DOI: 10.5061/dryad.k52h33d
title: Data from: Exploratory proteomic analysis implicates the alternative complement cascade in Primary CNS Vasculitis

description: Objective: To identify molecular correlates of primary angiitis of the
 central nervous system (PACNS) through proteomic analysis of cerebrospinal
 fluid (CSF) from a biopsy-proven patient cohort. Methods: Using mass
 spectrometry, the CSF proteome of biopsy-proven PACNS patients (n=8) was
 quantitatively compared to CSF from individuals with non-inflammatory
 conditions (n=11). Significantly enriched molecular pathways were
 identified using a gene ontology workflow, and high confidence hits within
 enriched pathways (fold change &gt;1.5 and concordant
 Benjamini-Hochberg-adjusted p-value &lt;0.05 on DeSeq and t-test) were
 identified as differentially regulated proteins. Results: Compared to
 non-inflammatory controls, 283 proteins were differentially expressed in
 PACNS patient CSF, with significant enrichment of the complement cascade
 pathway (C4-binding protein, CD55, CD59, properdin, complement C5,
 complement C8 and complement C9) and neural cell adhesion molecules. A
 subset of clinically relevant findings was validated by western blot and
 commercial ELISA. Conclusions: In this exploratory study we found evidence
 of deregulation of the alternative complement cascade in CSF from
 biopsy-proven PACNS as compared to non-inflammatory controls. More
 specifically, several regulators of the C3 and C5 convertases and
 components of the terminal cascade were significantly altered. These
 preliminary findings shed light on a previously unappreciated similarity
 between PACNS and systemic vasculitides, especially Anti-Neutrophil
 Cytoplasmic Antibody (ANCA)-associated vasculitis. The therapeutic
 implications of this common biology, and the diagnostic and/or therapeutic
 utility of individual proteomic findings warrant validation in larger
 cohorts.
description: Supplementary Appendix
 e-1: Extended Materials and MethodsSupplementary_Appendix_e1.docxSupplementary Appendix e-2: Mass spectrometry counts for all proteins across all samplesData file contains summary of mass spectrometry results by patient, aggregated by protein (UniProt ID and Gene name given), with number of unique peptides, peptide count, percent coverage, best discovery score, and best expectation value. For patient ID key, see main manuscript Table 1. (PACNS = ID 1-8, RCVS = ID 9-12, NIC = ID 13-23)Supplementary_Appendix_e2_Exploratory_Rev_Neurology.xlsxSupplementary Appendix e-3: Statistically significant differentially expressed proteins in PACNS CSF compared to NIC CSFData file contains results of of tests for differential expression of all observed proteins by t-test, and by DESeq. See methods for further detail. UniProt ID, adjusted p value for each test, and log2(fold change) are provided, for comparing PACNS (n=8) to NIC (n=11).Supplementary_Appendix_e3_Exploratory_Rev_Neurology.csvSupplemental Figure e-1: Orthogonal validation of elevated C5, IgM, IgA in CSF of PACNS patients using Western BlottingSupplementalFig_e1_ExplRev.pdfSupplemental Figure e-2: Orthogonal validation of elevated C5 by commercial ELISASupplemental_Figure_e2.pdf