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Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation.
Mol Cell Proteomics. 2015 Mar; 14(3):544-55.MC

Abstract

Finding robust biomarkers for Parkinson disease (PD) is currently hampered by inherent technical limitations associated with imaging or antibody-based protein assays. To circumvent the challenges, we adapted a staged pipeline, starting from our previous proteomic profiling followed by high-throughput targeted mass spectrometry (MS), to identify peptides in human cerebrospinal fluid (CSF) for PD diagnosis and disease severity correlation. In this multicenter study consisting of training and validation sets, a total of 178 subjects were randomly selected from a retrospective cohort, matching age and sex between PD patients, healthy controls, and neurological controls with Alzheimer disease (AD). From ∼14,000 unique peptides displaying differences between PD and healthy control in proteomic investigations, 126 peptides were selected based on relevance and observability in CSF using bioinformatic analysis and MS screening, and then quantified by highly accurate and sensitive selected reaction monitoring (SRM) in the CSF of 30 PD patients versus 30 healthy controls (training set), followed by diagnostic (receiver operating characteristics) and disease severity correlation analyses. The most promising candidates were further tested in an independent cohort of 40 PD patients, 38 AD patients, and 40 healthy controls (validation set). A panel of five peptides (derived from SPP1, LRP1, CSF1R, EPHA4, and TIMP1) was identified to provide an area under curve (AUC) of 0.873 (sensitivity = 76.7%, specificity = 80.0%) for PD versus healthy controls in the training set. The performance was essentially confirmed in the validation set (AUC = 0.853, sensitivity = 82.5%, specificity = 82.5%). Additionally, this panel could also differentiate the PD and AD groups (AUC = 0.990, sensitivity = 95.0%, specificity = 97.4%). Furthermore, a combination of two peptides belonging to proteins TIMP1 and APLP1 significantly correlated with disease severity as determined by the Unified Parkinson's Disease Rating Scale motor scores in both the training (r = 0.381, p = 0.038)j and the validation (r = 0.339, p = 0.032) sets. The novel panel of CSF peptides, if validated in independent cohorts, could be used to assist in clinical diagnosis of PD and has the potential to help monitoring or predicting disease progression.

Authors+Show Affiliations

From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104; §School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China;¶Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195;From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104;‖Geriatric and Parkinson's Disease Research, Education, and Clinical Centers, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108; **Department of Neurology, University of Washington School of Medicine, Seattle, Washington 98195;‡‡Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington 98195; §§Mental Illness Research, Education, and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108;‖Geriatric and Parkinson's Disease Research, Education, and Clinical Centers, Veterans Affairs Puget Sound Health Care System, Seattle, Washington 98108; **Department of Neurology, University of Washington School of Medicine, Seattle, Washington 98195;¶¶Department of Neurology, Oregon Health and Science University, Portland, Oregon 97239;‖‖Department of Neurosciences, University of California at San Diego, La Jolla, California 92093.From the ‡Department of Pathology, University of Washington School of Medicine, Seattle, Washington 98104; zhangj@u.washington.edu.

Pub Type(s)

Journal Article
Multicenter Study
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

25556233

Citation

Shi, Min, et al. "Cerebrospinal Fluid Peptides as Potential Parkinson Disease Biomarkers: a Staged Pipeline for Discovery and Validation." Molecular & Cellular Proteomics : MCP, vol. 14, no. 3, 2015, pp. 544-55.
Shi M, Movius J, Dator R, et al. Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. Mol Cell Proteomics. 2015;14(3):544-55.
Shi, M., Movius, J., Dator, R., Aro, P., Zhao, Y., Pan, C., Lin, X., Bammler, T. K., Stewart, T., Zabetian, C. P., Peskind, E. R., Hu, S. C., Quinn, J. F., Galasko, D. R., & Zhang, J. (2015). Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. Molecular & Cellular Proteomics : MCP, 14(3), 544-55. https://doi.org/10.1074/mcp.M114.040576
Shi M, et al. Cerebrospinal Fluid Peptides as Potential Parkinson Disease Biomarkers: a Staged Pipeline for Discovery and Validation. Mol Cell Proteomics. 2015;14(3):544-55. PubMed PMID: 25556233.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Cerebrospinal fluid peptides as potential Parkinson disease biomarkers: a staged pipeline for discovery and validation. AU - Shi,Min, AU - Movius,James, AU - Dator,Romel, AU - Aro,Patrick, AU - Zhao,Yanchun, AU - Pan,Catherine, AU - Lin,Xiangmin, AU - Bammler,Theo K, AU - Stewart,Tessandra, AU - Zabetian,Cyrus P, AU - Peskind,Elaine R, AU - Hu,Shu-Ching, AU - Quinn,Joseph F, AU - Galasko,Douglas R, AU - Zhang,Jing, Y1 - 2015/01/02/ PY - 2015/1/4/entrez PY - 2015/1/4/pubmed PY - 2015/12/15/medline SP - 544 EP - 55 JF - Molecular & cellular proteomics : MCP JO - Mol Cell Proteomics VL - 14 IS - 3 N2 - Finding robust biomarkers for Parkinson disease (PD) is currently hampered by inherent technical limitations associated with imaging or antibody-based protein assays. To circumvent the challenges, we adapted a staged pipeline, starting from our previous proteomic profiling followed by high-throughput targeted mass spectrometry (MS), to identify peptides in human cerebrospinal fluid (CSF) for PD diagnosis and disease severity correlation. In this multicenter study consisting of training and validation sets, a total of 178 subjects were randomly selected from a retrospective cohort, matching age and sex between PD patients, healthy controls, and neurological controls with Alzheimer disease (AD). From ∼14,000 unique peptides displaying differences between PD and healthy control in proteomic investigations, 126 peptides were selected based on relevance and observability in CSF using bioinformatic analysis and MS screening, and then quantified by highly accurate and sensitive selected reaction monitoring (SRM) in the CSF of 30 PD patients versus 30 healthy controls (training set), followed by diagnostic (receiver operating characteristics) and disease severity correlation analyses. The most promising candidates were further tested in an independent cohort of 40 PD patients, 38 AD patients, and 40 healthy controls (validation set). A panel of five peptides (derived from SPP1, LRP1, CSF1R, EPHA4, and TIMP1) was identified to provide an area under curve (AUC) of 0.873 (sensitivity = 76.7%, specificity = 80.0%) for PD versus healthy controls in the training set. The performance was essentially confirmed in the validation set (AUC = 0.853, sensitivity = 82.5%, specificity = 82.5%). Additionally, this panel could also differentiate the PD and AD groups (AUC = 0.990, sensitivity = 95.0%, specificity = 97.4%). Furthermore, a combination of two peptides belonging to proteins TIMP1 and APLP1 significantly correlated with disease severity as determined by the Unified Parkinson's Disease Rating Scale motor scores in both the training (r = 0.381, p = 0.038)j and the validation (r = 0.339, p = 0.032) sets. The novel panel of CSF peptides, if validated in independent cohorts, could be used to assist in clinical diagnosis of PD and has the potential to help monitoring or predicting disease progression. SN - 1535-9484 UR - https://www.unboundmedicine.com/medline/citation/25556233/Cerebrospinal_fluid_peptides_as_potential_Parkinson_disease_biomarkers:_a_staged_pipeline_for_discovery_and_validation_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1535-9476(20)33221-7 DB - PRIME DP - Unbound Medicine ER -