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LeWitt PA, Li J, Lu M, Guo L, Auinger P. Metabolomic biomarkers as strong correlates of Parkinson disease progression. Neurology 2017; 88:862-869. [PMID: 28179471 DOI: 10.1212/wnl.0000000000003663] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/29/2016] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To determine whether a Parkinson disease (PD)-specific biochemical signature might be found in the total body metabolic milieu or in the CSF compartment, especially since this disorder has systemic manifestations beyond the progressive loss of dopaminergic nigrostriatal neurons. METHODS Our goal was to discover biomarkers of PD progression. Using ultra-high-performance liquid chromatography linked to gas chromatography and tandem mass spectrometry, we measured concentrations of small-molecule (≤1.5 kDa) constituents of plasma and CSF from 49 unmedicated, mildly affected patients with PD (mean age 61.4 years; mean duration of PD 11.4 months). Specimens were collected twice (baseline and final) at intervals up to 24 months. During this time, mean Unified Parkinson's Disease Rating Scale (UPDRS) parts 2 + 3 scores increased 47% (from 28.8 to 42.2). Measured compounds underwent unbiased univariate and multivariate analyses, including fitting data into multiple linear regression with variable selection using least absolute shrinkage and selection operator (LASSO). RESULTS Of 575 identified plasma and 383 CSF biochemicals, LASSO led to selection of 15 baseline plasma constituents with high positive correlation (0.87, p = 2.2e-16) to baseline-to-final change in UPDRS parts 2 + 3 scores. Three of the compounds had xanthine structures, and 4 were either medium- or long-chain fatty acids. For the 15 LASSO-selected biomarkers, pathway enrichment software found no overrepresentation among metabolic pathways. CSF concentrations of the dopamine metabolite homovanillate showed little change between baseline and final collections and minimal correlation with worsening UPDRS parts 2 + 3 scores (0.29, p = 0.041). CONCLUSIONS Metabolomic profiling of plasma yielded strong prediction of PD progression and offered biomarkers that may provide new insights into PD pathogenesis.
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Affiliation(s)
- Peter A LeWitt
- From the Departments of Neurology (P.A.L.) and Public Health Science (J.L., M.L.), Henry Ford Health System; Wayne State University School of Medicine (P.A.L.), Detroit MI; Metabolon, Inc (L.G.), Durham, NC; and Center for Human Experimental Therapeutics (P.A.), University of Rochester, NY.
| | - Jia Li
- From the Departments of Neurology (P.A.L.) and Public Health Science (J.L., M.L.), Henry Ford Health System; Wayne State University School of Medicine (P.A.L.), Detroit MI; Metabolon, Inc (L.G.), Durham, NC; and Center for Human Experimental Therapeutics (P.A.), University of Rochester, NY
| | - Mei Lu
- From the Departments of Neurology (P.A.L.) and Public Health Science (J.L., M.L.), Henry Ford Health System; Wayne State University School of Medicine (P.A.L.), Detroit MI; Metabolon, Inc (L.G.), Durham, NC; and Center for Human Experimental Therapeutics (P.A.), University of Rochester, NY
| | - Lining Guo
- From the Departments of Neurology (P.A.L.) and Public Health Science (J.L., M.L.), Henry Ford Health System; Wayne State University School of Medicine (P.A.L.), Detroit MI; Metabolon, Inc (L.G.), Durham, NC; and Center for Human Experimental Therapeutics (P.A.), University of Rochester, NY
| | - Peggy Auinger
- From the Departments of Neurology (P.A.L.) and Public Health Science (J.L., M.L.), Henry Ford Health System; Wayne State University School of Medicine (P.A.L.), Detroit MI; Metabolon, Inc (L.G.), Durham, NC; and Center for Human Experimental Therapeutics (P.A.), University of Rochester, NY
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Tang D, Chen Y, He H, Huang J, Chen W, Peng W, Lu Q, Dai Y. Integrated analysis of mRNA, microRNA and protein in systemic lupus erythematosus-specific induced pluripotent stem cells from urine. BMC Genomics 2016; 17:488. [PMID: 27402083 PMCID: PMC4940874 DOI: 10.1186/s12864-016-2809-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 05/28/2016] [Indexed: 12/16/2022] Open
Abstract
Background In clinical practice, it is difficult to monitor the repeating relapse in patients who have been suffering from systemic lupus erythematosus (SLE). The underlying etiology remains largely unknown. Methods Aiming to understand the pathogenesis of SLE, a detailed study was conducted. Renal tubular cells–derived iPSCs were successfully obtained from the urine of SLE patients and healthy controls. With the purpose to identify simultaneous expression profiling of microRNA, mRNA and protein, Illumina HiSeq™ 2000 System and iTRAQ-coupled 2D LC-MS/MS analysis were utilized in systemic lupus erythematosus-specific induced pluripotent stem cells (SLE-iPSCs) and normal control-iPSCs (NC-iPSCs). The integration of multiple profiling datasets was realized since it could facilitate the identification of non-seed miRNA targets, as well as differentially expressed mRNAs and proteins. Results For this study, profiling datasets of 1099 differentially expressed mRNAs, 223 differentially expressed microRNAs and 94 differentially expressed proteins were integrated. In order to investigate the influence of miRNA on the processes of regulating mRNAs and proteins’ levels, potential targets of differentially expressed mRNAs and proteins were predicted using miRanda, TargetScan and Pictar. Multiple profiling datasets were integrated to facilitate the identification of miRNA targets, as well as differentially expressed mRNAs and proteins. Through gene ontology (GO) analysis of differentially expressed mRNAs and proteins, biological processes that drive proliferation were identified, such as mRNA processing and translation. Western blot and Q-PCR confirmed AK4 protein and mRNA up-regulation. The findings also showed that TAGLN’s protein and mRNA level were down-regulated in SLE-iPSCs, both miR-371a-5p and let-7a-5p in SLE-iPSC were down-regulated and verified using Q-PCR. The up-regulation of AK4 involved in nucleotide biosynthesis suggested a general acceleration of anabolic metabolism induced by down-regulated miR-371a-5p, which might contribute to SLE. Conclusion Based on high throughput analysis, integrated miRNA, mRNA, and protein expression data were generated. Differentially expressed dates were also adopted in conjunction with in-silico tools to identify potential candidates for SLE-iPSCs. Representative miRNA, mRNA and proteins were verified. It was also expected that the knowledge gained from this study can be applied to assess the usefulness of pathogenesis and novel biomarker candidates of SLE, which may develop a new way for SLE diagnosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2809-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Donge Tang
- Key Laboratory of Functional Protein Research of Guangdong Higher Education Institutes, Institute of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou, 510632, People's Republic of China
| | - Yuyu Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, People's Republic of China
| | - Huiyan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, People's Republic of China
| | - Jianrong Huang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, People's Republic of China
| | - Wenbiao Chen
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, People's Republic of China
| | - Wujian Peng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, People's Republic of China
| | - Qianjin Lu
- Department of Dermatology, Second Xiangya Hospital, Central South University, Hunan Key Laboratory of Medical Epigenomics, Changsha, Hunan, 410011, People's Republic of China
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, 518020, People's Republic of China.
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Ansoleaga B, Garcia-Esparcia P, Llorens F, Hernández-Ortega K, Carmona Tech M, Antonio Del Rio J, Zerr I, Ferrer I. Altered Mitochondria, Protein Synthesis Machinery, and Purine Metabolism Are Molecular Contributors to the Pathogenesis of Creutzfeldt-Jakob Disease. J Neuropathol Exp Neurol 2016; 75:755-769. [PMID: 27297670 DOI: 10.1093/jnen/nlw048] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Neuron loss, synaptic decline, and spongiform change are the hallmarks of sporadic Creutzfeldt-Jakob disease (sCJD), and may be related to deficiencies in mitochondria, energy metabolism, and protein synthesis. To investigate these relationships, we determined the expression levels of genes encoding subunits of the 5 protein complexes of the electron transport chain, proteins involved in energy metabolism, nucleolar and ribosomal proteins, and enzymes of purine metabolism in frontal cortex samples from 15 cases of sCJD MM1 and age-matched controls. We also assessed the protein expression levels of subunits of the respiratory chain, initiation and elongation translation factors of protein synthesis, and localization of selected mitochondrial components. We identified marked, generalized alterations of mRNA and protein expression of most subunits of all 5 mitochondrial respiratory chain complexes in sCJD cases. Expression of molecules involved in protein synthesis and purine metabolism were also altered in sCJD. These findings point to altered mRNA and protein expression of components of mitochondria, protein synthesis machinery, and purine metabolism as components of the pathogenesis of CJD.
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Affiliation(s)
- Belén Ansoleaga
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - Paula Garcia-Esparcia
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - Franc Llorens
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - Karina Hernández-Ortega
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - Margarita Carmona Tech
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - José Antonio Del Rio
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - Inga Zerr
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF)
| | - Isidro Ferrer
- From the Institute of Neuropathology, Service of Pathologic Anatomy, Hospital Universitari de Bellvitge, Hospitalet de Llobregat, Spain (BA, PG-E, KH-O, MC, IF); CIBERNED, Network Centre for Biomedical Research of Neurodegenerative Diseases, Institute Carlos III, Spain (PG-E, KH-O, MC, JAR, IF); Department of Neurology, Clinical Dementia Center, University Medical School, Georg-August University and German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany (FL, IZ); Molecular and Cellular Neurobiotechnology, Institute of Bioengineering of Catalonia (IBEC), Parc Científic de Barcelona, Department of Cell Biology, University of Barcelona, Barcelona, Spain (JAR); and Department of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain (IF).
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Garcia-Esparcia P, Hernández-Ortega K, Koneti A, Gil L, Delgado-Morales R, Castaño E, Carmona M, Ferrer I. Altered machinery of protein synthesis is region- and stage-dependent and is associated with α-synuclein oligomers in Parkinson's disease. Acta Neuropathol Commun 2015; 3:76. [PMID: 26621506 PMCID: PMC4666041 DOI: 10.1186/s40478-015-0257-4] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/14/2015] [Indexed: 01/17/2023] Open
Abstract
INTRODUCTION Parkinson's disease (PD) is characterized by the accumulation of abnormal α-synuclein in selected regions of the brain following a gradient of severity with disease progression. Whether this is accompanied by globally altered protein synthesis is poorly documented. The present study was carried out in PD stages 1-6 of Braak and middle-aged (MA) individuals without alterations in brain in the substantia nigra, frontal cortex area 8, angular gyrus, precuneus and putamen. RESULTS Reduced mRNA expression of nucleolar proteins nucleolin (NCL), nucleophosmin (NPM1), nucleoplasmin 3 (NPM3) and upstream binding transcription factor (UBF), decreased NPM1 but not NPM3 nucleolar protein immunostaining in remaining neurons; diminished 18S rRNA, 28S rRNA; reduced expression of several mRNAs encoding ribosomal protein (RP) subunits; and altered protein levels of initiation factor eIF3 and elongation factor eEF2 of protein synthesis was found in the substantia nigra in PD along with disease progression. Although many of these changes can be related to neuron loss in the substantia nigra, selective alteration of certain factors indicates variable degree of vulnerability of mRNAs, rRNAs and proteins in degenerating sustantia nigra. NPM1 mRNA and 18S rRNA was increased in the frontal cortex area 8 at stage 5-6; modifications were less marked and region-dependent in the angular gyrus and precuneus. Several RPs were abnormally regulated in the frontal cortex area 8 and precuneus, but only one RP in the angular gyrus, in PD. Altered levels of eIF3 and eIF1, and decrease eEF1A and eEF2 protein levels were observed in the frontal cortex in PD. No modifications were found in the putamen at any time of the study except transient modifications in 28S rRNA and only one RP mRNA at stages 5-6. These observations further indicate marked region-dependent and stage-dependent alterations in the cerebral cortex in PD. Altered solubility and α-synuclein oligomer formation, assessed in total homogenate fractions blotted with anti-α-synuclein oligomer-specific antibody, was demonstrated in the substantia nigra and frontal cortex, but not in the putamen, in PD. Dramatic increase in α-synuclein oligomers was also seen in fluorescent-activated cell sorter (FACS)-isolated nuclei in the frontal cortex in PD. CONCLUSIONS Altered machinery of protein synthesis is altered in the substantia nigra and cerebral cortex in PD being the frontal cortex area 8 more affected than the angular gyrus and precuneus; in contrast, pathways of protein synthesis are apparently preserved in the putamen. This is associated with the presence of α-synuclein oligomeric species in total homogenates; substantia nigra and frontal cortex are enriched, albeit with different band patterns, in α-synuclein oligomeric species, whereas α-synuclein oligomers are not detected in the putamen.
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Affiliation(s)
- Paula Garcia-Esparcia
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Karina Hernández-Ortega
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Anusha Koneti
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Laura Gil
- Department of Genetics, Medical School, Alfonso X el Sabio University, Villanueva de la Cañada, Madrid, Spain
| | - Raul Delgado-Morales
- Cancer Epigenetics and Biology Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ester Castaño
- Biology-Bellvitge Unit, Scientific and Technological Centers-University of Barcelona (CCiTUB), Hospitalet de Llobregat, Barcelona, Spain
| | - Margarita Carmona
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat; Biomedical Research Center of Neurodegenerative Diseases (CIBERNED), Barcelona, Spain.
- Institute of Neuropathology, Service of Pathologic Anatomy, Bellvitge University Hospital, carrer Feixa Llarga s/n, 08907, Hospitalet de Llobregat, Spain.
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