1
|
Yoon JH, Lee D, Lee C, Cho E, Lee S, Cazenave-Gassiot A, Kim K, Chae S, Dennis EA, Suh PG. Paradigm shift required for translational research on the brain. Exp Mol Med 2024; 56:1043-1054. [PMID: 38689090 PMCID: PMC11148129 DOI: 10.1038/s12276-024-01218-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: 10/13/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 05/02/2024] Open
Abstract
Biomedical research on the brain has led to many discoveries and developments, such as understanding human consciousness and the mind and overcoming brain diseases. However, historical biomedical research on the brain has unique characteristics that differ from those of conventional biomedical research. For example, there are different scientific interpretations due to the high complexity of the brain and insufficient intercommunication between researchers of different disciplines owing to the limited conceptual and technical overlap of distinct backgrounds. Therefore, the development of biomedical research on the brain has been slower than that in other areas. Brain biomedical research has recently undergone a paradigm shift, and conducting patient-centered, large-scale brain biomedical research has become possible using emerging high-throughput analysis tools. Neuroimaging, multiomics, and artificial intelligence technology are the main drivers of this new approach, foreshadowing dramatic advances in translational research. In addition, emerging interdisciplinary cooperative studies provide insights into how unresolved questions in biomedicine can be addressed. This review presents the in-depth aspects of conventional biomedical research and discusses the future of biomedical research on the brain.
Collapse
Affiliation(s)
- Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea.
| | - Dongha Lee
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Chany Lee
- Cognitive Science Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Eunji Cho
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Seulah Lee
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry and Precision Medicine Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore, 117456, Singapore
| | - Kipom Kim
- Research Strategy Office, Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Sehyun Chae
- Neurovascular Unit Research Group, Korean Brain Research Institute, Daegu, 41062, Republic of Korea
| | - Edward A Dennis
- Department of Pharmacology and Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093-0601, USA
| | - Pann-Ghill Suh
- Korea Brain Research Institute, Daegu, 41062, Republic of Korea
| |
Collapse
|
2
|
Mulroy E, Erro R, Bhatia KP, Hallett M. Refining the clinical diagnosis of Parkinson's disease. Parkinsonism Relat Disord 2024; 122:106041. [PMID: 38360507 PMCID: PMC11069446 DOI: 10.1016/j.parkreldis.2024.106041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Our ability to define, understand, and classify Parkinson's disease (PD) has undergone significant changes since the disorder was first described in 1817. Clinical features and neuropathologic signatures can now be supplemented by in-vivo interrogation of genetic and biological substrates of disease, offering great opportunity for further refining the diagnosis of PD. In this mini-review, we discuss the historical perspectives which shaped our thinking surrounding the definition and diagnosis of PD. We highlight the clinical, genetic, pathologic and biologic diversity which underpins the condition, and proceed to discuss how recent developments in our ability to define biologic and pathologic substrates of disease might impact PD definition, diagnosis, individualised prognostication, and personalised clinical care. We argue that Parkinson's 'disease', as currently diagnosed in the clinic, is actually a syndrome. It is the outward manifestation of any array of potential dysfunctional biologic processes, neuropathological changes, and disease aetiologies, which culminate in common outward clinical features which we term PD; each person has their own unique disease, which we can now define with increasing precision. This is an exciting time in PD research and clinical care. Our ability to refine the clinical diagnosis of PD, incorporating in-vivo assessments of disease biology, neuropathology, and neurogenetics may well herald the era of biologically-based, precision medicine approaches PD management. With this however comes a number of challenges, including how to integrate these technologies into clinical practice in a way which is acceptable to patients, promotes meaningful changes to care, and minimises health economic impact.
Collapse
Affiliation(s)
- Eoin Mulroy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Roberto Erro
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Baronissi, (SA), Italy
| | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Mark Hallett
- Human Motor Control Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
3
|
de Lope EG, Loo RTJ, Rauschenberger A, Ali M, Pavelka L, Marques TM, Gomes CPC, Krüger R, Glaab E. Comprehensive blood metabolomics profiling of Parkinson's disease reveals coordinated alterations in xanthine metabolism. NPJ Parkinsons Dis 2024; 10:68. [PMID: 38503737 PMCID: PMC10951366 DOI: 10.1038/s41531-024-00671-9] [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: 09/18/2023] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Parkinson's disease (PD) is a highly heterogeneous disorder influenced by several environmental and genetic factors. Effective disease-modifying therapies and robust early-stage biomarkers are still lacking, and an improved understanding of the molecular changes in PD could help to reveal new diagnostic markers and pharmaceutical targets. Here, we report results from a cohort-wide blood plasma metabolic profiling of PD patients and controls in the Luxembourg Parkinson's Study to detect disease-associated alterations at the level of systemic cellular process and network alterations. We identified statistically significant changes in both individual metabolite levels and global pathway activities in PD vs. controls and significant correlations with motor impairment scores. As a primary observation when investigating shared molecular sub-network alterations, we detect pronounced and coordinated increased metabolite abundances in xanthine metabolism in de novo patients, which are consistent with previous PD case/control transcriptomics data from an independent cohort in terms of known enzyme-metabolite network relationships. From the integrated metabolomics and transcriptomics network analysis, the enzyme hypoxanthine phosphoribosyltransferase 1 (HPRT1) is determined as a potential key regulator controlling the shared changes in xanthine metabolism and linking them to a mechanism that may contribute to pathological loss of cellular adenosine triphosphate (ATP) in PD. Overall, the investigations revealed significant PD-associated metabolome alterations, including pronounced changes in xanthine metabolism that are mechanistically congruent with alterations observed in independent transcriptomics data. The enzyme HPRT1 may merit further investigation as a main regulator of these network alterations and as a potential therapeutic target to address downstream molecular pathology in PD.
Collapse
Affiliation(s)
- Elisa Gómez de Lope
- Biomedical Data Science, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rebecca Ting Jiin Loo
- Biomedical Data Science, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Armin Rauschenberger
- Biomedical Data Science, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Muhammad Ali
- Biomedical Data Science, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Lukas Pavelka
- Parkinson's Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Tainá M Marques
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Clarissa P C Gomes
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Parkinson's Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- Biomedical Data Science, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg.
| |
Collapse
|
4
|
Pan X, Donaghy PC, Roberts G, Chouliaras L, O’Brien JT, Thomas AJ, Heslegrave AJ, Zetterberg H, McGuinness B, Passmore AP, Green BD, Kane JPM. Plasma metabolites distinguish dementia with Lewy bodies from Alzheimer's disease: a cross-sectional metabolomic analysis. Front Aging Neurosci 2024; 15:1326780. [PMID: 38239488 PMCID: PMC10794326 DOI: 10.3389/fnagi.2023.1326780] [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: 10/24/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Background In multifactorial diseases, alterations in the concentration of metabolites can identify novel pathological mechanisms at the intersection between genetic and environmental influences. This study aimed to profile the plasma metabolome of patients with dementia with Lewy bodies (DLB) and Alzheimer's disease (AD), two neurodegenerative disorders for which our understanding of the pathophysiology is incomplete. In the clinical setting, DLB is often mistaken for AD, highlighting a need for accurate diagnostic biomarkers. We therefore also aimed to determine the overlapping and differentiating metabolite patterns associated with each and establish whether identification of these patterns could be leveraged as biomarkers to support clinical diagnosis. Methods A panel of 630 metabolites (Biocrates MxP Quant 500) and a further 232 metabolism indicators (biologically informative sums and ratios calculated from measured metabolites, each indicative for a specific pathway or synthesis; MetaboINDICATOR) were analyzed in plasma from patients with probable DLB (n = 15; age 77.6 ± 8.2 years), probable AD (n = 15; 76.1 ± 6.4 years), and age-matched cognitively healthy controls (HC; n = 15; 75.2 ± 6.9 years). Metabolites were quantified using a reversed-phase ultra-performance liquid chromatography column and triple-quadrupole mass spectrometer in multiple reaction monitoring (MRM) mode, or by using flow injection analysis in MRM mode. Data underwent multivariate (PCA analysis), univariate and receiving operator characteristic (ROC) analysis. Metabolite data were also correlated (Spearman r) with the collected clinical neuroimaging and protein biomarker data. Results The PCA plot separated DLB, AD and HC groups (R2 = 0.518, Q2 = 0.348). Significant alterations in 17 detected metabolite parameters were identified (q ≤ 0.05), including neurotransmitters, amino acids and glycerophospholipids. Glutamine (Glu; q = 0.045) concentrations and indicators of sphingomyelin hydroxylation (q = 0.039) distinguished AD and DLB, and these significantly correlated with semi-quantitative measurement of cardiac sympathetic denervation. The most promising biomarker differentiating AD from DLB was Glu:lysophosphatidylcholine (lysoPC a 24:0) ratio (AUC = 0.92; 95%CI 0.809-0.996; sensitivity = 0.90; specificity = 0.90). Discussion Several plasma metabolomic aberrations are shared by both DLB and AD, but a rise in plasma glutamine was specific to DLB. When measured against plasma lysoPC a C24:0, glutamine could differentiate DLB from AD, and the reproducibility of this biomarker should be investigated in larger cohorts.
Collapse
Affiliation(s)
- Xiaobei Pan
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Paul C. Donaghy
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Gemma Roberts
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Leonidas Chouliaras
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - John T. O’Brien
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
| | - Alan J. Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Amanda J. Heslegrave
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, United Kingdom
- Dementia Research Institute, UCL, London, United Kingdom
| | - Henrik Zetterberg
- Department of Neurodegenerative Disease, University College London Queen Square Institute of Neurology, London, United Kingdom
- Dementia Research Institute, UCL, London, United Kingdom
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Hong Kong Center for Neurodegenerative Diseases, Kowloon, Hong Kong SAR, China
- Wisconsin Alzheimer’s Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anthony P. Passmore
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| | - Brian D. Green
- School of Biological Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Joseph P. M. Kane
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| |
Collapse
|
5
|
Kawahata I, Fukunaga K. Pathogenic Impact of Fatty Acid-Binding Proteins in Parkinson's Disease-Potential Biomarkers and Therapeutic Targets. Int J Mol Sci 2023; 24:17037. [PMID: 38069360 PMCID: PMC10707307 DOI: 10.3390/ijms242317037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/26/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Parkinson's disease is a neurodegenerative condition characterized by motor dysfunction resulting from the degeneration of dopamine-producing neurons in the midbrain. This dopamine deficiency gives rise to a spectrum of movement-related symptoms, including tremors, rigidity, and bradykinesia. While the precise etiology of Parkinson's disease remains elusive, genetic mutations, protein aggregation, inflammatory processes, and oxidative stress are believed to contribute to its development. In this context, fatty acid-binding proteins (FABPs) in the central nervous system, FABP3, FABP5, and FABP7, impact α-synuclein aggregation, neurotoxicity, and neuroinflammation. These FABPs accumulate in mitochondria during neurodegeneration, disrupting their membrane potential and homeostasis. In particular, FABP3, abundant in nigrostriatal dopaminergic neurons, is responsible for α-synuclein propagation into neurons and intracellular accumulation, affecting the loss of mesencephalic tyrosine hydroxylase protein, a rate-limiting enzyme of dopamine biosynthesis. This review summarizes the characteristics of FABP family proteins and delves into the pathogenic significance of FABPs in the pathogenesis of Parkinson's disease. Furthermore, it examines potential novel therapeutic targets and early diagnostic biomarkers for Parkinson's disease and related neurodegenerative disorders.
Collapse
Affiliation(s)
- Ichiro Kawahata
- Department of CNS Drug Innovation, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
| | - Kohji Fukunaga
- Department of CNS Drug Innovation, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan;
- BRI Pharma Inc., Sendai 982-0804, Japan
| |
Collapse
|
6
|
Lai H, Li XY, Xu F, Zhu J, Li X, Song Y, Wang X, Wang Z, Wang C. Applications of Machine Learning to Diagnosis of Parkinson's Disease. Brain Sci 2023; 13:1546. [PMID: 38002506 PMCID: PMC10670005 DOI: 10.3390/brainsci13111546] [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: 09/27/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Accurate diagnosis of Parkinson's disease (PD) is challenging due to its diverse manifestations. Machine learning (ML) algorithms can improve diagnostic precision, but their generalizability across medical centers in China is underexplored. OBJECTIVE To assess the accuracy of an ML algorithm for PD diagnosis, trained and tested on data from different medical centers in China. METHODS A total of 1656 participants were included, with 1028 from Beijing (training set) and 628 from Fuzhou (external validation set). Models were trained using the least absolute shrinkage and selection operator-logistic regression (LASSO-LR), decision tree (DT), random forest (RF), eXtreme gradient boosting (XGboost), support vector machine (SVM), and k-nearest neighbor (KNN) techniques. Hyperparameters were optimized using five-fold cross-validation and grid search techniques. Model performance was evaluated using the area under the curve (AUC) of the receiver operating characteristic (ROC) curve, accuracy, sensitivity (recall), specificity, precision, and F1 score. Variable importance was assessed for all models. RESULTS SVM demonstrated the best differentiation between healthy controls (HCs) and PD patients (AUC: 0.928, 95% CI: 0.908-0.947; accuracy: 0.844, 95% CI: 0.814-0.871; sensitivity: 0.826, 95% CI: 0.786-0.866; specificity: 0.861, 95% CI: 0.820-0.898; precision: 0.849, 95% CI: 0.807-0.891; F1 score: 0.837, 95% CI: 0.803-0.868) in the validation set. Constipation, olfactory decline, and daytime somnolence significantly influenced predictability. CONCLUSION We identified multiple pivotal variables and SVM as a precise and clinician-friendly ML algorithm for prediction of PD in Chinese patients.
Collapse
Affiliation(s)
- Hong Lai
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
- Department of Neurology, The First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Xu-Ying Li
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Fanxi Xu
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Junge Zhu
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Xian Li
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Yang Song
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Xianlin Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Zhanjun Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| | - Chaodong Wang
- Department of Neurology, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Diseases, Beijing 100053, China; (H.L.); (X.-Y.L.); (F.X.); (J.Z.); (X.L.); (Y.S.); (X.W.); (Z.W.)
| |
Collapse
|
7
|
Fonseca TH, Von Rekowski CP, Araújo R, Oliveira MC, Justino G, Bento L, Calado CRC. The Impact of the Serum Extraction Protocol on Metabolomic Profiling Using UPLC-MS/MS and FTIR Spectroscopy. ACS OMEGA 2023; 8:20755-20766. [PMID: 37323376 PMCID: PMC10237515 DOI: 10.1021/acsomega.3c01370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Biofluid metabolomics is a very appealing tool to increase the knowledge associated with pathophysiological mechanisms leading to better and new therapies and biomarkers for disease diagnosis and prognosis. However, due to the complex process of metabolome analysis, including the metabolome isolation method and the platform used to analyze it, there are diverse factors that affect metabolomics output. In the present work, the impact of two protocols to extract the serum metabolome, one using methanol and another using a mixture of methanol, acetonitrile, and water, was evaluated. The metabolome was analyzed by ultraperformance liquid chromatography associated with tandem mass spectrometry (UPLC-MS/MS), based on reverse-phase and hydrophobic chromatographic separations, and Fourier transform infrared (FTIR) spectroscopy. The two extraction protocols of the metabolome were compared over the analytical platforms (UPLC-MS/MS and FTIR spectroscopy) concerning the number of features, the type of features, common features, and the reproducibility of extraction replicas and analytical replicas. The ability of the extraction protocols to predict the survivability of critically ill patients hospitalized at an intensive care unit was also evaluated. The FTIR spectroscopy platform was compared to the UPLC-MS/MS platform and, despite not identifying metabolites and consequently not contributing as much as UPLC-MS/MS in terms of information concerning metabolic information, it enabled the comparison of the two extraction protocols as well as the development of very good predictive models of patient's survivability, such as the UPLC-MS/MS platform. Furthermore, FTIR spectroscopy is based on much simpler procedures and is rapid, economic, and applicable in the high-throughput mode, i.e., enabling the simultaneous analysis of hundreds of samples in the microliter range in a couple of hours. Therefore, FTIR spectroscopy represents a very interesting complementary technique not only to optimize processes as the metabolome isolation but also for obtaining biomarkers such as those for disease prognosis.
Collapse
Affiliation(s)
- Tiago
A. H. Fonseca
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Cristiana P. Von Rekowski
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Rúben Araújo
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - M. Conceição Oliveira
- Centro
de Química Estrutural, Institute of Molecular Sciences, Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal
| | - Gonçalo
C. Justino
- Centro
de Química Estrutural, Institute of Molecular Sciences, Instituto
Superior Técnico, Universidade de
Lisboa, Av. Rovisco Pais, 1, 1049-001 Lisboa, Portugal
| | - Luís Bento
- Intensive
Care Department, Centro Hospitalar Universitário
de Lisboa Central (CHULC), Rua José António Serrano, 1150-199 Lisboa, Portugal
- Integrated
Pathophysiological Mechanisms, CHRC, NOVA Medical School, Faculdade
de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Campo Mártires da Pátria, 130, 1169-056 Lisboa, Portugal
| | - Cecília R. C. Calado
- Instituto
Superior de Engenharia de Lisboa (ISEL), Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
- Centro
de Investigação em Modelação e Optimização
de Sistemas Multifuncionais (CIMOSM), Instituto Superior de Engenharia
de Lisboa (ISEL), Instituto Politécnico
de Lisboa, Rua Conselheiro
Emídio Navarro 1, 1959-007 Lisboa, Portugal
| |
Collapse
|
8
|
Lan TT, Chang L, Hou LW, Wang ZZ, Li DC, Ren ZH, Gu T, Wang JW, Chen GS. Serum metabolomics analysis revealed metabolic disorders in Parkinson's disease. Medicine (Baltimore) 2023; 102:e33715. [PMID: 37335671 DOI: 10.1097/md.0000000000033715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Parkinson's disease (PD) is by now the second of the most prevalent neurodegenerative diseases in the world, and its incidence is increasing rapidly as the global population ages, with 14.2 million PD patients expected worldwide by 2040. METHODS We gathered a completion of 45 serum samples, including 15 of healthy controls and 30 from the PD group. We used non-targeted metabolomics analysis based on liquid chromatography-mass spectrometry to identify the molecular changes in PD patients, and conducted bioinformatics analysis on this basis to explore the possible pathogenesis of PD. RESULTS We found significant metabolomics changes in the levels of 30 metabolites in PD patients compared with healthy controls. CONCLUSION Lipids and lipid-like molecules accounted for the majority of the 30 differentially expressed metabolites. Also, pathway enrichment analysis showed significant enrichment in sphingolipid metabolic pathway. These assessments can improve our perception on the underlying mechanism of PD as well as facilitate a better targeting on therapeutic interventions.
Collapse
Affiliation(s)
- Tian-Tian Lan
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Le Chang
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Li-Wei Hou
- People's Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Zhen-Zhen Wang
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Dong-Chu Li
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Zi-Han Ren
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Tao Gu
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Jian-Wen Wang
- Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Gui-Sheng Chen
- Department of Neurology, Ningxia Medical University General Hospital, Yinchuan, China
- Cranial Laboratory of Ningxia Medical University, Yinchuan, China
| |
Collapse
|
9
|
LeWitt PA, Li J, Wu KH, Lu M. Diagnostic metabolomic profiling of Parkinson's disease biospecimens. Neurobiol Dis 2023; 177:105962. [PMID: 36563791 DOI: 10.1016/j.nbd.2022.105962] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Reliable and sensitive biomarkers are needed for enhancing and predicting Parkinson's disease (PD) diagnosis. OBJECTIVE To investigate comprehensive metabolomic profiling of biochemicals in CSF and serum for determining diagnostic biomarkers of PD. METHODS Fifty subjects, symptomatic with PD for ≥5 years, were matched to 50 healthy controls (HCs). We used ultrahigh-performance liquid chromatography linked to tandem mass spectrometry (UHPLC-MS/MS) for measuring relative concentrations of ≤1.5 kDalton biochemicals. A reference library created from authentic standards facilitated chemical identifications. Analytes underwent univariate analysis for PD association, with false discovery rate-adjusted p-value (≤0.05) determinations. Multivariate analysis (for identifying a panel of biochemicals discriminating PD from HCs) used several biostatistical methods, including logistic LASSO regression. RESULTS Comparing PD and HCs, strong differentiation was achieved from CSF but not serum specimens. With univariate analysis, 21 CSF compounds exhibited significant differential concentrations. Logistic LASSO regression led to selection of 23 biochemicals (11 shared with those determined by the univariate analysis). The selected compounds, as a group, distinguished PD from HCs, with Area-Under-the-Receiver-Operating-Characteristic (ROC) curve of 0.897. With optimal cutoff, logistic LASSO achieved 100% sensitivity and 96% specificity (and positive and negative predictive values of 96% and 100%). Ten-fold cross-validation gave 84% sensitivity and 82% specificity (and 82% positive and 84% negative predictive values). From the logistic LASSO-chosen regression model, 2 polyamine metabolites (N-acetylcadaverine and N-acetylputrescine) were chosen and had the highest fold-changes in comparing PD to HCs. Another chosen biochemical, acisoga (N-(3-acetamidopropyl)pyrrolidine-2-one), also is a polyamine metabolism derivative. CONCLUSIONS UHPLC-MS/MS assays provided a metabolomic signature highly predictive of PD. These findings provide further evidence for involvement of polyamine pathways in the neurodegeneration of PD.
Collapse
Affiliation(s)
- Peter A LeWitt
- Departments of Neurology, Henry Ford Hospital, West Bloomfield, MI, USA; Wayne State University School of Medicine, West Bloomfield, MI, USA.
| | - Jia Li
- The Department of Public Health Science, Henry Ford Health System, Detroit, MI, USA
| | - Kuan-Han Wu
- The Department of Public Health Science, Henry Ford Health System, Detroit, MI, USA
| | - Mei Lu
- The Department of Public Health Science, Henry Ford Health System, Detroit, MI, USA
| |
Collapse
|
10
|
Zacharias HU, Kaleta C, Cossais F, Schaeffer E, Berndt H, Best L, Dost T, Glüsing S, Groussin M, Poyet M, Heinzel S, Bang C, Siebert L, Demetrowitsch T, Leypoldt F, Adelung R, Bartsch T, Bosy-Westphal A, Schwarz K, Berg D. Microbiome and Metabolome Insights into the Role of the Gastrointestinal-Brain Axis in Parkinson's and Alzheimer's Disease: Unveiling Potential Therapeutic Targets. Metabolites 2022; 12:metabo12121222. [PMID: 36557259 PMCID: PMC9786685 DOI: 10.3390/metabo12121222] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's disease (AD), the prevalence of which is rapidly rising due to an aging world population and westernization of lifestyles, are expected to put a strong socioeconomic burden on health systems worldwide. Clinical trials of therapies against PD and AD have only shown limited success so far. Therefore, research has extended its scope to a systems medicine point of view, with a particular focus on the gastrointestinal-brain axis as a potential main actor in disease development and progression. Microbiome and metabolome studies have already revealed important insights into disease mechanisms. Both the microbiome and metabolome can be easily manipulated by dietary and lifestyle interventions, and might thus offer novel, readily available therapeutic options to prevent the onset as well as the progression of PD and AD. This review summarizes our current knowledge on the interplay between microbiota, metabolites, and neurodegeneration along the gastrointestinal-brain axis. We further illustrate state-of-the art methods of microbiome and metabolome research as well as metabolic modeling that facilitate the identification of disease pathomechanisms. We conclude with therapeutic options to modulate microbiome composition to prevent or delay neurodegeneration and illustrate potential future research directions to fight PD and AD.
Collapse
Affiliation(s)
- Helena U. Zacharias
- Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, 30625 Hannover, Germany
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Correspondence: (H.U.Z.); (C.K.)
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Correspondence: (H.U.Z.); (C.K.)
| | | | - Eva Schaeffer
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Henry Berndt
- Research Group Comparative Immunobiology, Zoological Institute, Kiel University, 24118 Kiel, Germany
| | - Lena Best
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Thomas Dost
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Kiel University, 24105 Kiel, Germany
| | - Svea Glüsing
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
| | - Mathieu Groussin
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Mathilde Poyet
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sebastian Heinzel
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Institute of Medical Informatics and Statistics, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Leonard Siebert
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Functional Nanomaterials, Department of Materials Science, Kiel University, 24143 Kiel, Germany
| | - Tobias Demetrowitsch
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
- Kiel Network of Analytical Spectroscopy and Mass Spectrometry, Kiel University, 24118 Kiel, Germany
| | - Frank Leypoldt
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
- Neuroimmunology, Institute of Clinical Chemistry, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Rainer Adelung
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Functional Nanomaterials, Department of Materials Science, Kiel University, 24143 Kiel, Germany
| | - Thorsten Bartsch
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Anja Bosy-Westphal
- Institute of Human Nutrition and Food Science, Kiel University, 24107 Kiel, Germany
| | - Karin Schwarz
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Institute of Human Nutrition and Food Science, Food Technology, Kiel University, 24118 Kiel, Germany
- Kiel Network of Analytical Spectroscopy and Mass Spectrometry, Kiel University, 24118 Kiel, Germany
| | - Daniela Berg
- Kiel Nano, Surface and Interface Science—KiNSIS, Kiel University, 24118 Kiel, Germany
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| |
Collapse
|
11
|
Gątarek P, Sekulska-Nalewajko J, Bobrowska-Korczaka B, Pawełczyk M, Jastrzębski K, Głąbiński A, Kałużna-Czaplińska J. Plasma Metabolic Disturbances in Parkinson's Disease Patients. Biomedicines 2022; 10:biomedicines10123005. [PMID: 36551761 PMCID: PMC9775245 DOI: 10.3390/biomedicines10123005] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/24/2022] Open
Abstract
Plasma from patients with Parkinson's disease (PD) is a valuable source of information indicating altered metabolites associated with the risk or progression of the disease. Neurotoxicity of dopaminergic neurons, which is triggered by aggregation of α-synuclein, is the main pathogenic feature of PD. However, a growing body of scientific reports indicates that metabolic changes may precede and directly contribute to neurodegeneration. Identification and characterization of the abnormal metabolic pattern in patients' plasma are therefore crucial for the search for potential PD biomarkers. The aims of the present study were (1) to identify metabolic alterations in plasma metabolome in subjects with PD as compared with the controls; (2) to find new potential markers, some correlations among them; (3) to identify metabolic pathways relevant to the pathophysiology of PD. Plasma samples from patients with PD (n = 25) and control group (n = 12) were collected and the gas chromatography-time-of-flight-mass spectrometry GC-TOFMS-based metabolomics approach was used to evaluate the metabolic changes based on the identified 14 metabolites with significantly altered levels using univariate and multivariate statistical analysis. The panel, including 6 metabolites (L-3-methoxytyrosine, aconitic acid, L-methionine, 13-docosenamide, hippuric acid, 9,12-octadecadienoic acid), was identified to discriminate PD from controls with the area under the curve (AUC) of 0.975, with an accuracy of 92%. We also used statistical criteria to identify the significantly altered level of metabolites. The metabolic pathways involved were associated with linoleic acid metabolism, mitochondrial electron transport chain, glycerolipid metabolism, and bile acid biosynthesis. These abnormal metabolic changes in the plasma of patients with PD were mainly related to the amino acid metabolism, TCA cycle metabolism, and mitochondrial function.
Collapse
Affiliation(s)
- Paulina Gątarek
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
- CONEM Poland Chemistry and Nutrition Research Group, Lodz University of Technology, 90-924 Lodz, Poland
- Correspondence: (P.G.); (J.K.-C.); Tel.: +48-426-313-091 (J.K.-C.); Fax: +48-426-313-128 (J.K.-C.)
| | | | | | - Małgorzata Pawełczyk
- Department of Neurology and Stroke, Medical University of Lodz, 90-549 Lodz, Poland
| | - Karol Jastrzębski
- Department of Neurology and Stroke, Medical University of Lodz, 90-549 Lodz, Poland
| | - Andrzej Głąbiński
- Department of Neurology and Stroke, Medical University of Lodz, 90-549 Lodz, Poland
| | - Joanna Kałużna-Czaplińska
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
- CONEM Poland Chemistry and Nutrition Research Group, Lodz University of Technology, 90-924 Lodz, Poland
- Correspondence: (P.G.); (J.K.-C.); Tel.: +48-426-313-091 (J.K.-C.); Fax: +48-426-313-128 (J.K.-C.)
| |
Collapse
|
12
|
Solana-Manrique C, Sanz FJ, Torregrosa I, Palomino-Schätzlein M, Hernández-Oliver C, Pineda-Lucena A, Paricio N. Metabolic Alterations in a Drosophila Model of Parkinson's Disease Based on DJ-1 Deficiency. Cells 2022; 11:cells11030331. [PMID: 35159141 PMCID: PMC8834223 DOI: 10.3390/cells11030331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 12/13/2022] Open
Abstract
Parkinson’s disease (PD) is the second-most common neurodegenerative disorder, whose physiopathology is still unclear. Moreover, there is an urgent need to discover new biomarkers and therapeutic targets to facilitate its diagnosis and treatment. Previous studies performed in PD models and samples from PD patients already demonstrated that metabolic alterations are associated with this disease. In this context, the aim of this study is to provide a better understanding of metabolic disturbances underlying PD pathogenesis. To achieve this goal, we used a Drosophila PD model based on inactivation of the DJ-1β gene (ortholog of human DJ-1). Metabolomic analyses were performed in 1-day-old and 15-day-old DJ-1β mutants and control flies using 1H nuclear magnetic resonance spectroscopy, combined with expression and enzymatic activity assays of proteins implicated in altered pathways. Our results showed that the PD model flies exhibited protein metabolism alterations, a shift fromthe tricarboxylic acid cycle to glycolytic pathway to obtain ATP, together with an increase in the expression of some urea cycle enzymes. Thus, these metabolic changes could contribute to PD pathogenesis and might constitute possible therapeutic targets and/or biomarkers for this disease.
Collapse
Affiliation(s)
- Cristina Solana-Manrique
- Departamento de Genética, Facultad CC Biológicas, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, 46100 Burjassot, Spain; (C.S.-M.); (F.J.S.); (I.T.)
| | - Francisco José Sanz
- Departamento de Genética, Facultad CC Biológicas, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, 46100 Burjassot, Spain; (C.S.-M.); (F.J.S.); (I.T.)
| | - Isabel Torregrosa
- Departamento de Genética, Facultad CC Biológicas, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, 46100 Burjassot, Spain; (C.S.-M.); (F.J.S.); (I.T.)
| | | | - Carolina Hernández-Oliver
- Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (C.H.-O.); (A.P.-L.)
| | - Antonio Pineda-Lucena
- Instituto de Investigación Sanitaria La Fe, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain; (C.H.-O.); (A.P.-L.)
- Programa de Terapias Moleculares, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain
| | - Nuria Paricio
- Departamento de Genética, Facultad CC Biológicas, Instituto Universitario de Biotecnología y Biomedicina (BIOTECMED), Universidad de Valencia, 46100 Burjassot, Spain; (C.S.-M.); (F.J.S.); (I.T.)
- Correspondence: ; Tel.: +34-96-354-3005; Fax: +34-96-354-3029
| |
Collapse
|