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Zhang X, Wang B, Luo Y, Ding CF, Yan Y. An amino-rich polymer-coated magnetic nanomaterial for ultra-rapid separation of phosphorylated peptides in the serum of Parkinson's disease patients. Anal Bioanal Chem 2024; 416:3361-3371. [PMID: 38607383 DOI: 10.1007/s00216-024-05287-9] [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: 01/24/2024] [Revised: 03/31/2024] [Accepted: 04/02/2024] [Indexed: 04/13/2024]
Abstract
The elucidation of disease pathogenesis can be achieved by analyzing the low-abundance phosphopeptides in organisms. Herein, we developed a novel and easy-to-prepare polymer-coated nanomaterial. By improving the hydrophilicity and spatial conformation of the material, we effectively enhanced the adsorption of phosphopeptides and demonstrated excellent enrichment properties. The material was able to successfully enrich the phosphopeptides in only 1 min. Meanwhile, the material has high selectivity (1:2000), good loading capacity (100 μg/mg), excellent sensitivity (0.5 fmol), and great acid and alkali resistance. In addition, the material was applied to real samples, and 70 phosphopeptides were enriched from the serum of Parkinson's disease (PD) patients and 67 phosphopeptides were enriched from the serum of normal controls. Sequences Logo showed that PD is probably associated with threonine, glutamate, serine, and glutamine. Finally, gene ontology (GO) analysis was performed on phosphopeptides enriched in PD patients' serum. The results showed that PD patients expressed abnormal expression of the cholesterol metabolic process and cell-matrix adhesion in the biological process (BP), endoplasmic reticulum and lipoprotein in the cellular component (CC), and heparin-binding, lipid-binding, and receptor-binding in the molecular function (MF) as compared with normal individuals. All the experiments indicate that the nanomaterials have great potential in proteomics studies.
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Affiliation(s)
- Xiaoya Zhang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Bing Wang
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yiting Luo
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Chuan-Fan Ding
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China.
| | - Yinghua Yan
- Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis of Zhejiang Province, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, 315211, Zhejiang, China.
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2
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Chapman MA, Sorg BA. A Systematic Review of Extracellular Matrix-Related Alterations in Parkinson's Disease. Brain Sci 2024; 14:522. [PMID: 38928523 PMCID: PMC11201521 DOI: 10.3390/brainsci14060522] [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: 04/17/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
The role of the extracellular matrix (ECM) in Parkinson's disease (PD) is not well understood, even though it is critical for neuronal structure and signaling. This systematic review identified the top deregulated ECM-related pathways in studies that used gene set enrichment analyses (GSEA) to document transcriptomic, proteomic, or genomic alterations in PD. PubMed and Google scholar were searched for transcriptomics, proteomics, or genomics studies that employed GSEA on data from PD tissues or cells and reported ECM-related pathways among the top-10 most enriched versus controls. Twenty-seven studies were included, two of which used multiple omics analyses. Transcriptomics and proteomics studies were conducted on a variety of tissue and cell types. Of the 17 transcriptomics studies (16 data sets), 13 identified one or more adhesion pathways in the top-10 deregulated gene sets or pathways, primarily related to cell adhesion and focal adhesion. Among the 8 proteomics studies, 5 identified altered overarching ECM gene sets or pathways among the top 10. Among the 4 genomics studies, 3 identified focal adhesion pathways among the top 10. The findings summarized here suggest that ECM organization/structure and cell adhesion (particularly focal adhesion) are altered in PD and should be the focus of future studies.
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Affiliation(s)
| | - Barbara A. Sorg
- R.S. Dow Neurobiology, Legacy Research Institute, Portland, OR 97232, USA;
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3
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Krauskopf J, Eggermont K, Caiment F, Verfaillie C, de Kok TM. Molecular insights into PCB neurotoxicity: Comparing transcriptomic responses across dopaminergic neurons, population blood cells, and Parkinson's disease pathology. ENVIRONMENT INTERNATIONAL 2024; 186:108642. [PMID: 38608384 DOI: 10.1016/j.envint.2024.108642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/26/2024] [Accepted: 04/08/2024] [Indexed: 04/14/2024]
Abstract
Parkinson's disease (PD) is a complex neurodegenerative disorder influenced by genetic factors and environmental exposures. Polychlorinated biphenyls (PCBs), a group of synthetic organic compounds, have been identified as potential environmental risk factors for neurodegenerative diseases, including PD. We explored PCB-induced neurotoxicity mechanisms using iPSC-derived dopaminergic neurons and assessed their transcriptomic responses to varying PCB concentrations (0.01 μM, 0.5 μM, and 10 μM). Specifically, we focused on PCB-180, a congener known for its accumulation in human brains. The exposure durations were 24 h and 74 h, allowing us to capture both short-term and more prolonged effects on gene expression patterns. We observed that PCB exposure led to the suppression of oxidative phosphorylation, synaptic function, and neurotransmitter release, implicating these pathways in PCB-induced neurotoxicity. In our comparative analysis, we noted similarities in PCB-induced changes with other PD-related compounds like MPP+ and rotenone. Our findings also aligned with gene expression changes in human blood derived from a population exposed to PCBs, highlighting broader inflammatory responses. Additionally, molecular patterns seen in iPSC-derived neurons were confirmed in postmortem PD brain tissues, validating our in vitro results. In conclusion, our study offers novel insights into the multifaceted impacts of PCB-induced perturbations on various cellular contexts relevant to PD. The use of iPSC-derived dopaminergic neurons allowed us to decipher intricate transcriptomic alterations, bridging the gap between in vitro and in vivo findings. This work underscores the potential role of PCB exposure in neurodegenerative diseases like PD, emphasizing the need to consider both systemic and cell specific effects.
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Affiliation(s)
- Julian Krauskopf
- Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands; MHeNS, School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands. %
| | - Kristel Eggermont
- Stem Cell Institute, Department of Development and Regeneration, Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Florian Caiment
- Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
| | - Catherine Verfaillie
- Stem Cell Institute, Department of Development and Regeneration, Katholieke Universiteit Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Theo M de Kok
- Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands; MHeNS, School for Mental Health and Neuroscience, Maastricht University, Universiteitssingel 50, 6229 ER Maastricht, The Netherlands
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4
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Awuson-David B, Williams AC, Wright B, Hill LJ, Di Pietro V. Common microRNA regulated pathways in Alzheimer's and Parkinson's disease. Front Neurosci 2023; 17:1228927. [PMID: 37719162 PMCID: PMC10502311 DOI: 10.3389/fnins.2023.1228927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/02/2023] [Indexed: 09/19/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs involved in gene regulation. Recently, miRNA dysregulation has been found in neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). The diagnosis of Alzheimer's and Parkinson's is currently challenging, mainly occurring when pathology is already present, and although treatments are available for both diseases, the role of treatment is primarily to prevent or delay the progress of the diseases instead of fully overcoming the diseases. Therefore, the challenge in the near future will be to determine effective drugs to tackle the dysregulated biological pathways in neurodegenerative diseases. In the present study, we describe the dysregulation of miRNAs in blood of Alzheimer's and Parkinson's patients with the aim to identify common mechanisms between the 2 pathologies and potentially to identify common therapeutic targets which can stop or delay the progression of two most frequent neuropathologies. Two independent systematic reviews, bioinformatic analysis, and experiment validation were performed to identify whether AD and PD share common pathways. A total of 15 common miRNAs were found in the literature and 13 common KEGG pathways. Among the common miRNAs, two were selected for validation in a small cohort of AD and PD patients. Let-7f-5p and miR-29b-3p showed to be good predictors in blood of PD patients.
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Affiliation(s)
- Betina Awuson-David
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Adrian C. Williams
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Benjamin Wright
- Department of Neurology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Lisa J. Hill
- School of Biomedical Sciences, Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
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Bang D, Lim S, Lee S, Kim S. Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers. Nat Commun 2023; 14:3570. [PMID: 37322032 PMCID: PMC10272215 DOI: 10.1038/s41467-023-39301-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Computational drug repurposing aims to identify new indications for existing drugs by utilizing high-throughput data, often in the form of biomedical knowledge graphs. However, learning on biomedical knowledge graphs can be challenging due to the dominance of genes and a small number of drug and disease entities, resulting in less effective representations. To overcome this challenge, we propose a "semantic multi-layer guilt-by-association" approach that leverages the principle of guilt-by-association - "similar genes share similar functions", at the drug-gene-disease level. Using this approach, our model DREAMwalk: Drug Repurposing through Exploring Associations using Multi-layer random walk uses our semantic information-guided random walk to generate drug and disease-populated node sequences, allowing for effective mapping of both drugs and diseases in a unified embedding space. Compared to state-of-the-art link prediction models, our approach improves drug-disease association prediction accuracy by up to 16.8%. Moreover, exploration of the embedding space reveals a well-aligned harmony between biological and semantic contexts. We demonstrate the effectiveness of our approach through repurposing case studies for breast carcinoma and Alzheimer's disease, highlighting the potential of multi-layer guilt-by-association perspective for drug repurposing on biomedical knowledge graphs.
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Affiliation(s)
- Dongmin Bang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- AIGENDRUG Co., Ltd., Seoul, 08826, Republic of Korea
| | - Sangsoo Lim
- School of Artificial Intelligence Convergence, Dongguk University, Seoul, 04620, Republic of Korea
| | - Sangseon Lee
- Institute of Computer Technology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sun Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- AIGENDRUG Co., Ltd., Seoul, 08826, Republic of Korea.
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea.
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Zhang X, Zhou J, Xu W, Zhan W, Zou H, Lin J. Transcriptomic and Behavioral Studies of Small Yellow Croaker (Larimichthys polyactis) in Response to Noise Exposure. Animals (Basel) 2022; 12:ani12162061. [PMID: 36009652 PMCID: PMC9405241 DOI: 10.3390/ani12162061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 11/21/2022] Open
Abstract
Simple Summary Ocean noise pollution from marine traffic may affect the behavioral, ecological and biochemical parameters of marine fish species. Most studies have focused on behavioral changes and hearing damage in fishes, but the molecular mechanism of noise exposure in the impairment of the brain has rarely been reported. In this study, using small yellow croaker (L. polyactis) as a model, we used RNA-seq methods to characterize differently expressed genes between the control group and the noise exposure group. GO and KEGG pathway analysis found that synaptic transmission, neurotransmitter transport, endocytosis procession, cell adhesion molecules and the extracellular matrix receptor interaction pathway were over-represented in the DEGs. In addition, behavioral studies revealed that L. polyactis kept motionless on the surface of the water and lost the ability to keep their balance after noise exposure. Collectively, our results indicate that exposure to noise stressors contributes to neurological dysfunction in the brain and impaired locomotor ability in L. polyactis. Abstract Noise has the potential to induce physiological stress in marine fishes, which may lead to all sorts of ecological consequences. In the current study, we used the RNA-sequencing (RNA-seq) method to sequence the whole transcriptome of the brain in small yellow croaker (Larimichthys polyactis). The animals were exposed to a mix of noises produced by different types of boat played back in a tank, then the brain tissues were collected after the fish had been exposed to a 120 dB noise for 0.5 h. In total, 762 differently expressed genes (DEGs) between the two groups were identified, including 157 up regulated and 605 down regulated genes in the noise exposure group compared with the control group. Gene ontology (GO) enrichment analysis indicated that the most up regulated gene categories included synaptic membranes, receptor-mediated endocytosis and the neurotransmitter secretion process. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways found that endocytosis, cell adhesion molecules and the extracellular matrix (ECM) receptor interaction pathway were over-represented. Specifically, ECM-related genes, including lamin2, lamin3, lamin4, coll1a2, coll5a1 and col4a5 were down regulated in the noise exposure group, implying the impaired composition of the ECM. In addition, the behavioral experiment revealed that L. polyactis exhibited avoidance behaviors to run away from the noise source at the beginning of the noise exposure period. At the end of the noise exposure period, L. polyactis kept motionless on the surface of the water and lost the ability to keep their balance. Taken together, our results indicate that exposure to noise stress contributes to neurological dysfunction in the brain and impaired locomotor ability in L. polyactis.
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Affiliation(s)
- Xuguang Zhang
- Engineering Technology Research Center of Marine Ranching, College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Jun Zhou
- Engineering Technology Research Center of Marine Ranching, College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
| | - Wengang Xu
- School of Ocean, Yantai University, Yantai 264005, China
| | - Wei Zhan
- Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Huafeng Zou
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
- The Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (H.Z.); (J.L.)
| | - Jun Lin
- Engineering Technology Research Center of Marine Ranching, College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai 201306, China
- Correspondence: (H.Z.); (J.L.)
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7
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Fernández-Santiago R, Esteve-Codina A, Fernández M, Valldeoriola F, Sanchez-Gómez A, Muñoz E, Compta Y, Tolosa E, Ezquerra M, Martí MJ. Transcriptome analysis in LRRK2 and idiopathic Parkinson's disease at different glucose levels. NPJ Parkinsons Dis 2021; 7:109. [PMID: 34853332 PMCID: PMC8636510 DOI: 10.1038/s41531-021-00255-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/04/2021] [Indexed: 02/08/2023] Open
Abstract
Type-2 diabetes (T2D) and glucose metabolic imbalances have been linked to neurodegenerative diseases, including Parkinson's disease (PD). To detect potential effects of different glucose levels on gene expression, by RNA-seq we analyzed the transcriptome of dermal fibroblasts from idiopathic PD (iPD) patients, LRRK2-associated PD (L2PD) patients, and healthy controls (total n = 21 cell lines), which were cultured at two different glucose concentrations (25 and 5 mM glucose). In PD patients we identified differentially expressed genes (DEGs) that were related to biological processes mainly involving the plasmatic cell membrane, the extracellular matrix, and also neuronal functions. Such pathway deregulation was largely similar in iPD or L2PD fibroblasts. Overall, the gene expression changes detected in this study were associated with PD independently of glucose concentration.
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Affiliation(s)
- Rubén Fernández-Santiago
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain.
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028, Barcelona, Catalonia, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Catalonia, Spain
| | - Manel Fernández
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
| | - Francesc Valldeoriola
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Catalonia, Spain
| | - Almudena Sanchez-Gómez
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Catalonia, Spain
| | - Esteban Muñoz
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Catalonia, Spain
| | - Yaroslau Compta
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Catalonia, Spain
| | - Eduardo Tolosa
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Catalonia, Spain
| | - Mario Ezquerra
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain.
| | - María J Martí
- Lab of Parkinson disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research, Department of Neurology, Hospital Clínic of Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, 08036, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), 08036, Barcelona, Catalonia, Spain
- Parkinson's disease & Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, 08036, Barcelona, Catalonia, Spain
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8
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Marques TM, van Rumund A, Kersten I, Bruinsma IB, Wessels HJ, Gloerich J, Kaffa C, Esselink RAJ, Bloem BR, Kuiperij HB, Verbeek MM. Identification of cerebrospinal fluid biomarkers for parkinsonism using a proteomics approach. NPJ Parkinsons Dis 2021; 7:107. [PMID: 34848724 PMCID: PMC8633286 DOI: 10.1038/s41531-021-00249-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 10/27/2021] [Indexed: 01/25/2023] Open
Abstract
The aim of our study was to investigate cerebrospinal fluid (CSF) tryptic peptide profiles as potential diagnostic biomarkers for the discrimination of parkinsonian disorders. CSF samples were collected from individuals with parkinsonism, who had an uncertain diagnosis at the time of inclusion and who were followed for up to 12 years in a longitudinal study. We performed shotgun proteomics to identify tryptic peptides in CSF of Parkinson's disease (PD, n = 10), multiple system atrophy patients (MSA, n = 5) and non-neurological controls (n = 10). We validated tryptic peptides with differential levels between PD and MSA using a newly developed selected reaction monitoring (SRM) assay in CSF of PD (n = 46), atypical parkinsonism patients (AP; MSA, n = 17; Progressive supranuclear palsy; n = 8) and non-neurological controls (n = 39). We identified 191 tryptic peptides that differed significantly between PD and MSA, of which 34 met our criteria for SRM development. For 14/34 peptides we confirmed differences between PD and AP. These tryptic peptides discriminated PD from AP with moderate-to-high accuracy. Random forest modelling including tryptic peptides plus either clinical assessments or other CSF parameters (neurofilament light chain, phosphorylated tau protein) and age improved the discrimination of PD vs. AP. Our results show that the discovery of tryptic peptides by untargeted and subsequent validation by targeted proteomics is a suitable strategy to identify potential CSF biomarkers for PD versus AP. Furthermore, the tryptic peptides, and corresponding proteins, that we identified as differential biomarkers may increase our current knowledge about the disease-specific pathophysiological mechanisms of parkinsonism.
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Affiliation(s)
- Tainá M. Marques
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anouke van Rumund
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - Iris Kersten
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ilona B. Bruinsma
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hans J.C.T. Wessels
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jolein Gloerich
- grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Charlotte Kaffa
- grid.10417.330000 0004 0444 9382Center for Molecular and Biomolecular Informatics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rianne A. J. Esselink
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - Bastiaan R. Bloem
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands
| | - H. Bea Kuiperij
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Marcel M. Verbeek
- grid.10417.330000 0004 0444 9382Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands ,Radboudumc Center of Expertise for Parkinson & Movement Disorders, Nijmegen, The Netherlands ,grid.10417.330000 0004 0444 9382Department of Laboratory Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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Ruffini N, Klingenberg S, Schweiger S, Gerber S. Common Factors in Neurodegeneration: A Meta-Study Revealing Shared Patterns on a Multi-Omics Scale. Cells 2020; 9:E2642. [PMID: 33302607 PMCID: PMC7764447 DOI: 10.3390/cells9122642] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/24/2020] [Accepted: 12/04/2020] [Indexed: 02/06/2023] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS) are heterogeneous, progressive diseases with frequently overlapping symptoms characterized by a loss of neurons. Studies have suggested relations between neurodegenerative diseases for many years (e.g., regarding the aggregation of toxic proteins or triggering endogenous cell death pathways). We gathered publicly available genomic, transcriptomic, and proteomic data from 177 studies and more than one million patients to detect shared genetic patterns between the neurodegenerative diseases on three analyzed omics-layers. The results show a remarkably high number of shared differentially expressed genes between the transcriptomic and proteomic levels for all conditions, while showing a significant relation between genomic and proteomic data between AD and PD and AD and ALS. We identified a set of 139 genes being differentially expressed in several transcriptomic experiments of all four diseases. These 139 genes showed overrepresented gene ontology (GO) Terms involved in the development of neurodegeneration, such as response to heat and hypoxia, positive regulation of cytokines and angiogenesis, and RNA catabolic process. Furthermore, the four analyzed neurodegenerative diseases (NDDs) were clustered by their mean direction of regulation throughout all transcriptomic studies for this set of 139 genes, with the closest relation regarding this common gene set seen between AD and HD. GO-Term and pathway analysis of the proteomic overlap led to biological processes (BPs), related to protein folding and humoral immune response. Taken together, we could confirm the existence of many relations between Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis on transcriptomic and proteomic levels by analyzing the pathways and GO-Terms arising in these intersections. The significance of the connection and the striking relation of the results to processes leading to neurodegeneration between the transcriptomic and proteomic data for all four analyzed neurodegenerative diseases showed that exploring many studies simultaneously, including multiple omics-layers of different neurodegenerative diseases simultaneously, holds new relevant insights that do not emerge from analyzing these data separately. Furthermore, the results shed light on processes like the humoral immune response that have previously been described only for certain diseases. Our data therefore suggest human patients with neurodegenerative diseases should be addressed as complex biological systems by integrating multiple underlying data sources.
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Affiliation(s)
- Nicolas Ruffini
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
- Leibniz Institute for Resilience Research, Leibniz Association, Wallstraße 7, 55122 Mainz, Germany
| | - Susanne Klingenberg
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susann Schweiger
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
| | - Susanne Gerber
- Institute for Human Genetics, University Medical Center, Johannes Gutenberg University, 55131 Mainz, Germany; (N.R.); (S.K.); (S.S.)
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10
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Kumari B, Mandal M, Dholaniya PS. Analysis of multiple transcriptome data to determine age-associated genes for the progression of Parkinson's disease. Meta Gene 2020. [DOI: 10.1016/j.mgene.2020.100712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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González-Casacuberta I, Morén C, Juárez-Flores DL, Esteve-Codina A, Sierra C, Catalán-García M, Guitart-Mampel M, Tobías E, Milisenda JC, Pont-Sunyer C, Martí MJ, Cardellach F, Tolosa E, Artuch R, Ezquerra M, Fernández-Santiago R, Garrabou G. Transcriptional alterations in skin fibroblasts from Parkinson's disease patients with parkin mutations. Neurobiol Aging 2018; 65:206-216. [PMID: 29501959 DOI: 10.1016/j.neurobiolaging.2018.01.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 01/23/2018] [Accepted: 01/26/2018] [Indexed: 11/29/2022]
Abstract
Mutations in the parkin gene (PRKN) are the most common cause of autosomal-recessive juvenile Parkinson's disease (PD). PRKN encodes an E3 ubiquitin ligase that is involved in multiple regulatory functions including proteasomal-mediated protein turnover, mitochondrial function, mitophagy, and cell survival. However, the precise molecular events mediated by PRKN mutations in PRKN-associated PD (PRKN-PD) remain unknown. To elucidate the cellular impact of parkin mutations, we performed an RNA sequencing study in skin fibroblasts from PRKN-PD patients carrying different PRKN mutations (n = 4) and genetically unrelated healthy subjects (n = 4). We identified 343 differentially expressed genes in PRKN-PD fibroblasts. Gene ontology and canonical pathway analysis revealed enrichment of differentially expressed genes in processes such as cell adhesion, cell growth, and amino acid and folate metabolism among others. Our findings indicate that PRKN mutations are associated with large global gene expression changes as observed in fibroblasts from PRKN-PD patients and support the view of PD as a systemic disease affecting also non-neural peripheral tissues such as the skin.
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Affiliation(s)
- Ingrid González-Casacuberta
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Constanza Morén
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Diana-Luz Juárez-Flores
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Anna Esteve-Codina
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Sierra
- Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Marc Catalán-García
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mariona Guitart-Mampel
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Ester Tobías
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - José César Milisenda
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Claustre Pont-Sunyer
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - María José Martí
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Francesc Cardellach
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Eduard Tolosa
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Artuch
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain; Department of Clinical Biochemistry, Institut de Recerca Sant Joan de Déu, Esplugues de Llobregat, Barcelona, Spain
| | - Mario Ezquerra
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Rubén Fernández-Santiago
- Laboratory of Parkison Disease and Other Neurodegenerative Movement Disorders: Clinical and Experimental Research-CELLEX, IDIBAPS, Faculty of Medicine and Health Sciences, UB, Department of Neurology-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function-CELLEX, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Faculty of Medicine and Health Sciences, University of Barcelona (UB), Department of Internal Medicine-Hospital Clínic of Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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Yan Y, Cheng L, Chen X, Wang Q, Duan M, Ma J, Zhao L, Jiang X, Ai J. Estrogen deficiency is associated with hippocampal morphological remodeling of early postmenopausal mice. Oncotarget 2017; 8:21892-21902. [PMID: 28423534 PMCID: PMC5400632 DOI: 10.18632/oncotarget.15702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 01/24/2017] [Indexed: 01/10/2023] Open
Abstract
Estrogen (E2) deficiency is reported to involve in the impairment of cognition in postmenopausal women. However, the morphological basis is still unclear. In the present study, using transmission electron microscopy (TEM), we observed the ultrastructure of hippocampus in female C57BL/6 mice at the age of 18 months (18 M) which is considered as the early stage of postmenopause (n = 8). Compared with control mice aged 6 M (n = 8), we identified that the morphological changes in the hippocampus of these menopausal mice were mitochondrial damage, lipofuscin deposition and microtubule degradation. Notably, after E2 was subcutaneously injected into mice aged 16 M with a dosage of 3.5 μg/kg every three days for two months in the 18 M + E2 group (n = 8), mitochondrial damage and lipofuscin deposition in the DG region of hippocampus were prevented, but the degraded microtubules in the hippocampus of postmenopausal mice were failed to restore. These data suggest that hippocampal ultrastructure remodeling in mice can be initiated at the early stage of postmenopause, E2 supplementation could only have an effect on mitochondrial damage and lipofuscin increase.
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Affiliation(s)
- Yan Yan
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Heilongjiang Province, Harbin 150081, China
| | - Xin Chen
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Qin Wang
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Mingjing Duan
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Jichao Ma
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Linjing Zhao
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Xuemei Jiang
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
| | - Jing Ai
- Department of Pharmacology, Harbin Medical University, The State-Province Key Laboratories of Biomedicine-Pharmaceutics of China, Heilongjiang Province, Harbin 150081, China
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13
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Proteome Analysis of Potential Synaptic Vesicle Cycle Biomarkers in the Cerebrospinal Fluid of Patients with Sporadic Creutzfeldt-Jakob Disease. Mol Neurobiol 2016; 54:5177-5191. [PMID: 27562179 DOI: 10.1007/s12035-016-0029-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/01/2016] [Indexed: 01/01/2023]
Abstract
Sporadic Creutzfeldt-Jakob disease (sCJD) is the most frequent fatal human prion disease with a rapid progression and unknown mechanism. The synaptic vesicle (SV) cycle pathway has been a hot research field associated with many neurodegenerative diseases that affect synaptic function and thus may affect pathogenesis of the disorder. Here, we used the iTRAQ-based proteomic method and a KEGG pathway enrichment analysis to meticulously analyze all pathways involved in sCJD disease. In total, 1670 proteins were validated in pooled cerebrospinal fluid (CSF) from 20 patients with sCJD compared with that from 13 patients without CJD. The demographic analysis demonstrated that 557 proteins were upregulated and 595 proteins were downregulated with a 1.5-fold change, and 690 proteins involved in 39 pathways changed significantly (p ≤ 0.05) according to the enrichment analysis. The SV cycle pathway and proteins involved were further evaluated, and 14 proteins were confirmed to participate in the SV cycle pathway due to increased expression. Six key proteins, such as AP2A1, SYT1, SNAP25, STXBP1, CLTB, and Rab3a, showed the same trend by western blot as detected by iTRAQ. This is the first study to use high-throughput proteomics to accurately identify and quantify proteins in the SV cycle pathway of a neurodegenerative disease. These results will help define the mechanism and provide new insight into the pathogenetic factors involved in the SV cycle pathway in patients with sCJD. We hope that promising biomarkers can be identified in the CSF of patients with sCJD and other neurodegenerative disorders to help predict disease progression.
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14
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eSNPO: An eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Sci Rep 2016; 6:30595. [PMID: 27470167 PMCID: PMC4965794 DOI: 10.1038/srep30595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/04/2016] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWASs) have mined many common genetic variants associated with human complex traits like diseases. After that, the functional annotation and enrichment analysis of significant SNPs are important tasks. Classic methods are always based on physical positions of SNPs and genes. Expression quantitative trait loci (eQTLs) are genomic loci that contribute to variation in gene expression levels and have been proven efficient to connect SNPs and genes. In this work, we integrated the eQTL data and Gene Ontology (GO), constructed associations between SNPs and GO terms, then performed functional enrichment analysis. Finally, we constructed an eQTL-based SNP Ontology and SNP functional enrichment analysis platform. Taking Parkinson Disease (PD) as an example, the proposed platform and method are efficient. We believe eSNPO will be a useful resource for SNP functional annotation and enrichment analysis after we have got significant disease related SNPs.
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15
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Li XZ, Zhang SN, Lu F, Liu SM. Microarray Expression Analysis for the Paradoxical Roles of Acanthopanax senticosus Harms in Treating α-Synucleinopathies. Phytother Res 2015; 30:243-52. [PMID: 26612828 DOI: 10.1002/ptr.5522] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 10/26/2015] [Accepted: 11/01/2015] [Indexed: 01/04/2023]
Abstract
α-Synuclein is a key player in the pathogenesis of neurodegenerative disorders with Lewy bodies. Our previous studies have also showed that Acanthopanax senticosus harms (AS) could significantly suppress α-synuclein overexpression and toxicity. Identifying the RNAs related to α-synucleinopathies may facilitate understanding the pathogenesis of the diseases and the safe application of AS in the clinic. Microarray expression profiling of long non-coding RNAs (lncRNAs) and mRNAs was undertaken in control non-transgenic and human α-synuclein transgenic mice. The effects of AS on central nervous system (CNS) in pathology and physiology were investigated based on the lncRNA/mRNA targets analysis. In total, 341 lncRNAs and 279 mRNAs were differentially expressed by α-synuclein stimulus, among which 29 lncRNAs and 25 mRNAs were involved in the anti-α-synucleinopathies mechanism of AS. However, the levels of 19/29 lncRNAs and 12/25 mRNAs in AS group were similar to those in α-synuclein group, which may cause potential neurotoxicity analogous to α-synuclein. This study demonstrated that some of lncRNAs/mRNAs were involved in α-synuclein related pathophysiology, and AS produced the bidirectional effects on CNS under pathological and physiological conditions.
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Affiliation(s)
- Xu-zhao Li
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.,Department of Pharmacy, GuiYang College of Traditional Chinese Medicine, GuiYang, 550025, China
| | - Shuai-nan Zhang
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Fang Lu
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
| | - Shu-min Liu
- Chinese Medicine Toxicological Laboratory, Heilongjiang University of Chinese Medicine, Harbin, 150040, China.,Drug Safety Evaluation Center, Heilongjiang University of Chinese Medicine, Harbin, 150040, China
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