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Luo X, Liu Y, Balck A, Klein C, Fleming RMT. Identification of metabolites reproducibly associated with Parkinson's Disease via meta-analysis and computational modelling. NPJ Parkinsons Dis 2024; 10:126. [PMID: 38951523 PMCID: PMC11217404 DOI: 10.1038/s41531-024-00732-z] [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: 07/27/2023] [Accepted: 05/30/2024] [Indexed: 07/03/2024] Open
Abstract
Many studies have reported metabolomic analysis of different bio-specimens from Parkinson's disease (PD) patients. However, inconsistencies in reported metabolite concentration changes make it difficult to draw conclusions as to the role of metabolism in the occurrence or development of Parkinson's disease. We reviewed the literature on metabolomic analysis of PD patients. From 74 studies that passed quality control metrics, 928 metabolites were identified with significant changes in PD patients, but only 190 were replicated with the same changes in more than one study. Of these metabolites, 60 exclusively increased, such as 3-methoxytyrosine and glycine, 54 exclusively decreased, such as pantothenic acid and caffeine, and 76 inconsistently changed in concentration in PD versus control subjects, such as ornithine and tyrosine. A genome-scale metabolic model of PD and corresponding metabolic map linking most of the replicated metabolites enabled a better understanding of the dysfunctional pathways of PD and the prediction of additional potential metabolic markers from pathways with consistent metabolite changes to target in future studies.
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Affiliation(s)
- Xi Luo
- School of Medicine, University of Galway, University Rd, Galway, Ireland
| | - Yanjun Liu
- School of Medicine, University of Galway, University Rd, Galway, Ireland
| | - Alexander Balck
- Institute of Neurogenetics and Department of Neurology, University of Luebeck and University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Christine Klein
- Institute of Neurogenetics and Department of Neurology, University of Luebeck and University Hospital Schleswig-Holstein, Luebeck, Germany
| | - Ronan M T Fleming
- School of Medicine, University of Galway, University Rd, Galway, Ireland.
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands.
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2
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Jiang Z, Sun Y, Liu S. Association between human blood metabolites and cerebral cortex architecture: evidence from a Mendelian randomization study. Front Neurol 2024; 15:1386844. [PMID: 38784905 PMCID: PMC11111910 DOI: 10.3389/fneur.2024.1386844] [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: 02/16/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
Background Dysregulation of circulating metabolites may affect brain function and cognition, associated with alterations in the cerebral cortex architecture. However, the exact cause remains unclear. This study aimed to determine the causal effect of circulating metabolites on the cerebral cortex architecture. Methods This study utilized retrieved data from genome-wide association studies to investigate the relationship between blood metabolites and cortical architecture. A total of 1,091 metabolites and 309 metabolite ratios were used for exposure. The brain cortex surface area and cortex thickness were selected as the primary outcomes in this study. In this study, the inverse variance weighting method was used as the main analytical method, complemented by sensitivity analyses that were more robust to pleiotropy. Furthermore, metabolic pathway analysis was performed via MetaboAnalyst 6.0. Finally, reverse Mendelian randomization (MR) analysis was conducted to assess the potential for reverse causation. Results After correcting for the false discovery rate (FDR), we identified 37 metabolites and 9 metabolite ratios that showed significant causal associations with cortical structures. Among these, Oxalate was found to be most strongly associated with cortical surface area (β: 2387.532, 95% CI 756.570-4018.495, p = 0.037), while Tyrosine was most correlated with cortical thickness (β: -0.015, 95% CI -0.005 to -0.025, p = 0.025). Furthermore, pathway analysis based on metabolites identified six significant metabolic pathways associated with cortical structures and 13 significant metabolic pathways based on metabolite ratios. Conclusion The identified metabolites and relevant metabolic pathways reveal potential therapeutic pathways for reducing the risk of neurodegenerative diseases. These findings will help guide health policies and clinical practice in treating neurodegenerative diseases.
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Affiliation(s)
- Zongzhi Jiang
- Department of Neurology, China-Japan Union Hospital, Jilin University, Changchun, China
| | - Yining Sun
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Songyan Liu
- Department of Neurology, China-Japan Union Hospital, Jilin University, Changchun, China
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3
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Li S, Liu Y, Lu S, Xu J, Liu X, Yang D, Yang Y, Hou L, Li N. A crazy trio in Parkinson's disease: metabolism alteration, α-synuclein aggregation, and oxidative stress. Mol Cell Biochem 2024:10.1007/s11010-024-04985-3. [PMID: 38625515 DOI: 10.1007/s11010-024-04985-3] [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: 01/13/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024]
Abstract
Parkinson's disease (PD) is an aging-associated neurodegenerative disorder, characterized by the progressive loss of dopaminergic neurons in the pars compacta of the substantia nigra and the presence of Lewy bodies containing α-synuclein within these neurons. Oligomeric α-synuclein exerts neurotoxic effects through mitochondrial dysfunction, glial cell inflammatory response, lysosomal dysfunction and so on. α-synuclein aggregation, often accompanied by oxidative stress, is generally considered to be a key factor in PD pathology. At present, emerging evidences suggest that metabolism alteration is closely associated with α-synuclein aggregation and PD progression, and improvement of key molecules in metabolism might be potentially beneficial in PD treatment. In this review, we highlight the tripartite relationship among metabolic changes, α-synuclein aggregation, and oxidative stress in PD, and offer updated insights into the treatments of PD, aiming to deepen our understanding of PD pathogenesis and explore new therapeutic strategies for the disease.
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Affiliation(s)
- Sheng Li
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Yanbing Liu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Sen Lu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Jiayi Xu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiaokun Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Di Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Yuxuan Yang
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Lin Hou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China
| | - Ning Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, 266071, China.
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4
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de Souza HMR, Pereira TTP, de Sá HC, Alves MA, Garrett R, Canuto GAB. Critical Factors in Sample Collection and Preparation for Clinical Metabolomics of Underexplored Biological Specimens. Metabolites 2024; 14:36. [PMID: 38248839 PMCID: PMC10819689 DOI: 10.3390/metabo14010036] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
This review article compiles critical pre-analytical factors for sample collection and extraction of eight uncommon or underexplored biological specimens (human breast milk, ocular fluids, sebum, seminal plasma, sweat, hair, saliva, and cerebrospinal fluid) under the perspective of clinical metabolomics. These samples are interesting for metabolomics studies as they reflect the status of living organisms and can be applied for diagnostic purposes and biomarker discovery. Pre-collection and collection procedures are critical, requiring protocols to be standardized to avoid contamination and bias. Such procedures must consider cleaning the collection area, sample stimulation, diet, and food and drug intake, among other factors that impact the lack of homogeneity of the sample group. Precipitation of proteins and removal of salts and cell debris are the most used sample preparation procedures. This review intends to provide a global view of the practical aspects that most impact results, serving as a starting point for the designing of metabolomic experiments.
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Affiliation(s)
- Hygor M. R. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
| | - Tássia T. P. Pereira
- Departamento de Genética, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Hanna C. de Sá
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
| | - Marina A. Alves
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil;
| | - Rafael Garrett
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
- Department of Laboratory Medicine, Boston Children’s Hospital—Harvard Medical School, Boston, MA 02115, USA
| | - Gisele A. B. Canuto
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
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5
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Zagare A, Preciat G, Nickels SL, Luo X, Monzel AS, Gomez-Giro G, Robertson G, Jaeger C, Sharif J, Koseki H, Diederich NJ, Glaab E, Fleming RMT, Schwamborn JC. Omics data integration suggests a potential idiopathic Parkinson's disease signature. Commun Biol 2023; 6:1179. [PMID: 37985891 PMCID: PMC10662437 DOI: 10.1038/s42003-023-05548-w] [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: 06/30/2023] [Accepted: 11/06/2023] [Indexed: 11/22/2023] Open
Abstract
The vast majority of Parkinson's disease cases are idiopathic. Unclear etiology and multifactorial nature complicate the comprehension of disease pathogenesis. Identification of early transcriptomic and metabolic alterations consistent across different idiopathic Parkinson's disease (IPD) patients might reveal the potential basis of increased dopaminergic neuron vulnerability and primary disease mechanisms. In this study, we combine systems biology and data integration approaches to identify differences in transcriptomic and metabolic signatures between IPD patient and healthy individual-derived midbrain neural precursor cells. Characterization of gene expression and metabolic modeling reveal pyruvate, several amino acid and lipid metabolism as the most dysregulated metabolic pathways in IPD neural precursors. Furthermore, we show that IPD neural precursors endure mitochondrial metabolism impairment and a reduced total NAD pool. Accordingly, we show that treatment with NAD precursors increases ATP yield hence demonstrating a potential to rescue early IPD-associated metabolic changes.
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Affiliation(s)
- Alise Zagare
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - German Preciat
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA, Leiden, The Netherlands
| | - Sarah L Nickels
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Xi Luo
- School of Medicine, University of Galway, University Rd, Galway, Ireland
| | - Anna S Monzel
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Graham Robertson
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Christian Jaeger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS), Kanagawa, 230-0045, Japan
| | - Nico J Diederich
- Centre Hospitalier de Luxembourg (CHL), 4, Rue Nicolas Ernest Barblé, L-1210, Luxembourg, Luxembourg
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg
| | - Ronan M T Fleming
- Metabolomics and Analytics Center, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA, Leiden, The Netherlands
- School of Medicine, University of Galway, University Rd, Galway, Ireland
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, 7, Avenue des Hauts-Fourneaux, 4362, Esch-sur-Alzette, Luxembourg.
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Huang Q, Chen C, Zhang Z, Xue Q. Anti-inflammatory effects of myristic acid mediated by the NF-κB pathway in lipopolysaccharide-induced BV-2 microglial cells. Mol Omics 2023; 19:726-734. [PMID: 37466104 DOI: 10.1039/d3mo00063j] [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: 07/20/2023]
Abstract
Parkinson's disease (PD) is a serious neurodegenerative disorder wherein changes in metabolites related to lipids, glutathione, and energy metabolism occur. Currently, metabolite changes in PD have been reported, yet their role in the prognosis of disease remains poorly understood. Functional metabolites can be used to diagnose diseases, especially PD, and can exert neuroprotective effects. This study used a PD animal model and a lipopolysaccharide (LPS)-mediated inflammatory response model (using the BV-2 mouse microglial cell line) to identify functional metabolites that can identify important metabolic disorders during PD, and comprehensively evaluated their profiles using a metabolomics-based approach. Our results showed that co-treatment with myristic acid and heptadecanoic acid downregulated the expression of interleukin (IL)-1β, IL-6, and tumor necrosis factor-α in BV-2 cells. Additionally, myristic acid and 10 μM heptadecanoic acid significantly inhibited the LPS-induced inflammatory response through the nuclear factor-κB pathway in BV-2 microglial cells, which provides a potential approach for PD treatment. Myristic acid and heptadecanoic acid were the active metabolites found by active metabolomics technology, but at present, there is no research report about their function for PD treatment, and our findings offer a novel research strategy for PD diagnosis and treatment.
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Affiliation(s)
- Qiong Huang
- Department of Neurology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Chunyan Chen
- Department of Neurology, Tongren Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200336, China
| | - Zhongxiao Zhang
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China.
- Department of Anesthesiology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Qun Xue
- Department of Neurology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China.
- Institute of Clinical Immunology, Jiangsu Key Laboratory of Clinical Immunology, First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
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7
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Qiu J, Wei L, Su Y, Tang Y, Peng G, Wu Y, He Y, Liu H, Guo W, Wu Z, Xu P, Mo M. Lipid Metabolism Disorder in Cerebrospinal Fluid Related to Parkinson's Disease. Brain Sci 2023; 13:1166. [PMID: 37626522 PMCID: PMC10452343 DOI: 10.3390/brainsci13081166] [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: 04/24/2023] [Revised: 07/26/2023] [Accepted: 07/29/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Abnormal accumulation of lipids is found in dopamine neurons and resident microglia in the substantia nigra of patients with Parkinson's disease (PD). The accumulation of lipids is an important risk factor for PD. Previous studies have mainly focussed on lipid metabolism in peripheral blood, but little attention has been given to cerebrospinal fluid (CSF). We drew the lipidomic signature in CSF from PD patients and evaluated the role of lipids in CSF as biomarkers for PD diagnosis. METHODS Based on lipidomic approaches, we investigated and compared lipid metabolism in CSF from PD patients and healthy controls without dyslipidaemia in peripheral blood and explored the relationship of lipids between CSF and serum by Pearson correlation analysis. RESULTS A total of 231 lipid species were detected and classified into 13 families in the CSF. The lipid families, including phosphatidylcholine (PC), sphingomyelin (SM) and cholesterol ester (CE), had significantly increased expression compared with the control. Hierarchical clustering was performed to distinguish PD patients based on the significantly changed expression of 34 lipid species. Unsupervised and supervised methods were used to refine this classification. A total of 12 lipid species, including 3-hydroxy-dodecanoyl-carnitine, Cer(d18:1/24:1), CE(20:4), CE(22:6), PC(14:0/18:2), PC(O-18:3/20:2), PC(O-20:2/24:3), SM(d18:0/16:0), SM(d18:2/14:0), SM(d18:2/24:1), SM(d18:1/20:1) and SM(d18:1/12:0), were selected to draw the lipidomic signature of PD. Correlation analysis was performed and showed that the CE family and CE (22:6) in CSF had a positive association with total cholesterol in the peripheral blood from PD patients but not from healthy controls. CONCLUSIONS Our results revealed that the lipidomic signature in CSF may be considered a potential biomarker for PD diagnosis, and increased CE, PC and SM in CSF may reveal pathological changes in PD patients, such as blood-brain barrier leakage.
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Affiliation(s)
- Jiewen Qiu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Lijian Wei
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Yilin Su
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Yuting Tang
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Guoyou Peng
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Yimin Wu
- Department of General Medicine, Fengxian Community Health Service Center, Shanghai 210499, China;
| | - Yan He
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Hanqun Liu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Wenyuan Guo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Zhuohu Wu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Pingyi Xu
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
| | - Mingshu Mo
- Department of Neurology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China; (J.Q.); (L.W.); (Y.S.); (Y.T.); (G.P.); (Y.H.); (H.L.); (W.G.); (Z.W.)
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Kalecký K, Bottiglieri T. Targeted metabolomic analysis in Parkinson's disease brain frontal cortex and putamen with relation to cognitive impairment. NPJ Parkinsons Dis 2023; 9:84. [PMID: 37270646 PMCID: PMC10239505 DOI: 10.1038/s41531-023-00531-y] [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: 10/22/2022] [Accepted: 05/22/2023] [Indexed: 06/05/2023] Open
Abstract
We performed liquid chromatography tandem mass spectrometry analysis with the targeted metabolomic kit Biocrates MxP Quant 500, in human brain cortex (Brodmann area 9) and putamen, to reveal metabolic changes characteristic of Parkinson's disease (PD) and PD-related cognitive decline. This case-control study involved 101 subjects (33 PD without dementia, 32 PD with dementia (cortex only), 36 controls). We found changes associated with PD, cognitive status, levodopa levels, and disease progression. The affected pathways include neurotransmitters, bile acids, homocysteine metabolism, amino acids, TCA cycle, polyamines, β-alanine metabolism, fatty acids, acylcarnitines, ceramides, phosphatidylcholines, and several microbiome-derived metabolites. Previously reported levodopa-related homocysteine accumulation in cortex still best explains the dementia status in PD, which can be modified by dietary supplementation. Further investigation is needed to reveal the exact mechanisms behind this pathological change.
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Affiliation(s)
- Karel Kalecký
- Institute of Biomedical Studies, Baylor University, Waco, TX, 76712, USA.
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, 75204, USA.
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, 75204, USA
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9
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D'Ercole C, D'Angelo P, Ruggieri V, Proietti D, Virtanen L, Parisi C, Riera CS, Renzini A, Macone A, Marzullo M, Ciapponi L, Bonvissuto D, Sette C, Giordani L, Madaro L. Spatially resolved transcriptomics reveals innervation-responsive functional clusters in skeletal muscle. Cell Rep 2022; 41:111861. [PMID: 36543136 DOI: 10.1016/j.celrep.2022.111861] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 10/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Striated muscle is a highly organized structure composed of well-defined anatomical domains with integrated but distinct assignments. So far, the lack of a direct correlation between tissue architecture and gene expression has limited our understanding of how each unit responds to physio-pathologic contexts. Here, we show how the combined use of spatially resolved transcriptomics and immunofluorescence can bridge this gap by enabling the unbiased identification of such domains and the characterization of their response to external perturbations. Using a spatiotemporal analysis, we follow changes in the transcriptome of specific domains in muscle in a model of denervation. Furthermore, our approach enables us to identify the spatial distribution and nerve dependence of atrophic signaling pathway and polyamine metabolism to glycolytic fibers. Indeed, we demonstrate that perturbations of polyamine pathway can affect muscle function. Our dataset serves as a resource for future studies of the mechanisms underlying skeletal muscle homeostasis and innervation.
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Affiliation(s)
- Chiara D'Ercole
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy; Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Paolo D'Angelo
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy; Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Veronica Ruggieri
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy; Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Daisy Proietti
- Cell Therapy for Myopathies Unit, Division of Neurosciences, San Raffaele Hospital, 20132 Milano, Italy
| | - Laura Virtanen
- Sorbonne Université, INSERM UMRS 974, Association Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France
| | - Cristina Parisi
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy; Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Carles Sanchez Riera
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy
| | - Alessandra Renzini
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy
| | - Alberto Macone
- Department Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
| | - Marta Marzullo
- IBPM CNR c/o Department of Biology and Biotechnology, Sapienza University of Rome, 00185 Rome, Italy
| | - Laura Ciapponi
- Department of Biology and Biotechnologies, Sapienza University of Rome, 00185 Rome, Italy
| | - Davide Bonvissuto
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; GSTeP Organoids Research Core Facility, Fondazione Policlinico A. Gemelli, 00168 Rome, Italy
| | - Lorenzo Giordani
- Sorbonne Université, INSERM UMRS 974, Association Institut de Myologie, Centre de Recherche en Myologie, 75013 Paris, France.
| | - Luca Madaro
- Department of Anatomical, Histological, Forensic Sciences and Orthopedics, Sapienza University of Rome, 00161 Rome, Italy; Laboratory Affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, 00161 Rome, Italy.
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Talavera Andújar B, Aurich D, Aho VTE, Singh RR, Cheng T, Zaslavsky L, Bolton EE, Mollenhauer B, Wilmes P, Schymanski EL. Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study. Anal Bioanal Chem 2022; 414:7399-7419. [PMID: 35829770 PMCID: PMC9482909 DOI: 10.1007/s00216-022-04207-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/14/2022] [Accepted: 06/28/2022] [Indexed: 11/28/2022]
Abstract
Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease, with an increasing incidence in recent years due to the aging population. Genetic mutations alone only explain <10% of PD cases, while environmental factors, including small molecules, may play a significant role in PD. In the present work, 22 plasma (11 PD, 11 control) and 19 feces samples (10 PD, 9 control) were analyzed by non-target high-resolution mass spectrometry (NT-HRMS) coupled to two liquid chromatography (LC) methods (reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC)). A cheminformatics workflow was optimized using open software (MS-DIAL and patRoon) and open databases (all public MSP-formatted spectral libraries for MS-DIAL, PubChemLite for Exposomics, and the LITMINEDNEURO list for patRoon). Furthermore, five disease-specific databases and three suspect lists (on PD and related disorders) were developed, using PubChem functionality to identifying relevant unknown chemicals. The results showed that non-target screening with the larger databases generally provided better results compared with smaller suspect lists. However, two suspect screening approaches with patRoon were also good options to study specific chemicals in PD. The combination of chromatographic methods (RP and HILIC) as well as two ionization modes (positive and negative) enhanced the coverage of chemicals in the biological samples. While most metabolomics studies in PD have focused on blood and cerebrospinal fluid, we found a higher number of relevant features in feces, such as alanine betaine or nicotinamide, which can be directly metabolized by gut microbiota. This highlights the potential role of gut dysbiosis in PD development.
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Affiliation(s)
- Begoña Talavera Andújar
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, 4367, Belvaux, Luxembourg.
| | - Dagny Aurich
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, 4367, Belvaux, Luxembourg
| | - Velma T E Aho
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, 4367, Belvaux, Luxembourg
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, 4367, Belvaux, Luxembourg.,IFREMER (Institut Français de Recherche Pour L'Exploitation de La Mer), Unité Contamination Chimique Des Ecosystèmes Marins, Nantes, France
| | - Tiejun Cheng
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Leonid Zaslavsky
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Brit Mollenhauer
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany.,Paracelsus-Elena-Klinik, Kassel, Germany
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, 4367, Belvaux, Luxembourg.,Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Avenue du Swing 6, 4367, Belvaux, Luxembourg.
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11
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Kwon EH, Tennagels S, Gold R, Gerwert K, Beyer L, Tönges L. Update on CSF Biomarkers in Parkinson's Disease. Biomolecules 2022; 12:biom12020329. [PMID: 35204829 PMCID: PMC8869235 DOI: 10.3390/biom12020329] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/02/2022] [Accepted: 02/16/2022] [Indexed: 02/07/2023] Open
Abstract
Progress in developing disease-modifying therapies in Parkinson’s disease (PD) can only be achieved through reliable objective markers that help to identify subjects at risk. This includes an early and accurate diagnosis as well as continuous monitoring of disease progression and therapy response. Although PD diagnosis still relies mainly on clinical features, encouragingly, advances in biomarker discovery have been made. The cerebrospinal fluid (CSF) is a biofluid of particular interest to study biomarkers since it is closest to the brain structures and therefore could serve as an ideal source to reflect ongoing pathologic processes. According to the key pathophysiological mechanisms, the CSF status of α-synuclein species, markers of amyloid and tau pathology, neurofilament light chain, lysosomal enzymes and markers of neuroinflammation provide promising preliminary results as candidate biomarkers. Untargeted approaches in the field of metabolomics provide insights into novel and interconnected biological pathways. Markers based on genetic forms of PD can contribute to identifying subgroups suitable for gene-targeted treatment strategies that might also be transferable to sporadic PD. Further validation analyses in large PD cohort studies will identify the CSF biomarker or biomarker combinations with the best value for clinical and research purposes.
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Affiliation(s)
- Eun Hae Kwon
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, D-44791 Bochum, Germany; (E.H.K.); (S.T.); (R.G.)
| | - Sabrina Tennagels
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, D-44791 Bochum, Germany; (E.H.K.); (S.T.); (R.G.)
| | - Ralf Gold
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, D-44791 Bochum, Germany; (E.H.K.); (S.T.); (R.G.)
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, D-44801 Bochum, Germany; (K.G.); (L.B.)
| | - Klaus Gerwert
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, D-44801 Bochum, Germany; (K.G.); (L.B.)
- Faculty of Biology and Biotechnology, Department of Biophysics, Ruhr University Bochum, D-44801 Bochum, Germany
| | - Léon Beyer
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, D-44801 Bochum, Germany; (K.G.); (L.B.)
- Faculty of Biology and Biotechnology, Department of Biophysics, Ruhr University Bochum, D-44801 Bochum, Germany
| | - Lars Tönges
- Department of Neurology, St. Josef-Hospital, Ruhr-University Bochum, D-44791 Bochum, Germany; (E.H.K.); (S.T.); (R.G.)
- Center for Protein Diagnostics (ProDi), Ruhr University Bochum, D-44801 Bochum, Germany; (K.G.); (L.B.)
- Correspondence: ; Tel.: +49-234-509-2420; Fax: +49-234-509-2439
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12
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Kwon DH, Hwang JS, Kim SG, Jang YE, Shin TH, Lee G. Cerebrospinal Fluid Metabolome in Parkinson's Disease and Multiple System Atrophy. Int J Mol Sci 2022; 23:ijms23031879. [PMID: 35163800 PMCID: PMC8836409 DOI: 10.3390/ijms23031879] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Parkinson’s disease (PD) and multiple system atrophy (MSA) belong to the neurodegenerative group of synucleinopathies; differential diagnosis between PD and MSA is difficult, especially at early stages, owing to their clinical and biological similarities. Thus, there is a pressing need to identify metabolic biomarkers for these diseases. The metabolic profile of the cerebrospinal fluid (CSF) is reported to be altered in PD and MSA; however, the altered metabolites remain unclear. We created a single network with altered metabolites in PD and MSA based on the literature and assessed biological functions, including metabolic disorders of the nervous system, inflammation, concentration of ATP, and neurological disorder, through bioinformatics methods. Our in-silico prediction-based metabolic networks are consistent with Parkinsonism events. Although metabolomics approaches provide a more quantitative understanding of biochemical events underlying the symptoms of PD and MSA, limitations persist in covering molecules related to neurodegenerative disease pathways. Thus, omics data, such as proteomics and microRNA, help understand the altered metabolomes mechanism. In particular, integrated omics and machine learning approaches will be helpful to elucidate the pathological mechanisms of PD and MSA. This review discusses the altered metabolites between PD and MSA in the CSF and omics approaches to discover diagnostic biomarkers.
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Affiliation(s)
- Do Hyeon Kwon
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Ji Su Hwang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Seok Gi Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Yong Eun Jang
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
| | - Tae Hwan Shin
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
| | - Gwang Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea; (D.H.K.); (J.S.H.); (S.G.K.); (Y.E.J.)
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
- Correspondence: (T.H.S.); (G.L.)
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13
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Metabolic Features of Brain Function with Relevance to Clinical Features of Alzheimer and Parkinson Diseases. Molecules 2022; 27:molecules27030951. [PMID: 35164216 PMCID: PMC8839962 DOI: 10.3390/molecules27030951] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/04/2022] Open
Abstract
Brain metabolism is comprised in Alzheimer’s disease (AD) and Parkinson’s disease (PD). Since the brain primarily relies on metabolism of glucose, ketone bodies, and amino acids, aspects of these metabolic processes in these disorders—and particularly how these altered metabolic processes are related to oxidative and/or nitrosative stress and the resulting damaged targets—are reviewed in this paper. Greater understanding of the decreased functions in brain metabolism in AD and PD is posited to lead to potentially important therapeutic strategies to address both of these disorders, which cause relatively long-lasting decreased quality of life in patients.
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