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Dahabiyeh LA, Nimer RM, Wells JD, Abu-rish EY, Fiehn O. Diagnosing Parkinson's disease and monitoring its progression: Biomarkers from combined GC-TOF MS and LC-MS/MS untargeted metabolomics. Heliyon 2024; 10:e30452. [PMID: 38720721 PMCID: PMC11077040 DOI: 10.1016/j.heliyon.2024.e30452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 04/20/2024] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder with a poorly understood etiology. An accurate diagnosis of idiopathic PD remains challenging as misdiagnosis is common in routine clinical practice. Moreover, current therapeutics focus on symptomatic management rather than curing or slowing down disease progression. Therefore, identification of potential PD biomarkers and providing a better understanding of the underlying disease pathophysiology are urgent. Herein, hydrophilic interaction liquid chromatography-mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-TOF MS) based metabolomics approaches were used to profile the serum metabolome of 50 patients with different stages of idiopathic PD (early, mid and advanced) and 45 age-matched controls. Levels of 57 metabolites including cysteine-S-sulfate and N-acetyl tryptophan were significantly higher in patients with PD compared to controls, with lower amounts of additional 51 metabolites including vanillic acid, and N-acetylaspartic acid. Xanthines, including caffeine and its downstream metabolites, were lowered in patients with PD relative to controls indicating a potential role caffeine and its metabolites against neuronal damage. Seven metabolites, namely cysteine-S-sulfate, 1-methylxanthine, vanillic acid, N-acetylaspartic acid, 3-N-acetyl tryptophan, 5-methoxytryptophol, and 13-HODE yielded a ROC curve with a high classification accuracy (AUC 0.977). Comparison between different PD stages showed that cysteine-S-sulfate levels were significantly increasing with the advancement of PD stages while LPI 20:4 was significantly decreasing with disease progression. Our findings provide new biomarker candidates to assist in the diagnosis of PD and monitor its progression. Unusual metabolites like cysteine-S-sulfate might point to therapeutic targets that could enhance the development of novel PD treatments, such as NMDA antagonists.
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Affiliation(s)
- Lina A. Dahabiyeh
- Department of Pharmaceutical Sciences, School of Pharmacy, The University of Jordan, 11942, Amman, Jordan
- West Coast Metabolomics Center, University of California, Davis, Sacramento, CA, USA
| | - Refat M. Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, 22110, Irbid, Jordan
| | - Jeremiah D. Wells
- West Coast Metabolomics Center, University of California, Davis, Sacramento, CA, USA
| | - Eman Y. Abu-rish
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Sacramento, CA, USA
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Lu C, Cai X, Zhi S, Wen X, Shen J, Ercoli T, Simula ER, Masala C, Sechi LA, Solla P. Exploring the Association between Cathepsin B and Parkinson's Disease. Brain Sci 2024; 14:482. [PMID: 38790460 PMCID: PMC11119263 DOI: 10.3390/brainsci14050482] [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: 04/09/2024] [Revised: 04/30/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
OBJECTIVE The aim of this study is to investigate the association between Cathepsin B and Parkinson's Disease (PD), with a particular focus on determining the role of N-acetylaspartate as a potential mediator. METHODS We used summary-level data from Genome-Wide Association Studies (GWAS) for a two-sample Mendelian randomization (MR) analysis, exploring the association between Cathepsin B (3301 cases) and PD (4681 cases). A sequential two-step MR approach was applied (8148 cases) to study the role of N-acetylaspartate. RESULTS The MR analysis yielded that genetically predicted elevated Cathepsin B levels correlated with a reduced risk of developing PD (p = 0.0133, OR: 0.9171, 95% CI: 0.8563-0.9821). On the other hand, the analysis provided insufficient evidence to determine that PD affected Cathepsin B levels (p = 0.8567, OR: 1.0035, 95% CI: 0.9666-1.0418). The estimated effect of N-acetylaspartate in this process was 7.52% (95% CI = -3.65% to 18.69%). CONCLUSIONS This study suggested that elevated Cathepsin B levels decreased the risk of developing PD, with the mediation effect of N-acetylaspartate. Further research is needed to better understand this relationship.
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Affiliation(s)
- Changhao Lu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy;
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (E.R.S.); (L.A.S.)
| | - Xinyi Cai
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Department of Pathology, Shantou University Medical College, Shantou 515041, China;
| | - Shilin Zhi
- Department of Gastrointestinal Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China;
| | - Xiaofen Wen
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou 515041, China;
| | - Jiaxin Shen
- Department of Hematology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China;
| | - Tommaso Ercoli
- Department of Neurology, University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy
| | - Elena Rita Simula
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (E.R.S.); (L.A.S.)
| | - Carla Masala
- Department of Biomedical Sciences, University of Cagliari, SP 8 Cittadella Universitaria, 09042 Monserrato, Italy;
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (E.R.S.); (L.A.S.)
- Struttura Complessa di Microbiologia e Virologia, Azienda Ospedaliera Universitaria di Sassari, 07100 Sassari, Italy
| | - Paolo Solla
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy;
- Department of Neurology, University of Sassari, Viale S. Pietro 10, 07100 Sassari, Italy
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Choudhury FK, Premkumar V, Zecha J, Boyd J, Gaynor AS, Guo Z, Martin T, Cimbro R, Allman EL, Hess S. Multiomics Characterization of a Less Invasive Microfluidic-Based Cell Sorting Technique. J Proteome Res 2024. [PMID: 38417049 DOI: 10.1021/acs.jproteome.3c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Fluorescence-activated cell sorting (FACS) is a specialized technique to isolate specific cell subpopulations with a high level of recovery and accuracy. However, the cell sorting procedure can impact the viability and metabolic state of cells. Here, we performed a comparative study and evaluated the impact of traditional high-pressure charged droplet-based and microfluidic chip-based sorting on the metabolic and phosphoproteomic profile of different cell types. While microfluidic chip-based sorted cells more closely resembled the unsorted control group for most cell types tested, the droplet-based sorted cells showed significant metabolic and phosphoproteomic alterations. In particular, greater changes in redox and energy status were present in cells sorted with the droplet-based cell sorter along with larger shifts in proteostasis. 13C-isotope tracing analysis on cells recovering postsorting revealed that the sorter-induced suppression of mitochondrial TCA cycle activity recovered faster in the microfluidic chip-based sorted group. Apart from this, amino acid and lipid biosynthesis pathways were suppressed in sorted cells, with minimum impact and faster recovery in the microfluidic chip-based sorted group. These results indicate microfluidic chip-based sorting has a minimum impact on metabolism and is less disruptive compared to droplet-based sorting.
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Affiliation(s)
- Feroza K Choudhury
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Viji Premkumar
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jana Zecha
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Jonathan Boyd
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Andrew S Gaynor
- Oncology Cell Therapy, ICC, Oncology R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Zengli Guo
- Biologics Engineering, Cell Therapeutics and Viral Technologies, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Tom Martin
- Biologics Engineering, Oncology TTD, ADC, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Raffaello Cimbro
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB2 0AA, United Kingdom
| | - Erik L Allman
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
| | - Sonja Hess
- Dynamic Omics, Centre for Genomics Research (CGR), Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland 20878, United States
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Lu H, Zhang H, Wu Z, Li L. Microbiota-gut-liver-brain axis and hepatic encephalopathy. MICROBIOME RESEARCH REPORTS 2024; 3:17. [PMID: 38841407 PMCID: PMC11149093 DOI: 10.20517/mrr.2023.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 06/07/2024]
Abstract
Hepatic encephalopathy (HE) is a clinical manifestation of neurological and psychiatric abnormalities that are caused by complications of liver dysfunction including hyperammonemia, hyperuricemia, and portal hypertension. Accumulating evidence suggests that HE could be reversed through therapeutic modifications of gut microbiota. Multiple preclinical and clinical studies have indicated that gut microbiome affects the physiological function of the liver, such as the regulation of metabolism, secretion, and immunity, through the gut-liver crosstalk. In addition, gut microbiota also influences the brain through the gut-brain crosstalk, altering its physiological functions including the regulation of the immune, neuroendocrine, and vagal pathways. Thus, key molecules that are involved in the microbiota-gut-liver-brain axis might be able to serve as clinical biomarkers for early diagnosis of HE, and could be effective therapeutic targets for clinical interventions. In this review, we summarize the pathophysiology of HE and further propose approaches modulating the microbiota-gut-liver-brain axis in order to provide a comprehensive understanding of the prevention and potential clinical treatment for HE with a microbiota-targeted therapy.
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Affiliation(s)
| | | | | | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang, China
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Ramírez-Acosta S, Huertas-Abril PV, Selma-Royo M, Prieto-Álamo MJ, Collado MC, Abril N, García-Barrera T. The role of selenium in shaping mice brain metabolome and selenoproteome through the gut-brain axis by combining metabolomics, metallomics, gene expression and amplicon sequencing. J Nutr Biochem 2023; 117:109323. [PMID: 36958417 DOI: 10.1016/j.jnutbio.2023.109323] [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: 08/18/2022] [Revised: 02/17/2023] [Accepted: 03/16/2023] [Indexed: 03/25/2023]
Abstract
Selenium (Se) is a trace element crucial for human health. Recently, the impact of Se supplementation on gut microbiota has been pointed out as well as its influence on the expression of certain selenoproteins and gut metabolites. This study aims to elucidate the link between Se supplementation, brain selenoproteins and brain metabolome as well as the possible connection with the gut-brain axis. To this end, an in vivo study with 40 BALB/c mice was carried out. The study included conventional (n=20) and mice model with microbiota depleted by antibiotics (n=20) under a regular or Se supplemented diet. Brain selenoproteome was determined by a transcriptomic/gene expression profile, while brain metabolome and gut microbiota profiles were accomplished by untargeted metabolomics and amplicon sequencing, respectively. The total content of Se in brain was also determined. The selenoproteins genes Dio and Gpx isoenzymes, SelenoH, SelenoI, SelenoT, SelenoV and SelenoW and 31 metabolites were significantly altered in the brain after Se supplementation in conventional mice, while 11 selenoproteins and 26 metabolites were altered in microbiota depleted mice. The main altered brain metabolites were related to glyoxylate and dicarboxylate metabolism, amino acid metabolism, and gut microbiota that have been previously related with the gut-brain axis (e.g., members of Lachnospiraceae and Ruminococcaceae families). Moreover, specific associations were determined between brain selenoproteome and metabolome, which correlated with the same bacteria, suggesting an intertwined mechanism. Our results demonstrated the effect of Se on brain metabolome through specific selenoproteins gene expression and gut microbiota.
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Affiliation(s)
- Sara Ramírez-Acosta
- Research Center of Natural Resources, Health and the Environment (RENSMA). Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., 21007, Huelva, Spain
| | - Paula V Huertas-Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Marta Selma-Royo
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Department of Biotechnology, Agustin Escardino 7. 46980 Paterna, Valencia, Spain
| | - Maria J Prieto-Álamo
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - M Carmen Collado
- Institute of Agrochemistry and Food Technology (IATA-CSIC), Department of Biotechnology, Agustin Escardino 7. 46980 Paterna, Valencia, Spain
| | - Nieves Abril
- Department of Biochemistry and Molecular Biology, University of Córdoba, Campus de Rabanales, Edificio Severo Ochoa, E-14071, Córdoba, Spain
| | - Tamara García-Barrera
- Research Center of Natural Resources, Health and the Environment (RENSMA). Department of Chemistry, Faculty of Experimental Sciences, University of Huelva, Fuerzas Armadas Ave., 21007, Huelva, Spain.
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Wang Y, Yang H, Geerts C, Furtos A, Waters P, Cyr D, Wang S, Mitchell GA. The multiple facets of acetyl-CoA metabolism: Energetics, biosynthesis, regulation, acylation and inborn errors. Mol Genet Metab 2023; 138:106966. [PMID: 36528988 DOI: 10.1016/j.ymgme.2022.106966] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022]
Abstract
Acetyl-coenzyme A (Ac-CoA) is a core metabolite with essential roles throughout cell physiology. These functions can be classified into energetics, biosynthesis, regulation and acetylation of large and small molecules. Ac-CoA is essential for oxidative metabolism of glucose, fatty acids, most amino acids, ethanol, and of free acetate generated by endogenous metabolism or by gut bacteria. Ac-CoA cannot cross lipid bilayers, but acetyl groups from Ac-CoA can shuttle across membranes as part of carrier molecules like citrate or acetylcarnitine, or as free acetate or ketone bodies. Ac-CoA is the basic unit of lipid biosynthesis, providing essentially all of the carbon for the synthesis of fatty acids and of isoprenoid-derived compounds including cholesterol, coenzyme Q and dolichols. High levels of Ac-CoA in hepatocytes stimulate lipid biosynthesis, ketone body production and the diversion of pyruvate metabolism towards gluconeogenesis and away from oxidation; low levels exert opposite effects. Acetylation changes the properties of molecules. Acetylation is necessary for the synthesis of acetylcholine, acetylglutamate, acetylaspartate and N-acetyl amino sugars, and to metabolize/eliminate some xenobiotics. Acetylation is a major post-translational modification of proteins. Different types of protein acetylation occur. The most-studied form occurs at the epsilon nitrogen of lysine residues. In histones, lysine acetylation can alter gene transcription. Acetylation of other proteins has diverse, often incompletely-documented effects. Inborn errors related to Ac-CoA feature a broad spectrum of metabolic, neurological and other features. To date, a small number of studies of animals with inborn errors of CoA thioesters has included direct measurement of acyl-CoAs. These studies have shown that low levels of tissue Ac-CoA correlate with the development of clinical signs, hinting that shortage of Ac-CoA may be a recurrent theme in these conditions. Low levels of Ac-CoA could potentially disrupt any of its roles.
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Affiliation(s)
- Youlin Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Hao Yang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Chloé Geerts
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Alexandra Furtos
- Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - Paula Waters
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Denis Cyr
- Medical Genetics Service, Department of Laboratory Medicine, CHU Sherbrooke and Department of Pediatrics, Université de Sherbrooke, Québec, Canada
| | - Shupei Wang
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada
| | - Grant A Mitchell
- Medical Genetics Service, Department of Pediatrics and Research Center, CHU Sainte-Justine and Université de Montréal, Montréal, Québec, Canada.
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TMAO to the rescue of pathogenic protein variants. Biochim Biophys Acta Gen Subj 2022; 1866:130214. [PMID: 35902028 DOI: 10.1016/j.bbagen.2022.130214] [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: 02/03/2022] [Revised: 07/11/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Trimethylamine N-oxide (TMAO) is a chemical chaperone found in various organisms including humans. Various studies unveiled that it is an excellent protein-stabilizing agent, and induces folding of unstructured proteins. It is also well established that it can counteract the deleterious effects of urea, salt, and hydrostatic pressure on macromolecular integrity. There is also existence of large body of data regarding its ability to restore functional deficiency of various mutant proteins or pathogenic variants by correcting misfolding defects and inhibiting the formation of high-order toxic protein oligomers. Since an important class of human disease called "protein conformational disorders" is due to protein misfolding and/or formation of high-order oligomers, TMAO stands as a promising molecule for the therapeutic intervention of such diseases. The present review has been designed to gather a comprehensive knowledge of the TMAO's effect on the functional restoration of various mutants, identify its shortcomings and explore its potentiality as a lead molecule. Future prospects have also been suitably incorporated.
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Li X, Fan X, Yang H, Liu Y. Review of Metabolomics-Based Biomarker Research for Parkinson's Disease. Mol Neurobiol 2021; 59:1041-1057. [PMID: 34826053 DOI: 10.1007/s12035-021-02657-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/17/2021] [Indexed: 01/12/2023]
Abstract
Parkinson's disease (PD), as the second most common neurodegenerative disease, is seriously affecting the life quality of the elderly. However, there is still a lack of efficient medical methods to diagnosis PD before apparent symptoms occur. In recent years, clinical biomarkers including genetic, imaging, and tissue markers have exhibited remarkable benefits in assisting PD diagnoses. Due to the advantages of high-throughput detection of metabolites and almost non-invasive sample collection, metabolomics research of PD is widely used for diagnostic biomarker discovery. However, there are also a few shortages for those identified biomarkers, such as the scarcity of verifications regarding the sensitivity and specificity. Thus, reviewing the research progress of PD biomarkers based on metabolomics techniques is of great significance for developing PD diagnosis. To comprehensively clarify the progress of current metabolic biomarker studies in PD, we reviewed 20 research articles regarding the discovery and validation of biomarkers for PD diagnosis from three mainstream academic databases (NIH PubMed, ISI Web of Science, and Elsevier ScienceDirect). By analyzing those materials, we summarized the metabolic biomarkers identified by those metabolomics studies and discussed the potential approaches used for biomarker verifications. In conclusion, this review provides a comprehensive and updated overview of PD metabolomics research in the past two decades and particularly discusses the validation of disease biomarkers. We hope those discussions might provide inspiration for PD biomarker discovery and verification in the future.
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Affiliation(s)
- Xin Li
- School of Pharmaceutical Sciences, Liaoning University, No. 66 Chongshan Middle Road, Huanggu District, Liaoning Province, 110036, Shenyang, People's Republic of China
| | - Xiaoying Fan
- School of Pharmaceutical Sciences, Liaoning University, No. 66 Chongshan Middle Road, Huanggu District, Liaoning Province, 110036, Shenyang, People's Republic of China
| | - Hongtian Yang
- School of Pharmaceutical Sciences, Liaoning University, No. 66 Chongshan Middle Road, Huanggu District, Liaoning Province, 110036, Shenyang, People's Republic of China
| | - Yufeng Liu
- School of Pharmaceutical Sciences, Liaoning University, No. 66 Chongshan Middle Road, Huanggu District, Liaoning Province, 110036, Shenyang, People's Republic of China. .,Natural Products Pharmaceutical Engineering Technology Research Center of Liaoning Province, Shenyang, 110036, People's Republic of China.
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