation(s)
- Yang Tian
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ning Wan
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hanqing Zhang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chang Shao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Ming Ding
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qiuyu Bao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Haiyang Hu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Huiyong Sun
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Chenguang Liu
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Kun Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Shuai Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Cardiology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Guangji Wang
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China
| | - Hui Ye
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
| | - Haiping Hao
- Jiangsu Provincial Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China.
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Gao Y, Zhang Y, Liu W, Zhang N, Gao Q, Shangguan J, Li N, Zhao Y, Jia Y. Danggui Buxue decoction alleviates cyclophosphamide-induced myelosuppression by regulating β-hydroxybutyric acid metabolism and suppressing oxidative stress. PHARMACEUTICAL BIOLOGY 2023; 61:710-721. [PMID: 37096658 PMCID: PMC10132245 DOI: 10.1080/13880209.2023.2201606] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
CONTEXT Danggui Buxue Decoction (DBD) is an effective complementary medicine in alleviating myelosuppression after chemotherapy (MAC). However, its mechanism of action is elusive. OBJECTIVE To illustrate that regulating β-hydroxybutyric acid (β-OHB) metabolism and suppressing oxidative stress could be a potential mechanism of action for DBD in alleviating MAC. MATERIALS AND METHODS After HPLC quantification and dose testing (3, 6 and 10 g/kg, gavage) of DBD, Sprague-Dawley rats were divided into control, cyclophosphamide (CTX) (30 mg/kg CTX for 5 days, intraperitoneal administration) and CTX + DBD groups (6 g/kg DBD for 14 days, gavage). Blood cell counts, thigh bone histological examination, β-OHB levels, oxidative stress indices and HDAC1 activity were tested. The biological function of β-OHB was verified in vitro (hBMSC cells were incubated in culture mediums that contained 40 μM CTX and β-OHB in 0, 1, 2.5, 5, 10 mM) and in vivo (MAC rat model, 3 g/kg β-OHB for 14 days, gavage). RESULTS Rats in the CTX + DBD group showed upregulated blood cell counts (118-243%), β-OHB levels (495 nmol/mL in blood, 122 nmol/mg in marrow supernatant) and downregulated HDAC1 activity (59%), and oxidative stress indices (60-85%). In vitro, 5 mM β-OHB improved hBMSC cell migration (123%) and proliferation (131%). In vivo, rats treated with 3 g/kg β-OHB showed upregulated blood cell counts (121-182%) and downregulated HDAC1 activity (64%) and oxidative stress indices (65-83%). DISCUSSION AND CONCLUSIONS DBD, a traditional Chinese medicine, alleviates MAC by intervening in β-OHB metabolism and oxidative stress.
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Affiliation(s)
- Yiqiao Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
- Xinxiang Key Laboratory of Clinical Psychopharmacology, Xinxiang Medical University, Xinxiang, P. R. China
- CONTACT Yiqiao Gao
| | - Yixin Zhang
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
- Xinxiang Key Laboratory of Clinical Psychopharmacology, Xinxiang Medical University, Xinxiang, P. R. China
| | - Wei Liu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
| | - Nan Zhang
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
| | - Qinghe Gao
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
| | | | - Na Li
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
- Xinxiang Key Laboratory of Clinical Psychopharmacology, Xinxiang Medical University, Xinxiang, P. R. China
| | - Ying Zhao
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
- Xinxiang Key Laboratory of Clinical Psychopharmacology, Xinxiang Medical University, Xinxiang, P. R. China
| | - Yanlong Jia
- School of Pharmacy, Xinxiang Medical University, Xinxiang, P. R. China
- Yanlong Jia School of Pharmacy, Xinxiang Medical University, Xinxiang, Henan453003, P. R. China
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Vignoli A, Tenori L. NMR-based metabolomics in Alzheimer's disease research: a review. Front Mol Biosci 2023; 10:1308500. [PMID: 38099198 PMCID: PMC10720579 DOI: 10.3389/fmolb.2023.1308500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder and represents the most common cause of dementia in the elderly population worldwide. Currently, there is no cure for AD, and the continuous increase in the number of susceptible individuals poses one of the most significant emerging threats to public health. However, the molecular pathways involved in the onset and progression of AD are not fully understood. This information is crucial for developing less invasive diagnostic instruments and discovering novel potential therapeutic targets. Metabolomics studies the complete ensemble of endogenous and exogenous metabolites present in biological specimens and may provide an interesting approach to identify alterations in multiple biochemical processes associated with AD onset and evolution. In this mini review, we summarize the results from metabolomic studies conducted using nuclear magnetic resonance (NMR) spectroscopy on human biological samples (blood derivatives, cerebrospinal fluid, urine, saliva, and tissues) from AD patients. We describe the metabolic alterations identified in AD patients compared to controls and to patients diagnosed with mild cognitive impairment (MCI). Moreover, we discuss the challenges and issues associated with the application of NMR-based metabolomics in the context of AD research.
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Affiliation(s)
- Alessia Vignoli
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
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112
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Liang J, Wei X, Hou W, Wang H, Ma R, Gao Y, Du Y, Zhang Q. Liver metabolomics reveals potential mechanism of Jieduan-Niwan formula against acute-on-chronic liver failure (ACLF) by improving mitochondrial damage and TCA cycle. Chin Med 2023; 18:157. [PMID: 38037150 PMCID: PMC10691013 DOI: 10.1186/s13020-023-00858-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Acute-on-chronic liver failure (ACLF) is a refractory disease with high mortality, which is characterized by a pathophysiological process of inflammation-related dysfunction of energy metabolism. Jieduan-Niwan formula (JDNWF) is a eutherapeutic Chinese medicine formula for ACLF. However, the intrinsic mechanism of its anti-ACLF effect still need to be studied systematically. PURPOSE This study aimed to investigate the mechanism of JDNWF against ACLF based on altered substance metabolic profile in ACLF the expression levels of related molecules. MATERIALS AND METHODS The chemical characteristics of JDNWF were characterized using ultra performance liquid chromatography (UPLC) coupled with triple quadrupole mass spectrometry. Wistar rats subjected to a long-term CCL4 stimulation followed by a combination of an acute attack with LPS/D-GalN were used to establish the ACLF model. Liver metabolites were analyzed by LC-MS/MS and multivariate analysis. Liver function, coagulation function, histopathology, mitochondrial metabolic enzyme activity and mitochondrial damage markers were evaluated. The protein expression of mitochondrial quality control (MQC) was investigated by western blot. RESULTS Liver function, coagulation function, inflammation, oxidative stress and mitochondrial enzyme activity were significantly improved by JDNWF. 108 metabolites are considered as biomarkers of JDNWF in treating ACLF, which were closely related to TCA cycle. It was further suggested that JDNWF alleviated mitochondrial damage and MQC may be potential mechanism of JDNWF improving mitochondrial function. CONCLUSIONS Metabolomics revealed that TCA cycle was impaired in ACLF rats, and JDNWF had a regulatory effect on it. The potential mechanism may be improving the mitochondrial function through MQC pathway, thus restoring energy metabolism.
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Affiliation(s)
- Jiajun Liang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of TCM Collateral Disease Theory Research, Beijing, 100069, China
| | - Xiaoyi Wei
- Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Weixin Hou
- Department of Gastroenterology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hanjing Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of TCM Collateral Disease Theory Research, Beijing, 100069, China
| | - Ruimin Ma
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
- Beijing Key Laboratory of TCM Collateral Disease Theory Research, Beijing, 100069, China
| | - Yanbin Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China.
- Beijing Key Laboratory of TCM Collateral Disease Theory Research, Beijing, 100069, China.
| | - Yuqiong Du
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China.
- Beijing Key Laboratory of TCM Collateral Disease Theory Research, Beijing, 100069, China.
| | - Qiuyun Zhang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China.
- Beijing Key Laboratory of TCM Collateral Disease Theory Research, Beijing, 100069, China.
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Liu X, Wu Y, Guo L, Wang X, Shan C, Liu Y, An H, Kang X, Ding R, Cai Z, Dong J, Zhao Y, Gao X. Comprehensive Profiling of Amine-Containing Metabolite Isomers with Chiral Phosphorus Reagents. Anal Chem 2023; 95:16830-16839. [PMID: 37943818 DOI: 10.1021/acs.analchem.3c02325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Metabolite isomers play diverse and crucial roles in various metabolic processes. However, in untargeted metabolomics analysis, it remains a great challenge to distinguish between the constitutional isomers and enantiomers of amine-containing metabolites due to their similar chemical structures and physicochemical properties. In this work, the triplex stable isotope N-phosphoryl amino acids labeling (SIPAL) is developed to identify and relatively quantify the amine-containing metabolites and their isomers by using chiral phosphorus reagents coupled with high-resolution tandem mass spectroscopy. The constitutional isomers could be effectively distinguished with stereo isomers by using the diagnosis ions in MS/MS spectra. The in-house software MS-Isomerism has been parallelly developed for high-throughput screening and quantification. The proposed strategy enables the unbiased detection and relative quantification of isomers of amine-containing metabolites. Based on the characteristic triplet peaks with SIPAL tags, a total of 854 feature peaks with 154 isomer groups are successfully recognized as amine-containing metabolites in liver cells, in which 37 amine-containing metabolites, including amino acids, polyamines, and small peptides, are found to be significantly different between liver cancer cells and normal cells. Notably, it is the first time to identify S-acetyl-glutathione as an endogenous metabolite in liver cells. The SIPAL strategy could provide spectacular insight into the chemical structures and biological functions of the fascinating amine-containing metabolite isomers. The feasibility of SIPAL in isomeric metabolomics analysis may reach a deeper understanding of the mirror-chemistry in life and further advance the discovery of novel biomarkers for disease diagnosis.
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Affiliation(s)
- Xingxing Liu
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Yifan Wu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Lei Guo
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Xiaoyu Wang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Changkai Shan
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yaru Liu
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Hanxiang An
- Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361102, China
| | - Xinmei Kang
- Xiang'an Hospital of Xiamen University, Xiamen University, Xiamen 361102, China
| | - Rong Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, SAR 999077, China
| | - Jiyang Dong
- Department of Electronic Science, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen 361005, China
| | - Yufen Zhao
- Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315221, China
| | - Xiang Gao
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
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Lu AX, Lin Y, Li J, Liu JX, Yan CH, Zhang L. Effects of food-borne docosahexaenoic acid supplementation on bone lead mobilisation, mitochondrial function and serum metabolomics in pre-pregnancy lead-exposed lactating rats. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122613. [PMID: 37757928 DOI: 10.1016/j.envpol.2023.122613] [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: 07/17/2023] [Revised: 09/01/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Large bone lead (Pb) resulting from high environmental exposure during childhood is an important source of endogenous Pb during pregnancy and lactation. Docosahexaenoic acid (DHA) attenuates Pb toxicity, however, the effect of DHA on bone Pb mobilisation during lactation has not been investigated. We aimed to study the effects of DHA supplementation during pregnancy and lactation on bone Pb mobilisation during lactation and its potential mechanisms. Weaning female rats were randomly divided into control (0.05% sodium acetate) and Pb-exposed (0.05% Pb acetate) groups, after a 4-week exposure by ad libitum drinking and a subsequent 4-week washout period, all female rats were mated with healthy males until pregnancy. Then exposed rats were randomly divided into Pb and Pb + DHA groups, and the latter was given a 0.14% DHA diet, while the remaining groups were given normal feed until the end of lactation. Pb and calcium levels, bone microarchitecture, bone turnover markers, mitochondrial function and serum metabolomics were analyzed. The results showed that higher blood and bone Pb levels were observed in the Pb group compared to the control, and there was a significant negative correlation between blood and bone Pb. Also, Pb increased trabecular bone loss along with slightly elevated serum C-telopeptide of type I collagen (CTX-I) levels. However, DHA reduced CTX-I levels and improved trabecular bone microarchitecture. Metabolomics showed that Pb affected mitochondrial function, which was further demonstrated in bone tissue by significant reductions in ATP levels, Na+-K+-ATPase, Ca2+-Mg2+-ATPase and CAT activities, and elevated levels of MDA, IL-1β and IL-18. However, these alterations were partially mitigated by DHA. In conclusion, DHA supplementation during pregnancy and lactation improved bone Pb mobilisation and mitochondrial dysfunction in lactating rats induced by pre-pregnancy Pb exposure, providing potential means of mitigating bone Pb mobilisation levels during lactation, but the mechanism still needs further study.
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Affiliation(s)
- An-Xin Lu
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Yin Lin
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Jing Li
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jun-Xia Liu
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Chong-Huai Yan
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China; Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Lin Zhang
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China.
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Wang R, Lu M, An S, Wang J, Yu C. G-Aligner: a graph-based feature alignment method for untargeted LC-MS-based metabolomics. BMC Bioinformatics 2023; 24:431. [PMID: 37964228 PMCID: PMC10644574 DOI: 10.1186/s12859-023-05525-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/09/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Liquid chromatography-mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature alignment algorithms to observe the intensity variations across runs. However, most of the existing feature alignment methods focus more on accurate retention time correction, while underestimating the importance of feature matching. None of the existing methods can comprehensively consider feature correspondences among all runs and achieve optimal matching. RESULTS To comprehensively analyze feature correspondences among runs, we propose G-Aligner, a graph-based feature alignment method for untargeted LC-MS data. In the feature matching stage, G-Aligner treats features and potential correspondences as nodes and edges in a multipartite graph, considers the multi-run feature matching problem an unbalanced multidimensional assignment problem, and provides three combinatorial optimization algorithms to find optimal matching solutions. In comparison with the feature alignment methods in OpenMS, MZmine2 and XCMS on three public metabolomics benchmark datasets, G-Aligner achieved the best feature alignment performance on all the three datasets with up to 9.8% and 26.6% increase in accurately aligned features and analytes, and helped all comparison software obtain more accurate results on their self-extracted features by integrating G-Aligner to their analysis workflow. G-Aligner is open-source and freely available at https://github.com/CSi-Studio/G-Aligner under a permissive license. Benchmark datasets, manual annotation results, evaluation methods and results are available at https://doi.org/10.5281/zenodo.8313034 CONCLUSIONS: In this study, we proposed G-Aligner to improve feature matching accuracy for untargeted metabolomics LC-MS data. G-Aligner comprehensively considered potential feature correspondences between all runs, converting the feature matching problem as a multidimensional assignment problem (MAP). In evaluations on three public metabolomics benchmark datasets, G-Aligner achieved the highest alignment accuracy on manual annotated and popular software extracted features, proving the effectiveness and robustness of the algorithm.
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Affiliation(s)
- Ruimin Wang
- Fudan University, Shanghai, 200433, Shanghai, China
- School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
| | - Miaoshan Lu
- School of Engineering, Westlake University, Hangzhou, 310030, Zhejiang, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
- Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Shaowei An
- Fudan University, Shanghai, 200433, Shanghai, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Jinyin Wang
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China
- Zhejiang University, Hangzhou, 310058, Zhejiang, China
- School of Life Sciences, Westlake University, Hangzhou, 310030, Zhejiang, China
| | - Changbin Yu
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250021, Shandong, China.
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Roquencourt C, Lamy E, Bardin E, Devillier P, Grassin-Delyle S. A benchmark study of data normalisation methods for PTR-TOF-MS exhaled breath metabolomics. J Breath Res 2023; 18:016006. [PMID: 37917990 DOI: 10.1088/1752-7163/ad08ce] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/02/2023] [Indexed: 11/04/2023]
Abstract
Volatilomics is the branch of metabolomics dedicated to the analysis of volatile organic compounds in exhaled breath for medical diagnostic or therapeutic monitoring purposes. Real-time mass spectrometry (MS) technologies such as proton transfer reaction (PTR) MS are commonly used, and data normalisation is an important step to discard unwanted variation from non-biological sources, as batch effects and loss of sensitivity over time may be observed. As normalisation methods for real-time breath analysis have been poorly investigated, we aimed to benchmark known metabolomic data normalisation methods and apply them to PTR-MS data analysis. We compared seven normalisation methods, five statistically based and two using multiple standard metabolites, on two datasets from clinical trials for COVID-19 diagnosis in patients from the emergency department or intensive care unit. We evaluated different means of feature selection to select the standard metabolites, as well as the use of multiple repeat measurements of ambient air to train the normalisation methods. We show that the normalisation tools can correct for time-dependent drift. The methods that provided the best corrections for both cohorts were probabilistic quotient normalisation and normalisation using optimal selection of multiple internal standards. Normalisation also improved the diagnostic performance of the machine learning models, significantly increasing sensitivity, specificity and area under the receiver operating characteristic (ROC) curve for the diagnosis of COVID-19. Our results highlight the importance of adding an appropriate normalisation step during the processing of PTR-MS data, which allows significant improvements in the predictive performance of statistical models.Clinical trials: VOC-COVID-Diag (EudraCT 2020-A02682-37); RECORDS trial (EudraCT 2020-000296-21).
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Affiliation(s)
| | - Elodie Lamy
- Département de Biotechnologie de la Santé, Université Paris-Saclay, UVSQ, INSERM U1173, Infection et inflammation, Montigny le Bretonneux, France
| | - Emmanuelle Bardin
- Hôpital Foch, Exhalomics®, Suresnes, France
- Département de Biotechnologie de la Santé, Université Paris-Saclay, UVSQ, INSERM U1173, Infection et inflammation, Montigny le Bretonneux, France
- Institut Necker-Enfants Malades, Paris, France
| | - Philippe Devillier
- Hôpital Foch, Exhalomics®, Suresnes, France
- Laboratoire de recherche en Pharmacologie Respiratoire-VIM Suresnes, UMR 0892, Université Paris-Saclay, Suresnes, France
| | - Stanislas Grassin-Delyle
- Hôpital Foch, Exhalomics®, Suresnes, France
- Département de Biotechnologie de la Santé, Université Paris-Saclay, UVSQ, INSERM U1173, Infection et inflammation, Montigny le Bretonneux, France
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Niazi SK. A Critical Analysis of the FDA's Omics-Driven Pharmacodynamic Biomarkers to Establish Biosimilarity. Pharmaceuticals (Basel) 2023; 16:1556. [PMID: 38004421 PMCID: PMC10675618 DOI: 10.3390/ph16111556] [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: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 11/26/2023] Open
Abstract
Demonstrating biosimilarity entails comprehensive analytical assessment, clinical pharmacology profiling, and efficacy testing in patients for at least one medical indication, as required by the U.S. Biologics Price Competition and Innovation Act (BPCIA). The efficacy testing can be waived if the drug has known pharmacodynamic (PD) markers, leaving most therapeutic proteins out of this concession. To overcome this, the FDA suggests that biosimilar developers discover PD biomarkers using omics technologies such as proteomics, glycomics, transcriptomics, genomics, epigenomics, and metabolomics. This approach is redundant since the mode-action-action biomarkers of approved therapeutic proteins are already available, as compiled in this paper for the first time. Other potential biomarkers are receptor binding and pharmacokinetic profiling, which can be made more relevant to ensure biosimilarity without requiring biosimilar developers to conduct extensive research, for which they are rarely qualified.
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Affiliation(s)
- Sarfaraz K Niazi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL 60612, USA
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Wang Y, Wei W, Du W, Cai J, Liao Y, Lu H, Kong B, Zhang Z. Deep-Learning-Based Mixture Identification for Nuclear Magnetic Resonance Spectroscopy Applied to Plant Flavors. Molecules 2023; 28:7380. [PMID: 37959799 PMCID: PMC10648966 DOI: 10.3390/molecules28217380] [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: 09/27/2023] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Nuclear magnetic resonance (NMR) is a crucial technique for analyzing mixtures consisting of small molecules, providing non-destructive, fast, reproducible, and unbiased benefits. However, it is challenging to perform mixture identification because of the offset of chemical shifts and peak overlaps that often exist in mixtures such as plant flavors. Here, we propose a deep-learning-based mixture identification method (DeepMID) that can be used to identify plant flavors (mixtures) in a formulated flavor (mixture consisting of several plant flavors) without the need to know the specific components in the plant flavors. A pseudo-Siamese convolutional neural network (pSCNN) and a spatial pyramid pooling (SPP) layer were used to solve the problems due to their high accuracy and robustness. The DeepMID model is trained, validated, and tested on an augmented data set containing 50,000 pairs of formulated and plant flavors. We demonstrate that DeepMID can achieve excellent prediction results in the augmented test set: ACC = 99.58%, TPR = 99.48%, FPR = 0.32%; and two experimentally obtained data sets: one shows ACC = 97.60%, TPR = 92.81%, FPR = 0.78% and the other shows ACC = 92.31%, TPR = 80.00%, FPR = 0.00%. In conclusion, DeepMID is a reliable method for identifying plant flavors in formulated flavors based on NMR spectroscopy, which can assist researchers in accelerating the design of flavor formulations.
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Affiliation(s)
- Yufei Wang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
| | - Weiwei Wei
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Wen Du
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Jiaxiao Cai
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Yuxuan Liao
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
| | - Hongmei Lu
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
| | - Bo Kong
- Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410014, China; (W.W.); (W.D.); (J.C.)
| | - Zhimin Zhang
- College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China; (Y.W.); (Y.L.); (H.L.)
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119
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Cheng H, Tang Y, Li Z, Guo Z, Heath JR, Xue M, Wei W. Non-Mass Spectrometric Targeted Single-Cell Metabolomics. Trends Analyt Chem 2023; 168:117300. [PMID: 37840599 PMCID: PMC10569257 DOI: 10.1016/j.trac.2023.117300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Metabolic assays serve as pivotal tools in biomedical research, offering keen insights into cellular physiological and pathological states. While mass spectrometry (MS)-based metabolomics remains the gold standard for comprehensive, multiplexed analyses of cellular metabolites, innovative technologies are now emerging for the targeted, quantitative scrutiny of metabolites and metabolic pathways at the single-cell level. In this review, we elucidate an array of these advanced methodologies, spanning synthetic and surface chemistry techniques, imaging-based methods, and electrochemical approaches. We summarize the rationale, design principles, and practical applications for each method, and underscore the synergistic benefits of integrating single-cell metabolomics (scMet) with other single-cell omics technologies. Concluding, we identify prevailing challenges in the targeted scMet arena and offer a forward-looking commentary on future avenues and opportunities in this rapidly evolving field.
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Affiliation(s)
- Hanjun Cheng
- Institute for Systems Biology, Seattle, WA, 98109, United States
| | - Yin Tang
- Institute for Systems Biology, Seattle, WA, 98109, United States
| | - Zhonghan Li
- Department of Chemistry, University of California, Riverside, CA, 92521, United States
| | - Zhili Guo
- Department of Chemistry, University of California, Riverside, CA, 92521, United States
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA, 98109, United States
| | - Min Xue
- Department of Chemistry, University of California, Riverside, CA, 92521, United States
| | - Wei Wei
- Institute for Systems Biology, Seattle, WA, 98109, United States
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120
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Liu R, Luo S, Zhang YS, Tsang CK. Plasma metabolomic profiling of patients with transient ischemic attack reveals positive role of neutrophils in ischemic tolerance. EBioMedicine 2023; 97:104845. [PMID: 37890369 PMCID: PMC10630611 DOI: 10.1016/j.ebiom.2023.104845] [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: 04/13/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Transient ischemic attack (TIA) induces ischemic tolerance that can reduce the subsequent ischemic damage and improve prognosis of patients with stroke. However, the underlying mechanisms remain elusive. Recent advances in plasma metabolomics analysis have made it a powerful tool to investigate human pathophysiological phenotypes and mechanisms of diseases. In this study, we aimed to identify the bioactive metabolites from the plasma of patients with TIA for determination of their prophylactic and therapeutic effects on protection against cerebral ischemic stroke, and the mechanism of TIA-induced ischemic tolerance against subsequent stroke. METHODS Metabolomic profiling using liquid chromatography-mass spectrometry was performed to identify the TIA-induced differential bioactive metabolites in the plasma samples of 20 patients at day 1 (time for basal metabolites) and day 7 (time for established chronic ischemic tolerance-associated metabolites) after onset of TIA. Mouse middle cerebral artery occlusion (MCAO)-induced stroke model was used to verify their prophylactic and therapeutic potentials. Transcriptomics changes in circulating neutrophils of patients with TIA were determined by RNA-sequencing. Multivariate statistics and integrative analysis of metabolomics and transcriptomics were performed to elucidate the potential mechanism of TIA-induced ischemic tolerance. FINDINGS Plasma metabolomics analysis identified five differentially upregulated metabolites associated with potentially TIA-induced ischemic tolerance, namely all-trans 13,14 dihydroretinol (atDR), 20-carboxyleukotriene B4, prostaglandin B2, cortisol and 9-KODE. They were associated with the metabolic pathways of retinol, arachidonic acid, and neuroactive ligand-receptor interaction. Prophylactic treatment of MCAO mice with these five metabolites significantly improved neurological functions. Additionally, post-stroke treatment with atDR or 9-KODE significantly reduced the cerebral infarct size and enhanced sensorimotor functions, demonstrating the therapeutic potential of these bioactive metabolites. Mechanistically, we found in patients with TIA that these metabolites were positively correlated with circulating neutrophil counts. Integrative analysis of plasma metabolomics and neutrophil transcriptomics further revealed that TIA-induced metabolites are significantly correlated with specific gene expression in circulating neutrophils which showed prominent enrichment in FoxO signaling pathway and upregulation of the anti-inflammatory cytokine IL-10. Finally, we demonstrated that the protective effect of atDR-pretreatment on MCAO mice was abolished when circulating neutrophils were depleted. INTERPRETATION TIA-induced potential ischemic tolerance is associated with upregulation of plasma bioactive metabolites which can protect against cerebral ischemic damage and improve neurological functions through a positive role of circulating neutrophils. FUNDING National Natural Science Foundation of China (81974210), Science and Technology Planning Project of Guangdong Province, China (2020A0505100045), Natural Science Foundation of Guangdong Province (2019A1515010671), Science and Technology Program of Guangzhou, China (2023A03J0577), and Natural Science Foundation of Jiangxi, China(20224BAB216043).
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Affiliation(s)
- Rongrong Liu
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China; Department of Neurology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Siwei Luo
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China; Department of Neurology, The First Clinical Medical School of Jinan University, Guangzhou, China
| | - Yu-Sheng Zhang
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China; Department of Neurology, The First Clinical Medical School of Jinan University, Guangzhou, China.
| | - Chi Kwan Tsang
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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Reece AS, Hulse GK. Perturbation of 3D nuclear architecture, epigenomic aging and dysregulation, and cannabinoid synaptopathy reconfigures conceptualization of cannabinoid pathophysiology: part 2-Metabolome, immunome, synaptome. Front Psychiatry 2023; 14:1182536. [PMID: 37854446 PMCID: PMC10579598 DOI: 10.3389/fpsyt.2023.1182536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
The second part of this paper builds upon and expands the epigenomic-aging perspective presented in Part 1 to describe the metabolomic and immunomic bases of the epigenomic-aging changes and then considers in some detail the application of these insights to neurotoxicity, neuronal epigenotoxicity, and synaptopathy. Cannabinoids are well-known to have bidirectional immunomodulatory activities on numerous parts of the immune system. Immune perturbations are well-known to impact the aging process, the epigenome, and intermediate metabolism. Cannabinoids also impact metabolism via many pathways. Metabolism directly impacts immune, genetic, and epigenetic processes. Synaptic activity, synaptic pruning, and, thus, the sculpting of neural circuits are based upon metabolic, immune, and epigenomic networks at the synapse, around the synapse, and in the cell body. Many neuropsychiatric disorders including depression, anxiety, schizophrenia, bipolar affective disorder, and autistic spectrum disorder have been linked with cannabis. Therefore, it is important to consider these features and their complex interrelationships in reaching a comprehensive understanding of cannabinoid dependence. Together these findings indicate that cannabinoid perturbations of the immunome and metabolome are important to consider alongside the well-recognized genomic and epigenomic perturbations and it is important to understand their interdependence and interconnectedness in reaching a comprehensive appreciation of the true nature of cannabinoid pathophysiology. For these reasons, a comprehensive appreciation of cannabinoid pathophysiology necessitates a coordinated multiomics investigation of cannabinoid genome-epigenome-transcriptome-metabolome-immunome, chromatin conformation, and 3D nuclear architecture which therefore form the proper mechanistic underpinning for major new and concerning epidemiological findings relating to cannabis exposure.
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Affiliation(s)
- Albert Stuart Reece
- Division of Psychiatry, University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Gary Kenneth Hulse
- Division of Psychiatry, University of Western Australia, Crawley, WA, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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Astarita G, Kelly RS, Lasky-Su J. Metabolomics and lipidomics strategies in modern drug discovery and development. Drug Discov Today 2023; 28:103751. [PMID: 37640150 PMCID: PMC10543515 DOI: 10.1016/j.drudis.2023.103751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.
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Affiliation(s)
- Giuseppe Astarita
- Georgetown University, Washington, DC, USA; Arkuda Therapeutics, Watertown, MA, USA.
| | - Rachel S Kelly
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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123
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Qian F, Zhao L, Zhang D, Yu M, Zhou W, Jin J. Serum metabolomics detected by LDI-TOF-MS can be used to distinguish between diabetic patients with and without diabetic kidney disease. FEBS Open Bio 2023; 13:1844-1858. [PMID: 37525631 PMCID: PMC10549217 DOI: 10.1002/2211-5463.13683] [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: 04/15/2023] [Revised: 06/21/2023] [Accepted: 07/31/2023] [Indexed: 08/02/2023] Open
Abstract
Diabetic kidney disease (DKD) is an important cause of end-stage renal disease with changes in metabolic characteristics. The objective of this study was to study changes in serum metabolic characteristics in patients with DKD and to examine metabolite panels to distinguish DKD from diabetes with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). We recruited 40 type II diabetes mellitus (T2DM) patients with or without DKD from a single center for a cross-sectional study. Serum metabolic profiling was performed with MALDI-TOF-MS using a vertical silicon nanowire array. Differential metabolites between DKD and diabetes patients were selected, and their relevance to the clinical parameters of DKD was analyzed. We applied machine learning methods to the differential metabolite panels to distinguish DKD patients from diabetes patients. Twenty-four differential serum metabolites between DKD patients and diabetes patients were identified, which were mainly enriched in butyrate metabolism, TCA cycle, and alanine, aspartate, and glutamate metabolism. Among the metabolites, l-kynurenine was positively correlated with urinary microalbumin, urinary microalbumin/creatinine ratio (UACR), creatinine, and urea nitrogen content. l-Serine, pimelic acid, 5-methylfuran-2-carboxylic acid, 4-methylbenzaldehyde, and dihydrouracil were associated with the estimated glomerular filtration rate (eGFR). The panel of differential metabolites could be used to distinguish between DKD and diabetes patients with an AUC value reaching 0.9899-0.9949. Among the differential metabolites, l-kynurenine was related to the progression of DKD. The differential metabolites exhibited excellent performance at distinguishing between DKD and diabetes. This study provides a novel direction for metabolomics-based clinical detection of DKD.
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Affiliation(s)
- Fengmei Qian
- The Second School of Clinical MedicineZhejiang Chinese Medical UniversityHangzhouChina
| | - Li Zhao
- Department of Nephrology, Urology & Nephrology CenterZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)China
| | - Di Zhang
- Department of Nephrology, Urology & Nephrology CenterZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)China
| | - Mengjie Yu
- Department of Nephrology, Urology & Nephrology CenterZhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College)China
| | - Wei Zhou
- Department of NephrologyThe First People's Hospital of Hangzhou Lin'an District, Affiliated Lin'an People's Hospital, Hangzhou Medical CollegeChina
| | - Juan Jin
- Department of NephrologyThe First People's Hospital of Hangzhou Lin'an District, Affiliated Lin'an People's Hospital, Hangzhou Medical CollegeChina
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Kussmann M. Mass spectrometry as a lens into molecular human nutrition and health. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2023; 29:370-379. [PMID: 37587732 DOI: 10.1177/14690667231193555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Mass spectrometry (MS) has developed over the last decades into the most informative and versatile analytical technology in molecular and structural biology (). The platform enables discovery, identification, and characterisation of non-volatile biomolecules, such as proteins, peptides, DNA, RNA, nutrients, metabolites, and lipids at both speed and scale and can elucidate their interactions and effects. The versatility, robustness, and throughput have rendered MS a major research and development platform in molecular human health and biomedical science. More recently, MS has also been established as the central tool for 'Molecular Nutrition', enabling comprehensive and rapid identification and characterisation of macro- and micronutrients, bioactives, and other food compounds. 'Molecular Nutrition' thereby helps understand bioaccessibility, bioavailability, and bioefficacy of macro- and micronutrients and related health effects. Hence, MS provides a lens through which the fate of nutrients can be monitored along digestion via absorption to metabolism. This in turn provides the bioanalytical foundation for 'Personalised Nutrition' or 'Precision Nutrition' in which design and development of diets and nutritional products is tailored towards consumer and patient groups sharing similar genetic and environmental predisposition, health/disease conditions and lifestyles, and/or objectives of performance and wellbeing. The next level of integrated nutrition science is now being built as 'Systems Nutrition' where public and personal health data are correlated with life condition and lifestyle factors, to establish directional relationships between nutrition, lifestyle, environment, and health, eventually translating into science-based public and personal heath recommendations and actions. This account provides a condensed summary of the contributions of MS to a precise, quantitative, and comprehensive nutrition and health science and sketches an outlook on its future role in this fascinating and relevant field.
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Affiliation(s)
- Martin Kussmann
- Abteilung Wissenschaft, Kompetenzzentrum für Ernährung (KErn), Germany
- Kussmann Biotech GmbH, Germany
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125
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Jariyasopit N, Khoomrung S. Mass spectrometry-based analysis of gut microbial metabolites of aromatic amino acids. Comput Struct Biotechnol J 2023; 21:4777-4789. [PMID: 37841334 PMCID: PMC10570628 DOI: 10.1016/j.csbj.2023.09.032] [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: 05/04/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 10/17/2023] Open
Abstract
Small molecules derived from gut microbiota have been increasingly investigated to better understand the functional roles of the human gut microbiome. Microbial metabolites of aromatic amino acids (AAA) have been linked to many diseases, such as metabolic disorders, chronic kidney diseases, inflammatory bowel disease, diabetes, and cancer. Important microbial AAA metabolites are often discovered via global metabolite profiling of biological specimens collected from humans or animal models. Subsequent metabolite identity confirmation and absolute quantification using targeted analysis enable comparisons across different studies, which can lead to the establishment of threshold concentrations of potential metabolite biomarkers. Owing to their excellent selectivity and sensitivity, hyphenated mass spectrometry (MS) techniques are often employed to identify and quantify AAA metabolites in various biological matrices. Here, we summarize the developments over the past five years in MS-based methodology for analyzing gut microbiota-derived AAA. Sample preparation, method validation, analytical performance, and statistical methods for correlation analysis are discussed, along with future perspectives.
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Affiliation(s)
- Narumol Jariyasopit
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
| | - Sakda Khoomrung
- Siriraj Center of Research Excellence in Metabolomics and Systems Biology (SiCORE-MSB), Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital Mahidol University, Bangkok 10700, Thailand
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126
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Almalki AH. Recent Analytical Advances for Decoding Metabolic Reprogramming in Lung Cancer. Metabolites 2023; 13:1037. [PMID: 37887362 PMCID: PMC10609104 DOI: 10.3390/metabo13101037] [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: 08/24/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Metabolic reprogramming is a fundamental trait associated with lung cancer development that fuels tumor proliferation and survival. Monitoring such metabolic pathways and their intermediate metabolites can provide new avenues concerning treatment strategies, and the identification of prognostic biomarkers that could be utilized to monitor drug responses in clinical practice. In this review, recent trends in the analytical techniques used for metabolome mapping of lung cancer are capitalized. These techniques include nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and imaging mass spectrometry (MSI). The advantages and limitations of the application of each technique for monitoring the metabolite class or type are also highlighted. Moreover, their potential applications in the analysis of many biological samples will be evaluated.
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Affiliation(s)
- Atiah H. Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
- Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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127
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Estrada-Pérez AR, García-Vázquez JB, Mendoza-Figueroa HL, Rosales-Hernández MC, Fernández-Pomares C, Correa-Basurto J. Untargeted LC-MS/MS Metabolomics Study of HO-AAVPA and VPA on Breast Cancer Cell Lines. Int J Mol Sci 2023; 24:14543. [PMID: 37833990 PMCID: PMC10572250 DOI: 10.3390/ijms241914543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/05/2023] [Accepted: 09/06/2023] [Indexed: 10/15/2023] Open
Abstract
Breast cancer (BC) is one of the biggest health problems worldwide, characterized by intricate metabolic and biochemical complexities stemming from pronounced variations across dysregulated molecular pathways. If BC is not diagnosed early, complications may lead to death. Thus, the pursuit of novel therapeutic avenues persists, notably focusing on epigenetic pathways such as histone deacetylases (HDACs). The compound N-(2-hydroxyphenyl)-2-propylpentanamide (HO-AAVPA), a derivative of valproic acid (VPA), has emerged as a promising candidate warranting pre-clinical investigation. HO-AAVPA is an HDAC inhibitor with antiproliferative effects on BC, but its molecular mechanism has yet to be deciphered. Furthermore, in the present study, we determined the metabolomic effects of HO-AAVPA and VPA on cells of luminal breast cancer (MCF-7) and triple-negative breast cancer (MDA-MB-231) subtypes. The LC-MS untargeted metabolomic study allowed for the simultaneous measurement of multiple metabolites and pathways, identifying that both compounds affect glycerophospholipid and sphingolipid metabolism in the MCF-7 and MDA-MB-231 cell lines, suggesting that other biological targets were different from HDACs. In addition, there are different dysregulate metabolites, possibly due to the physicochemical differences between HO-AAVPA and VPA.
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Affiliation(s)
- Alan Rubén Estrada-Pérez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Juan Benjamín García-Vázquez
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Humberto L. Mendoza-Figueroa
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Martha Cecilia Rosales-Hernández
- Laboratorio de Biofísica y Biocatálisis, Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - Cynthia Fernández-Pomares
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotecnológica, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Casco de Santo Tomás, Ciudad de México 11340, Mexico
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Wang Z, Wan Q, Xie B, Zhu Z, Xu X, Fu P, Liu R. Integrated network pharmacology and fecal metabolomic analysis of the combinational mechanisms of Shexiang Baoxin Pill against atherosclerosis. Mol Omics 2023; 19:653-667. [PMID: 37357557 DOI: 10.1039/d3mo00067b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Shexiang Baoxin Pill (SBP) has an excellent therapeutic effect on atherosclerosis (AS), but the combinational mechanisms of SBP against AS remain unclear. This study aimed to investigate the combinational mechanisms of SBP against AS by comprehensive network pharmacology and fecal metabolomic analysis. Bufonis venenum, one of the adjuvant medicines in SBP, is an animal medicine with a narrow therapeutic window. Considering animal protection, we evaluated the anti-AS effect of SBP without BV (SBP-BV) using ApoE-/- mouse models, culture cells, and metabolomic methods. Our data suggested that SBP showed remarkable anti-atherosclerotic effects through multiple targets and multiple pathways, while each component in SBP played different roles in their synergistic effect. Notably, SBP-BV showed comparable effects with SBP in the treatment of AS. Both SBP and SBP-BV could reduce cholesterol uptake in RAW264.7 cells and prevent the occurrence and development of AS in WD-induced ApoE-/- mice by attenuating the atherosclerotic plaque area, and reducing inflammatory cytokines and cholesterol levels in vivo. Our finding might provide new insights into the research and development of new anti-atherosclerosis drugs.
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Affiliation(s)
- Zhicong Wang
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China.
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Qianqian Wan
- Department of Integrated Chinese and Western Medicine, The Third Affiliated Hospital of Naval Medical University, Shanghai 200438, China.
| | - Bin Xie
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China.
| | - Zifan Zhu
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China.
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
| | - Xike Xu
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China.
| | - Peng Fu
- Changhai Hospital, Naval Medical University, Shanghai, 200433, China.
| | - Runhui Liu
- School of Pharmacy, Naval Medical University, Shanghai, 200433, China.
- School of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou, 350122, China
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Yang X, Zhang B, Wang S, Lu Y, Chen K, Luo C, Sun A, Zhang H. OTTM: an automated classification tool for translational drug discovery from omics data. Brief Bioinform 2023; 24:bbad301. [PMID: 37594310 PMCID: PMC10516341 DOI: 10.1093/bib/bbad301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/22/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023] Open
Abstract
Omics data from clinical samples are the predominant source of target discovery and drug development. Typically, hundreds or thousands of differentially expressed genes or proteins can be identified from omics data. This scale of possibilities is overwhelming for target discovery and validation using biochemical or cellular experiments. Most of these proteins and genes have no corresponding drugs or even active compounds. Moreover, a proportion of them may have been previously reported as being relevant to the disease of interest. To facilitate translational drug discovery from omics data, we have developed a new classification tool named Omics and Text driven Translational Medicine (OTTM). This tool can markedly narrow the range of proteins or genes that merit further validation via drug availability assessment and literature mining. For the 4489 candidate proteins identified in our previous proteomics study, OTTM recommended 40 FDA-approved or clinical trial drugs. Of these, 15 are available commercially and were tested on hepatocellular carcinoma Hep-G2 cells. Two drugs-tafenoquine succinate (an FDA-approved antimalarial drug targeting CYC1) and branaplam (a Phase 3 clinical drug targeting SMN1 for the treatment of spinal muscular atrophy)-showed potent inhibitory activity against Hep-G2 cell viability, suggesting that CYC1 and SMN1 may be potential therapeutic target proteins for hepatocellular carcinoma. In summary, OTTM is an efficient classification tool that can accelerate the discovery of effective drugs and targets using thousands of candidate proteins identified from omics data. The online and local versions of OTTM are available at http://otter-simm.com/ottm.html.
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Affiliation(s)
- Xiaobo Yang
- ShanghaiTech University
- School of Life Science and Technology, ShanghaiTech University, 393 Huaxiazhong Road, Shanghai 200031, China
| | - Bei Zhang
- Shanghai Institute of Materia Medica
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049, China
| | - Siqi Wang
- Beijing Proteome Research Center
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, and National Center for Protein Sciences (Beijing)
| | - Ye Lu
- Nanjing University of Chinese Medicine
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China; Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kaixian Chen
- academician medicinal scientist of the Chinese Academy of Sciences
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; School of Life Science and Technology, ShanghaiTech University, 393 Huaxiazhong Road, Shanghai 200031, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Cheng Luo
- Shanghai Institute of Materia Medica
- Chemical Biology Research Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Aihua Sun
- Beijing Proteome Research Center
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics; Research Unit of Proteomics-driven Cancer Precision Medicine, Chinese Academy of Medical Sciences
| | - Hao Zhang
- Shanghai Institute of Materia Medica
- Chemical Biology Research Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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130
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He S, Sun L, Chen J, Ouyang Y. Recent Advances and Perspectives in Relation to the Metabolomics-Based Study of Diabetic Retinopathy. Metabolites 2023; 13:1007. [PMID: 37755287 PMCID: PMC10536395 DOI: 10.3390/metabo13091007] [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: 08/13/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Diabetic retinopathy (DR), a prevalent microvascular complication of diabetes, is a major cause of acquired blindness in adults. Currently, a clinical diagnosis of DR primarily relies on fundus fluorescein angiography, with a limited availability of effective biomarkers. Metabolomics, a discipline dedicated to scrutinizing the response of various metabolites within living organisms, has shown noteworthy advancements in uncovering metabolic disorders and identifying key metabolites associated with DR in recent years. Consequently, this review aims to present the latest advancements in metabolomics techniques and comprehensively discuss the principal metabolic outcomes derived from analyzing blood, vitreous humor, aqueous humor, urine, and fecal samples.
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Affiliation(s)
| | | | | | - Yang Ouyang
- Department of Health Inspection and Quarantine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (S.H.)
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131
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Joshi AD, Rahnavard A, Kachroo P, Mendez KM, Lawrence W, Julián-Serrano S, Hua X, Fuller H, Sinnott-Armstrong N, Tabung FK, Shutta KH, Raffield LM, Darst BF. An epidemiological introduction to human metabolomic investigations. Trends Endocrinol Metab 2023; 34:505-525. [PMID: 37468430 PMCID: PMC10527234 DOI: 10.1016/j.tem.2023.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
Metabolomics holds great promise for uncovering insights around biological processes impacting disease in human epidemiological studies. Metabolites can be measured across biological samples, including plasma, serum, saliva, urine, stool, and whole organs and tissues, offering a means to characterize metabolic processes relevant to disease etiology and traits of interest. Metabolomic epidemiology studies face unique challenges, such as identifying metabolites from targeted and untargeted assays, defining standards for quality control, harmonizing results across platforms that often capture different metabolites, and developing statistical methods for high-dimensional and correlated metabolomic data. In this review, we introduce metabolomic epidemiology to the broader scientific community, discuss opportunities and challenges presented by these studies, and highlight emerging innovations that hold promise to uncover new biological insights.
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Affiliation(s)
- Amit D Joshi
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ali Rahnavard
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, The George Washington University, Washington, DC, USA
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kevin M Mendez
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wayne Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sachelly Julián-Serrano
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Public Health, University of Massachusetts Lowell, Lowell, MA, USA
| | - Xinwei Hua
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; Department of Cardiology, Peking University Third Hospital, Beijing, China
| | - Harriett Fuller
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nasa Sinnott-Armstrong
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Fred K Tabung
- The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH, USA
| | - Katherine H Shutta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Burcu F Darst
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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132
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Li W, Shao C, Li C, Zhou H, Yu L, Yang J, Wan H, He Y. Metabolomics: A useful tool for ischemic stroke research. J Pharm Anal 2023; 13:968-983. [PMID: 37842657 PMCID: PMC10568109 DOI: 10.1016/j.jpha.2023.05.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/14/2023] [Accepted: 05/29/2023] [Indexed: 10/17/2023] Open
Abstract
Ischemic stroke (IS) is a multifactorial and heterogeneous disease. Despite years of studies, effective strategies for the diagnosis, management and treatment of stroke are still lacking in clinical practice. Metabolomics is a growing field in systems biology. It is starting to show promise in the identification of biomarkers and in the use of pharmacometabolomics to help patients with certain disorders choose their course of treatment. The development of metabolomics has enabled further and more biological applications. Particularly, metabolomics is increasingly being used to diagnose diseases, discover new drug targets, elucidate mechanisms, and monitor therapeutic outcomes and its potential effect on precision medicine. In this review, we reviewed some recent advances in the study of metabolomics as well as how metabolomics might be used to identify novel biomarkers and understand the mechanisms of IS. Then, the use of metabolomics approaches to investigate the molecular processes and active ingredients of Chinese herbal formulations with anti-IS capabilities is summarized. We finally summarized recent developments in single cell metabolomics for exploring the metabolic profiles of single cells. Although the field is relatively young, the development of single cell metabolomics promises to provide a powerful tool for unraveling the pathogenesis of IS.
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Affiliation(s)
- Wentao Li
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chongyu Shao
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Chang Li
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Huifen Zhou
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Li Yu
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Jiehong Yang
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Haitong Wan
- School of Basic Medicine Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
| | - Yu He
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, 310053, China
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133
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Busi SB, Lei Z, Sumner LW, Amos-Landgraf JM. Integrated multi-omic analyses provide insight into colon adenoma susceptibility modulation by the gut microbiota. mSystems 2023; 8:e0015123. [PMID: 37458451 PMCID: PMC10469915 DOI: 10.1128/msystems.00151-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 06/06/2023] [Indexed: 09/01/2023] Open
Abstract
Colon cancer onset is strongly associated with the differences in microbial taxa in the gastrointestinal tract. Although recent studies highlight the role of individual taxa, the effect of a complex gut microbiome (GM) on the metabolome and host transcriptome is still unknown. We used a multi-omics approach to determine how differences in the GM affect the susceptibility to adenoma development in a rat model of human colon cancer. Ultra-high performance liquid chromatography mass spectrometry of feces collected prior to observable disease onset identified putative metabolite profiles that likely predict future disease severity. Transcriptome analyses performed after disease onset from normal colonic epithelium and tumor tissues show a correlation between GM and host gene expression. Integrated pathway analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis is enriched in rats with high tumors along with increased fatty acid metabolism and mucin biosynthesis. Targeted pyrosequencing of the Pirc allele indicates that the GM alters the mechanism of adenoma development and may drive an epigenetic pathway of tumor suppressor silencing. This study reveals how untargeted metabolomics identifies signatures of susceptibility and integrated analyses uncover pathways of differential mechanisms of loss of tumor suppressor gene function and for potential prevention and therapeutic intervention. IMPORTANCE The association between the gut microbiome and colon cancer is significant but difficult to test in model systems. This study highlights the association of differences in the pathogen-free gut microbiome to changes in the host transcriptome and metabolome that correlate with colon adenoma initiation and development in a rat genetic model of early colon cancer. The utilization of a multi-omics approach integrating metabolomics and transcriptomics reveals differences in pathways including bile acid biosynthesis and fatty acid metabolism. The study also shows that differences in gut microbiomes significantly alter the mechanism of adenoma formation, shifting from genetic changes to epigenetic changes that initiate the early loss of tumor suppressor function. These findings enhance our understanding of the gut microbiome's role in colon cancer susceptibility, offer insights into potential biomarkers and therapeutic targets, and may pave the way for future prevention and intervention strategies.
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Affiliation(s)
- Susheel Bhanu Busi
- University of Missouri School of Medicine, Columbia, Missouri, USA
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zhentian Lei
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- University of Missouri Metabolomics Center, Columbia, Missouri, USA
| | - Lloyd W. Sumner
- Department of Biochemistry, University of Missouri, Columbia, Missouri, USA
- University of Missouri Metabolomics Center, Columbia, Missouri, USA
| | - James M. Amos-Landgraf
- University of Missouri School of Medicine, Columbia, Missouri, USA
- University of Missouri College of Veterinary Medicine, Columbia, Missouri, USA
- Rat Resource and Research Center, University of Missouri, Columbia, Missouri, USA
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134
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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.
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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.
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135
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Choi E, Yoo WJ, Jang HY, Kim TY, Lee SK, Oh HB. Machine learning liquid chromatography retention time prediction model augments the dansylation strategy for metabolite analysis of urine samples. J Chromatogr A 2023; 1705:464167. [PMID: 37348224 DOI: 10.1016/j.chroma.2023.464167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/10/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
Herein, a standalone software equipped with a graphic user interface (GUI) is developed to predict liquid chromatography mass spectrometry (LC-MS) retention times (RTs) of dansylated metabolites. Dansylation metabolomics strategy developed by Li et al. narrows down a vast chemical space of metabolites into the metabolites containing amines and phenolic hydroxyls. Combined with differential isotope labeling, e.g., 12C-reagent labeled individual samples spiked with a 13C-reagent labeled reference or pooled sample, LC-MS analysis of the dansylated samples enables accurate relative quantification of all labeled metabolites. Herein, the LC-RTs for dansylated metabolites are predicted using an artificial neural network (ANN) machine-learning model. For the ANN modeling, 315 dansylated urine metabolites obtained from the DnsID database are used. The ANN LC-RT prediction model was reliable, with a mean absolute deviation of 0.74 min for the 30 min LC run. In the RT model, a deviation of more than 2 min was observed in only 3.2% of the total 315 metabolites, while a deviation of 1.5 min or more was observed in 11% of the metabolites. Furthermore, it was found that the LC-RT prediction was also reliable even for metabolites containing both amine and phenolic functional groups that can undergo dansylation on either one of the two functional groups, resulting in the generation of two isomeric forms. This RT-prediction model is embedded into a user-friendly GUI and can be used for identifying nontargeted dansylated metabolites with unknown RTs, along with accurate mass measurements. Furthermore, it is demonstrated that the developed software can help identify metabolites from a urine sample of an anonymous healthy pregnant woman.
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Affiliation(s)
- Eunwoo Choi
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Won Jun Yoo
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Hwa-Yong Jang
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea
| | - Tae-Young Kim
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Sung Ki Lee
- Department of Obstetrics and Gynecology, College of Medicine, Konyang University, Daejeon 35365, Republic of Korea.
| | - Han Bin Oh
- Department of Chemistry, Sogang University, Seoul 04107, Republic of Korea.
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136
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Pei C, Su R, Lu S, Chen X, Ding Y, Li R, Shu W, Zeng Y, Lin Y, Xu L, Mi Y, Wan J. Hollow multishelled heterostructures with enhanced performance for laser desorption/ionization mass spectrometry based metabolic diagnosis. J Mater Chem B 2023; 11:8206-8215. [PMID: 37554072 DOI: 10.1039/d3tb00766a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
High-performance metabolic diagnosis-based laser desorption/ionization mass spectrometry (LDI-MS) improves the precision diagnosis of diseases and subsequent treatment. Inorganic matrices are promising for the detection of metabolites by LDI-MS, while the structure and component impacts of the matrices on the LDI process are still under investigation. Here, we designed a multiple-shelled ZnMn2O4/(Co, Mn)(Co, Mn)2O4 (ZMO/CMO) as the matrix from calcined MOF-on-MOF for detecting metabolites in LDI-MS and clarified the synergistic impacts of multiple-shells and the heterostructure on LDI efficiency. The ZMO/CMO heterostructure allowed 3-5 fold signal enhancement compared with ZMO and CMO with the same morphology. Furthermore, the ZMO/CMO heterostructure with a triple-shelled hollow structure displayed a 3-fold signal enhancement compared to its nanoparticle counterpart. Taken together, the triple-shelled hollow ZMO/CMO exhibits 102-fold signal enhancement compared to the commercial matrix products (e.g., DHB and DHAP), allowing for sensitive metabolic profiling in bio-detection. We directly extracted metabolic patterns by the optimized triple-shelled hollow ZMO/CMO particle-assisted LDI-MS within 1 s using 100 nL of serum and used machine learning as the readout to distinguish hepatocellular carcinoma from healthy controls with the area under the curve value of 0.984. Our approach guides us in matrix design for LDI-MS metabolic analysis and drives the development of a nanomaterial-based LDI-MS platform toward precision diagnosis.
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Affiliation(s)
- Congcong Pei
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Rui Su
- Tianjin Second People's Hospital, Tianjin Medical University, Tianjin 300192, China.
- Tianjin Institute of Hepatology, Tianjin 300192, China
| | - Songting Lu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Xiaonan Chen
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Yajie Ding
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Rongxin Li
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Weikang Shu
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Yu Zeng
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Yingying Lin
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
| | - Liang Xu
- Tianjin Second People's Hospital, Tianjin Medical University, Tianjin 300192, China.
| | - Yuqiang Mi
- Tianjin Second People's Hospital, Tianjin Medical University, Tianjin 300192, China.
- Tianjin Institute of Hepatology, Tianjin 300192, China
| | - Jingjing Wan
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, P. R. China.
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137
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Khattab RH, Abo-Hammam RH, Salah M, Hanora AM, Shabayek S, Zakeer S. Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study. BMC Microbiol 2023; 23:238. [PMID: 37644393 PMCID: PMC10464353 DOI: 10.1186/s12866-023-02991-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique. RESULTS Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites. CONCLUSIONS Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.
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Affiliation(s)
- Randa H Khattab
- Department of Microbiology and Immunology, Al-Salam University, Tanta, Egypt
| | - Rana H Abo-Hammam
- Forensic toxicologist and narcotics expert, Ministry of Justice, Tanta, Egypt
| | - Mohammed Salah
- Department of Microbiology and Immunology, Faculty of pharmacy, Port-Said University, Port-Said, Egypt
| | - Amro M Hanora
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt.
| | - Sarah Shabayek
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
| | - Samira Zakeer
- Department of Microbiology and Immunology, Faculty of pharmacy, Suez Canal University, Ismailia, Egypt
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138
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Koussiouris J, Looby N, Kulasingam V, Chandran V. A Solid-Phase Microextraction-Liquid Chromatography-Mass Spectrometry Method for Analyzing Serum Lipids in Psoriatic Disease. Metabolites 2023; 13:963. [PMID: 37623906 PMCID: PMC10456752 DOI: 10.3390/metabo13080963] [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: 07/13/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Approximately 25% of psoriasis patients have an inflammatory arthritis termed psoriatic arthritis (PsA). There is strong interest in identifying and validating biomarkers that can accurately and reliably predict conversion from psoriasis to PsA using novel technologies such as metabolomics. Lipids, in particular, are of key interest in psoriatic disease. We sought to develop a liquid chromatography-mass spectrometry (LC-MS) method to be used in conjunction with solid-phase microextraction (SPME) for analyzing fatty acids and similar molecules. A total of 25 chromatographic methods based on published lipid studies were tested on two LC columns. As a proof of concept, serum samples from psoriatic disease patients (n = 27 psoriasis and n = 26 PsA) were processed using SPME and run on the selected LC-MS method. The method that was best for analyzing fatty acids and fatty acid-like molecules was optimized and applied to serum samples. A total of 18 tentatively annotated features classified as fatty acids and other lipid compounds were statistically significant between psoriasis and PsA groups using both multivariate and univariate approaches. The SPME-LC-MS method developed and optimized was capable of detecting fatty acids and similar lipids that may aid in differentiating psoriasis and PsA patients.
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Affiliation(s)
- John Koussiouris
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Nikita Looby
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Clinical Biochemistry, Laboratory Medicine Program, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Vinod Chandran
- Schroeder Arthritis Institute, Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada; (J.K.); (N.L.)
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada;
- Division of Rheumatology, Department of Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medicine, Memorial University, St. John’s, NL A1B 3V6, Canada
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139
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Corona G, Di Gregorio E, Buonadonna A, Lombardi D, Scalone S, Steffan A, Miolo G. Pharmacometabolomics of trabectedin in metastatic soft tissue sarcoma patients. Front Pharmacol 2023; 14:1212634. [PMID: 37637412 PMCID: PMC10450632 DOI: 10.3389/fphar.2023.1212634] [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: 04/26/2023] [Accepted: 07/20/2023] [Indexed: 08/29/2023] Open
Abstract
Objective: Trabectedin is an anti-cancer drug commonly used for the treatment of patients with metastatic soft tissue sarcoma (mSTS). Despite its recognized efficacy, significant variability in pharmacological response has been observed among mSTS patients. To address this issue, this pharmacometabolomics study aimed to identify pre-dose plasma metabolomics signatures that can explain individual variations in trabectedin pharmacokinetics and overall clinical response to treatment. Methods: In this study, 40 mSTS patients treated with trabectedin administered by 24 h-intravenous infusion at a dose of 1.5 mg/m2 were enrolled. The patients' baseline plasma metabolomics profiles, which included derivatives of amino acids and bile acids, were analyzed using multiple reaction monitoring LC-MS/MS together with their pharmacokinetics profile of trabectedin. Multivariate Partial least squares regression and univariate statistical analyses were utilized to identify correlations between baseline metabolite concentrations and trabectedin pharmacokinetics, while Partial Least Squares-Discriminant Analysis was employed to evaluate associations with clinical response. Results: The multiple regression model, derived from the correlation between the AUC of trabectedin and pre-dose metabolomics, exhibited the best performance by incorporating cystathionine, hemoglobin, taurocholic acid, citrulline, and the phenylalanine/tyrosine ratio. This model demonstrated a bias of 4.6% and a precision of 17.4% in predicting drug AUC, effectively accounting for up to 70% of the inter-individual pharmacokinetic variability. Through the use of Partial least squares-Discriminant Analysis, cystathionine and hemoglobin were identified as specific metabolic signatures that effectively distinguish patients with stable disease from those with progressive disease. Conclusions: The findings from this study provide compelling evidence to support the utilization of pre-dose metabolomics in uncovering the underlying causes of pharmacokinetic variability of trabectedin, as well as facilitating the identification of patients who are most likely to benefit from this treatment.
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Affiliation(s)
- Giuseppe Corona
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Emanuela Di Gregorio
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Angela Buonadonna
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Davide Lombardi
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Simona Scalone
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Gianmaria Miolo
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
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140
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Morales-González V, Galeano-Sánchez D, Covaleda-Vargas JE, Rodriguez Y, Monsalve DM, Pardo-Rodriguez D, Cala MP, Acosta-Ampudia Y, Ramírez-Santana C. Metabolic fingerprinting of systemic sclerosis: a systematic review. Front Mol Biosci 2023; 10:1215039. [PMID: 37614441 PMCID: PMC10442829 DOI: 10.3389/fmolb.2023.1215039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/27/2023] [Indexed: 08/25/2023] Open
Abstract
Introduction: Systemic sclerosis (SSc) is a chronic autoimmune disease, marked by an unpredictable course, high morbidity, and increased mortality risk that occurs especially in the diffuse and rapidly progressive forms of the disease, characterized by fibrosis of the skin and internal organs and endothelial dysfunction. Recent studies suggest that the identification of altered metabolic pathways may play a key role in understanding the pathophysiology of the disease. Therefore, metabolomics might be pivotal in a better understanding of these pathogenic mechanisms. Methods: Through a systematic review of the literature following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Guidelines (PRISMA), searches were done in the PubMed, EMBASE, Web of Science, and Scopus databases from 2000 to September 2022. Three researchers independently reviewed the literature and extracted the data based on predefined inclusion and exclusion criteria. Results: Of the screened studies, 26 fulfilled the inclusion criteria. A total of 151 metabolites were differentially distributed between SSc patients and healthy controls (HC). The main deregulated metabolites were those derived from amino acids, specifically homocysteine (Hcy), proline, alpha-N-phenylacetyl-L-glutamine, glutamine, asymmetric dimethylarginine (ADMA), citrulline and ornithine, kynurenine (Kyn), and tryptophan (Trp), as well as acylcarnitines associated with long-chain fatty acids and tricarboxylic acids such as citrate and succinate. Additionally, differences in metabolic profiling between SSc subtypes were identified. The diffuse cutaneous systemic sclerosis (dcSSc) subtype showed upregulated amino acid-related pathways involved in fibrosis, endothelial dysfunction, and gut dysbiosis. Lastly, potential biomarkers were evaluated for the diagnosis of SSc, the identification of the dcSSc subtype, pulmonary arterial hypertension, and interstitial lung disease. These potential biomarkers are within amino acids, nucleotides, carboxylic acids, and carbohydrate metabolism. Discussion: The altered metabolite mechanisms identified in this study mostly point to perturbations in amino acid-related pathways, fatty acid beta-oxidation, and in the tricarboxylic acid cycle, possibly associated with inflammation, vascular damage, fibrosis, and gut dysbiosis. Further studies in targeted metabolomics are required to evaluate potential biomarkers for diagnosis, prognosis, and treatment response.
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Affiliation(s)
- Victoria Morales-González
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Daniel Galeano-Sánchez
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Jaime Enrique Covaleda-Vargas
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Yhojan Rodriguez
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Diana M. Monsalve
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Daniel Pardo-Rodriguez
- Metabolomics Core Facility—MetCore, Vicepresidency for Research, Universidad de Los Andes, Bogotá, Colombia
| | - Mónica P. Cala
- Metabolomics Core Facility—MetCore, Vicepresidency for Research, Universidad de Los Andes, Bogotá, Colombia
| | - Yeny Acosta-Ampudia
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
| | - Carolina Ramírez-Santana
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad Del Rosario, Bogotá, Colombia
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141
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Eichie FO, Taiwo G, Idowu M, Sidney T, Treon E, Ologunagba D, Leal Y, Ogunade IM. Effects of bovine respiratory disease on the plasma metabolome of beef steers during the receiving period. Front Vet Sci 2023; 10:1239651. [PMID: 37601765 PMCID: PMC10436613 DOI: 10.3389/fvets.2023.1239651] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
The study aimed to investigate the impact of Bovine Respiratory Disease (BRD) on the metabolism of beef steers during a 35-d receiving period using plasma metabolomics. In this study, 77 newly weaned crossbred (Angus × Hereford) beef steers (BW = 206 ± 12 kg and age = 180 ± 17 days) were categorized into two groups: Healthy and Sick groups. The Sick group comprised beef steers diagnosed with BRD at any time during the 35-day period (n = 31), while the Healthy group did not show any signs of BRD (n = 46). Blood samples were collected from the coccygeal vessels on day 35, and plasma samples were subjected to targeted metabolomics analysis using Nuclear Magnetic Resonance spectroscopy. Data and statistical analyses, including biomarker and pathway enrichment analyses, were performed using Metaboanalyst 5.0. Results of the growth performance showed that sick steers had lower (p ≤ 0.05) ADG (1.44 vs. 1.64 kg/d) and higher (p = 0.01) feed:gain ratio (3.57 vs. 3.13) compared to healthy steers. A total of 50 metabolites were quantified. The partial least squares discriminant scores plot showed a slight separation between the two groups of steers, indicating some metabolic differences. Furthermore, the plasma concentrations of four metabolites (sarcosine, methionine, dimethyl sulfone, and L-histidine) were greater (p ≤ 0.05) in healthy steers compared to sick steers. Among these metabolites, sarcosine and methionine qualified as candidate biomarkers associated with BRD infection based on an area under the curve >0.70. Additionally, quantitative enrichment analysis revealed that cysteine and methionine metabolism was enriched in healthy steers compared to sick steers. This suggests that these metabolic pathways may play a role in the response to BRD infection. The findings of this study highlight the altered plasma metabolome in steers with BRD during the receiving period. Understanding these metabolic changes can contribute to the development of effective management strategies and nutritional interventions to mitigate the negative impact of BRD on beef cattle health and immune function.
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Affiliation(s)
| | | | | | | | | | | | | | - Ibukun M. Ogunade
- Division of Animal Science and Nutritional Science, West Virginia University, Morgantown, WV, United States
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142
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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.
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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
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143
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Selegato DM, Zanatta AC, Pilon AC, Veloso JH, Castro-Gamboa I. Application of feature-based molecular networking and MassQL for the MS/MS fragmentation study of depsipeptides. Front Mol Biosci 2023; 10:1238475. [PMID: 37593127 PMCID: PMC10427501 DOI: 10.3389/fmolb.2023.1238475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023] Open
Abstract
The Feature-based Molecular Networking (FBMN) is a well-known approach for mapping and identifying structures and analogues. However, in the absence of prior knowledge about the molecular class, assessing specific fragments and clusters requires time-consuming manual validation. This study demonstrates that combining FBMN and Mass Spec Query Language (MassQL) is an effective strategy for accelerating the decoding mass fragmentation pathways and identifying molecules with comparable fragmentation patterns, such as beauvericin and its analogues. To accomplish this objective, a spectral similarity network was built from ESI-MS/MS experiments of Fusarium oxysporum at various collision energies (CIDs) and paired with a MassQL search query for conserved beauvericin ions. FBMN analysis revealed that sodiated and protonated ions clustered differently, with sodiated adducts needing more collision energy and exhibiting a distinct fragmentation pattern. Based on this distinction, two sets of particular fragments were discovered for the identification of these hexadepsipeptides: ([M + H]+) m/z 134, 244, 262, and 362 and ([M + Na]+) m/z 266, 284 and 384. By using these fragments, MassQL accurately found other analogues of the same molecular class and annotated beauvericins that were not classified by FBMN alone. Furthermore, FBMN analysis of sodiated beauvericins at 70 eV revealed subclasses with distinct amino acid residues, allowing distinction between beauvericins (beauvericin and beauvericin D) and two previously unknown structural isomers with an unusual methionine sulfoxide residue. In summary, our integrated method revealed correlations between adduct types and fragmentation patterns, facilitated the detection of beauvericin clusters, including known and novel analogues, and allowed for the differentiation between structural isomers.
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Affiliation(s)
- Denise M. Selegato
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Ana C. Zanatta
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos (NPPNS), Faculdade de Ciências Farmacêuticas, São Paulo University (USP), São Paulo, Brazil
| | - Alan C. Pilon
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Juvenal H. Veloso
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
| | - Ian Castro-Gamboa
- Nucleus of Bioassays, Biosynthesis, and Ecophysiology of Natural Products (NuBBE), Institute of Chemistry, São Paulo State University (UNESP), Araraquara, Brazil
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144
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Singh A, Kinnebrew G, Hsu PC, Weng DY, Song MA, Reisinger SA, McElroy JP, Keller-Hamilton B, Ferketich AK, Freudenheim JL, Shields PG. Untargeted Metabolomics and Body Mass in Adolescents: A Cross-Sectional and Longitudinal Analysis. Metabolites 2023; 13:899. [PMID: 37623843 PMCID: PMC10456720 DOI: 10.3390/metabo13080899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Obesity in children and adolescents has increased globally. Increased body mass index (BMI) during adolescence carries significant long-term adverse health outcomes, including chronic diseases such as cardiovascular disease, stroke, diabetes, and cancer. Little is known about the metabolic consequences of changes in BMI in adolescents outside of typical clinical parameters. Here, we used untargeted metabolomics to assess changing BMI in male adolescents. Untargeted metabolomic profiling was performed on urine samples from 360 adolescents using UPLC-QTOF-MS. The study includes a baseline of 235 subjects in a discovery set and 125 subjects in a validation set. Of them, a follow-up of 81 subjects (1 year later) as a replication set was studied. Linear regression analysis models were used to estimate the associations of metabolic features with BMI z-score in the discovery and validation sets, after adjusting for age, race, and total energy intake (kcal) at false-discovery-rate correction (FDR) ≤ 0.1. We identified 221 and 16 significant metabolic features in the discovery and in the validation set, respectively. The metabolites associated with BMI z-score in validation sets are glycylproline, citrulline, 4-vinylsyringol, 3'-sialyllactose, estrone sulfate, carnosine, formiminoglutamic acid, 4-hydroxyproline, hydroxyprolyl-asparagine, 2-hexenoylcarnitine, L-glutamine, inosine, N-(2-Hydroxyphenyl) acetamide glucuronide, and galactosylhydroxylysine. Of those 16 features, 9 significant metabolic features were associated with a positive change in BMI in the replication set 1 year later. Histidine and arginine metabolism were the most affected metabolic pathways. Our findings suggest that obesity and its metabolic outcomes in the urine metabolome of children are linked to altered amino acids, lipid, and carbohydrate metabolism. These identified metabolites may serve as biomarkers and aid in the investigation of obesity's underlying pathological mechanisms. Whether these features are associated with the development of obesity, or a consequence of changing BMI, requires further study.
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Affiliation(s)
- Amarnath Singh
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210-1240, USA; (A.S.); (D.Y.W.)
| | - Garrett Kinnebrew
- Department of Biomedical Informatics, Biomedical Informatics Shared Resources (BISR), The Ohio State University, Columbus, OH 43210-1240, USA;
| | - Ping-Ching Hsu
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Daniel Y. Weng
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210-1240, USA; (A.S.); (D.Y.W.)
| | - Min-Ae Song
- College of Public Health, The Ohio State University, Columbus, OH 43210-1240, USA; (M.-A.S.); (A.K.F.)
| | - Sarah A. Reisinger
- Center for Tobacco Research, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210-1240, USA; (S.A.R.); (B.K.-H.)
| | - Joseph P. McElroy
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210-1240, USA;
| | - Brittney Keller-Hamilton
- Center for Tobacco Research, Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210-1240, USA; (S.A.R.); (B.K.-H.)
- Department of Internal Medicine, College of Medicine, The Ohio State University, Columbus, OH 43210-1240, USA
| | - Amy K. Ferketich
- College of Public Health, The Ohio State University, Columbus, OH 43210-1240, USA; (M.-A.S.); (A.K.F.)
| | - Jo L. Freudenheim
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY 14214, USA;
| | - Peter G. Shields
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210-1240, USA; (A.S.); (D.Y.W.)
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145
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Mirveis Z, Howe O, Cahill P, Patil N, Byrne HJ. Monitoring and modelling the glutamine metabolic pathway: a review and future perspectives. Metabolomics 2023; 19:67. [PMID: 37482587 PMCID: PMC10363518 DOI: 10.1007/s11306-023-02031-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023]
Abstract
BACKGROUND Analysis of the glutamine metabolic pathway has taken a special place in metabolomics research in recent years, given its important role in cell biosynthesis and bioenergetics across several disorders, especially in cancer cell survival. The science of metabolomics addresses the intricate intracellular metabolic network by exploring and understanding how cells function and respond to external or internal perturbations to identify potential therapeutic targets. However, despite recent advances in metabolomics, monitoring the kinetics of a metabolic pathway in a living cell in situ, real-time and holistically remains a significant challenge. AIM This review paper explores the range of analytical approaches for monitoring metabolic pathways, as well as physicochemical modeling techniques, with a focus on glutamine metabolism. We discuss the advantages and disadvantages of each method and explore the potential of label-free Raman microspectroscopy, in conjunction with kinetic modeling, to enable real-time and in situ monitoring of the cellular kinetics of the glutamine metabolic pathway. KEY SCIENTIFIC CONCEPTS Given its important role in cell metabolism, the ability to monitor and model the glutamine metabolic pathways are highlighted. Novel, label free approaches have the potential to revolutionise metabolic biosensing, laying the foundation for a new paradigm in metabolomics research and addressing the challenges in monitoring metabolic pathways in living cells.
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Affiliation(s)
- Zohreh Mirveis
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland.
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland.
| | - Orla Howe
- School of Biological, Health and Sport Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Paul Cahill
- School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Nitin Patil
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
- School of Physics and Optometric & Clinical Sciences, Technological University Dublin, City Campus, Grangegorman, Dublin 7, Ireland
| | - Hugh J Byrne
- FOCAS Research Institute, Technological University Dublin, City Campus, Camden Row, Dublin 8, Ireland
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146
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Chen Y, Xu W, Zhang W, Tong R, Yuan A, Li Z, Jiang H, Hu L, Huang L, Xu Y, Zhang Z, Sun M, Yan X, Chen AF, Qian K, Pu J. Plasma metabolic fingerprints for large-scale screening and personalized risk stratification of metabolic syndrome. Cell Rep Med 2023; 4:101109. [PMID: 37467725 PMCID: PMC10394172 DOI: 10.1016/j.xcrm.2023.101109] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/01/2023] [Accepted: 06/16/2023] [Indexed: 07/21/2023]
Abstract
Direct diagnosis and accurate assessment of metabolic syndrome (MetS) allow for prompt clinical interventions. However, traditional diagnostic strategies overlook the complex heterogeneity of MetS. Here, we perform metabolomic analysis in 13,554 participants from the natural cohort and identify 26 hub plasma metabolic fingerprints (PMFs) associated with MetS and its early identification (pre-MetS). By leveraging machine-learning algorithms, we develop robust diagnostic models for pre-MetS and MetS with convincing performance through independent validation. We utilize these PMFs to assess the relative contributions of the four major MetS risk factors in the general population, ranked as follows: hyperglycemia, hypertension, dyslipidemia, and obesity. Furthermore, we devise a personalized three-dimensional plasma metabolic risk (PMR) stratification, revealing three distinct risk patterns. In summary, our study offers effective screening tools for identifying pre-MetS and MetS patients in the general community, while defining the heterogeneous risk stratification of metabolic phenotypes in real-world settings.
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Affiliation(s)
- Yifan Chen
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Wei Xu
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Wei Zhang
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Renyang Tong
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Ancai Yuan
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Zheng Li
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Huiru Jiang
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Liuhua Hu
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Lin Huang
- Country Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yudian Xu
- School of Biomedical Engineering, Institute of Medical Robotics and Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ziyue Zhang
- School of Biomedical Engineering, Institute of Medical Robotics and Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Mingze Sun
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China
| | - Xiaoxiang Yan
- Department of Cardiovascular Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Alex F Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China.
| | - Kun Qian
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China; School of Biomedical Engineering, Institute of Medical Robotics and Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Jun Pu
- Division of Cardiology, State Key Laboratory of Systems Medicine for Cancer, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai 200127, China.
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147
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Fecke A, Saw NMMT, Kale D, Kasarla SS, Sickmann A, Phapale P. Quantitative Analytical and Computational Workflow for Large-Scale Targeted Plasma Metabolomics. Metabolites 2023; 13:844. [PMID: 37512551 PMCID: PMC10383057 DOI: 10.3390/metabo13070844] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/04/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Quantifying metabolites from various biological samples is necessary for the clinical and biomedical translation of metabolomics research. One of the ongoing challenges in biomedical metabolomics studies is the large-scale quantification of targeted metabolites, mainly due to the complexity of biological sample matrices. Furthermore, in LC-MS analysis, the response of compounds is influenced by their physicochemical properties, chromatographic conditions, eluent composition, sample preparation, type of MS ionization source, and analyzer used. To facilitate large-scale metabolite quantification, we evaluated the relative response factor (RRF) approach combined with an integrated analytical and computational workflow. This approach considers a compound's individual response in LC-MS analysis relative to that of a non-endogenous reference compound to correct matrix effects. We created a quantitative LC-MS library using the Skyline/Panorama web platform for data processing and public sharing of data. In this study, we developed and validated a metabolomics method for over 280 standard metabolites and quantified over 90 metabolites. The RRF quantification was validated and compared with conventional external calibration approaches as well as literature reports. The Skyline software environment was adapted for processing such metabolomics data, and the results are shared as a "quantitative chromatogram library" with the Panorama web application. This new workflow was found to be suitable for large-scale quantification of metabolites in human plasma samples. In conclusion, we report a novel quantitative chromatogram library with a targeted data analysis workflow for biomedical metabolomic applications.
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Affiliation(s)
- Antonia Fecke
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
- Department Hamm 2, Hochschule Hamm-Lippstadt, Marker-Allee 76-78, 59063 Hamm, Germany
| | - Nay Min Min Thaw Saw
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Dipali Kale
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Siva Swapna Kasarla
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
| | - Prasad Phapale
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Str. 6b, 44227 Dortmund, Germany
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148
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Li S, Siddiqa A, Thapa M, Chi Y, Zheng S. Trackable and scalable LC-MS metabolomics data processing using asari. Nat Commun 2023; 14:4113. [PMID: 37433854 DOI: 10.1038/s41467-023-39889-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 06/30/2023] [Indexed: 07/13/2023] Open
Abstract
Significant challenges remain in the computational processing of data from liquid chomratography-mass spectrometry (LC-MS)-based metabolomic experiments into metabolite features. In this study, we examine the issues of provenance and reproducibility using the current software tools. Inconsistency among the tools examined is attributed to the deficiencies of mass alignment and controls of feature quality. To address these issues, we develop the open-source software tool asari for LC-MS metabolomics data processing. Asari is designed with a set of specific algorithmic framework and data structures, and all steps are explicitly trackable. Asari compares favorably to other tools in feature detection and quantification. It offers substantial improvement in computational performance over current tools, and it is highly scalable.
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Affiliation(s)
- Shuzhao Li
- Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA.
- University of Connecticut School of Medicine, Farmington, CT, USA.
| | - Amnah Siddiqa
- Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Maheshwor Thapa
- Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Yuanye Chi
- Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
| | - Shujian Zheng
- Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, 06032, USA
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149
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Akash MSH, Yaqoob A, Rehman K, Imran M, Assiri MA, Al-Rashed F, Al-Mulla F, Ahmad R, Sindhu S. Metabolomics: a promising tool for deciphering metabolic impairment in heavy metal toxicities. Front Mol Biosci 2023; 10:1218497. [PMID: 37484533 PMCID: PMC10357477 DOI: 10.3389/fmolb.2023.1218497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023] Open
Abstract
Heavy metals are the metal compounds found in earth's crust and have densities higher than that of water. Common heavy metals include the lead, arsenic, mercury, cadmium, copper, manganese, chromium, nickel, and aluminum. Their environmental levels are consistently rising above the permissible limits and they are highly toxic as enter living systems via inhalation, ingestion, or inoculation. Prolonged exposures cause the disruption of metabolism, altered gene and/or protein expression, and dysregulated metabolite profiles. Metabolomics is a state of the art analytical tool widely used for pathomolecular inv22estigations, biomarkers, drug discovery and validation of biotransformation pathways in the fields of biomedicine, nutrition, agriculture, and industry. Here, we overview studies using metabolomics as a dynamic tool to decipher the mechanisms of metabolic impairment related to heavy metal toxicities caused by the environmental or experimental exposures in different living systems. These investigations highlight the key role of metabolomics in identifying perturbations in pathways of lipid and amino acid metabolism, with a critical role of oxidative stress in metabolic impairment. We present the conclusions with future perspectives on metabolomics applications in meeting emerging needs.
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Affiliation(s)
| | - Azka Yaqoob
- Department of Pharmaceutical Chemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Kanwal Rehman
- Department of Pharmacy, The Women University, Multan, Pakistan
| | - Muhammad Imran
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Mohammed A. Assiri
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
| | - Fatema Al-Rashed
- Immunology and Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Fahd Al-Mulla
- Research Division, Dasman Diabetes Institute, Dasman, Kuwait
| | - Rasheed Ahmad
- Immunology and Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
| | - Sardar Sindhu
- Immunology and Microbiology Department, Dasman Diabetes Institute, Dasman, Kuwait
- Animal and Imaging Core Facilities, Dasman Diabetes Institute, Dasman, Kuwait
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150
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Vahid F, Hajizadeghan K, Khodabakhshi A. Nutritional Metabolomics in Diet-Breast Cancer Relations: Current Research, Challenges, and Future Directions-A Review. Biomedicines 2023; 11:1845. [PMID: 37509485 PMCID: PMC10377267 DOI: 10.3390/biomedicines11071845] [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: 05/24/2023] [Revised: 06/21/2023] [Accepted: 06/24/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer is one of the most common types of cancer in women worldwide, and its incidence is increasing. Diet has been identified as a modifiable risk factor for breast cancer, but the complex interplay between diet, metabolism, and cancer development is not fully understood. Nutritional metabolomics is a rapidly evolving field that can provide insights into the metabolic changes associated with dietary factors and their impact on breast cancer risk. The review's objective is to provide a comprehensive overview of the current research on the application of nutritional metabolomics in understanding the relationship between diet and breast cancer. The search strategy involved querying several electronic databases, including PubMed, Scopus, Web of Science, and Google Scholar. The search terms included combinations of relevant keywords such as "nutritional metabolomics", "diet", "breast cancer", "metabolites", and "biomarkers". In this review, both in vivo and in vitro studies were included, and we summarize the current state of knowledge on the role of nutritional metabolomics in understanding the diet-breast cancer relationship, including identifying specific metabolites and metabolic pathways associated with breast cancer risk. We also discuss the challenges associated with nutritional metabolomics research, including standardization of analytical methods, interpretation of complex data, and integration of multiple-omics approaches. Finally, we highlight future directions for nutritional metabolomics research in studying diet-breast cancer relations, including investigating the role of gut microbiota and integrating multiple-omics approaches. The application of nutritional metabolomics in the study of diet-breast cancer relations, including 2-amino-4-cyano butanoic acid, piperine, caprate, rosten-3β,17β-diol-monosulfate, and γ-carboxyethyl hydrochroman, among others, holds great promise for advancing our understanding of the role of diet in breast cancer development and identifying personalized dietary recommendations for breast cancer prevention, control, and treatment.
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Affiliation(s)
- Farhad Vahid
- Nutrition and Health Research Group, Precision Health Department, Luxembourg Institute of Health, 1445 Strassen, Luxembourg
| | - Kimia Hajizadeghan
- Department of Nutrition, Faculty of Public Health, Kerman University of Medical Sciences, Kerman 7616913555, Iran
| | - Adeleh Khodabakhshi
- Department of Nutrition, Faculty of Public Health, Kerman University of Medical Sciences, Kerman 7616913555, Iran
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