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Affinity Proteomic Profiling of Plasma, Cerebrospinal Fluid, and Brain Tissue within Multiple Sclerosis

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† Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH − Royal Institute of Technology, Stockholm 171 21, Sweden
‡ Department of Neuroscience, SciLifeLab, Karolinska Institute, Stockholm 171 77, Sweden
§ Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institute, Tomtebodavägen 18A, Stockholm 171 77, Sweden
∥ Pathology Department, VU Medical Center, De Boelelaan 1117, Amsterdam 1081 HV, The Netherlands
*E-mail: [email protected]. Tel: +46 (0)8 5248 1482.
Cite this: J. Proteome Res. 2014, 13, 11, 4607–4619
Publication Date (Web):September 18, 2014
https://doi.org/10.1021/pr500609e
Copyright © 2014 American Chemical Society
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Abstract

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The brain is a vital organ and because it is well shielded from the outside environment, possibilities for noninvasive analysis are often limited. Instead, fluids taken from the spinal cord or circulatory system are preferred sources for the discovery of candidate markers within neurological diseases. In the context of multiple sclerosis (MS), we applied an affinity proteomic strategy and screened 22 plasma samples with 4595 antibodies (3450 genes) on bead arrays, then defined 375 antibodies (334 genes) for targeted analysis in a set of 172 samples and finally used 101 antibodies (43 genes) on 443 plasma as well as 573 cerebrospinal spinal fluid (CSF) samples. This revealed alteration of protein profiles in relation to MS subtypes for IRF8, IL7, METTL14, SLC30A7, and GAP43. Respective antibodies were subsequently used for immunofluorescence on human post-mortem brain tissue with MS pathology for expression and association analysis. There, antibodies for IRF8, IL7, and METTL14 stained neurons in proximity of lesions, which highlighted these candidate protein targets for further studies within MS and brain tissue. The affinity proteomic translation of profiles discovered by profiling human body fluids and tissue provides a powerful strategy to suggest additional candidates to studies of neurological disorders.

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S-Table 1: Demographics of brain tissue samples. S-Table 2A: Antibodies suggested by discovery screening. S-Table 2B: Antibodies used for second, focused 101-plex bead array. S-Table 3: Antibody performance in plasma and CSF. S-Table 4: Antibodies used for analysis of brain tissue. S-Table 5: RNA expression levels (FPKM) related to candidate proteins. S-Figure 1: Protein profiles prior normalization. S-Figure 2: Experimental reproducibility of candidate profiles. S-Figure 3: ROC curves from multivariate analysis. S-Figure 4: Western blot and epitope mapping of IRF8. S-Figure 5: Candidate profiles in CSF. S-Figure 6: Hierarchical clustering of SPMS and CIS in CSF. This material is available free of charge via the Internet at http://pubs.acs.org.

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