Euclidian distance with single linkage was used for hierarchical clustering

Euclidian distance with single linkage was used for hierarchical clustering. 67)?Time since diagnosis, y, median (range)9 (8 to 13)?EDSS score, median (range)1.5 (1 to 2 2)MS ELISpot-pos?Total (%)6 (75)?Age, y, median (range)46.5 (34 to 51)?Time since diagnosis, y, median (range)7.5 (2.5 to 26)?EDSS score, median (range)1 (0 to 4) Open in a separate window Polyclonal Stimulation of B Cells. PBMCs and plasma were separated from heparinized blood by density gradient centrifugation. Plasma samples were stored at C80 C. PBMCs were cultured at a concentration ATV of 3 106 cells/mL in complete RPMI-1640 supplemented with IL-2 at 15 ng/mL (Peprotech), the TLR7 and TLR8 agonist R-848 at 2.5 g/mL (Enzo Life Sciences), ACR 16 hydrochloride and -mercaptoethanol at 1 mM (Sigma-Aldrich) for 96 h at 37 C and 7% CO2, according to the protocol described by Pinna et al. (53). Culture supernatants were collected for subsequent array analysis, and polyclonally stimulated B cells were further processed for ELISpot analysis. ELISpot Assay. Here 96-well PVDF ELISpot plates (MultiScreen HTS; Millipore) were coated overnight with whole human brain lysate (30 g/mL; Novus Biologicals). Coating with anti-human Ig (Southern Biotech) served as a positive control at a concentration of 10 g/mL, and 10% FBS served as unfavorable control. Plates were blocked with 10% FBS for 2 h at room temperature. Each sample was plated in triplicate with 1 106 cells/well and incubated at 37 C and 7% CO2 for 26 h. After culture, the plates were incubated with biotinylated anti-human IgG (clone MT78/145; Mabtech) at 0.2 g/mL in 1% BSA. Subsequently, all plates were developed with AP-KIT III substrate (Vector Blue; Vector Laboratories). Spots were counted on an ImmunoSpot Series 6 Analyzer (Cellular Technology Limited). Array Production and Probing. Myelin antigen protein/peptide arrays were printed on SuperEpoxy slides (ArrayIt) (54). Between 4 and 12 replicates of each compound were printed. A list of all antigens ACR 16 hydrochloride included is usually provided in SI Appendix, Table S1. Arrays were circumscribed with a hydrophobic marker, blocked overnight at 4 C in PBS made up of 3% FCS and 0.1% Tween-20, incubated with B cell culture supernatants at 1:3 dilution or plasma samples at 1:125 dilution in blocking buffer for 1 h at 4 C, and then washed twice for 20 min in blocking buffer on a rotating shaker. Arrays were incubated with cyanin-3 dye-conjugated goat anti-human IgG + IgM (Jackson ImmunoResearch) at a concentration of 0.8 g/mL for 1 h at 4 C, then washed twice for 30 min in blocking buffer, twice for 30 min in PBS, and twice for 15 s in water. Arrays were spun dry and scanned with a GenePix 4000B scanner (Axon Instruments). The protocol has been described in detail previously (54) and is available at Array Data Analysis. GenePix Pro-3.0 software (Axon Instruments) was used to determine the net median pixel intensities for individual features. Normalized median net digital fluorescence units represent median values from 4 to 12 identical antigen features on each array normalized to the median intensity of 8 anti-IgG features, so that the normalized anti-IgG reactivity was 25,000 for all those arrays. SAM analysis for microarrays was used to identify antigens with significantly different antibody reactivities between individual groups (samr package in R6.1; (33, 55). SAM was run with two class unpaired settings, using the MannCWhitneyCWilcoxon test, a delta value of 0.25, and a minimum fold change of 2.5 and (12.5 for comparison of supernatants ELISpot-neg vs. ELISpot-pos, cohort 1). Heatmaps were generated with Morpheus software (The Broad Institute; Heatmap colors were adjusted ACR 16 hydrochloride for batch-dependent differences in intensities, as described in the physique legends. Euclidian distance with single linkage was used for hierarchical clustering. For time point analyses, data for each time point were normalized by division with the mean of all the data points for that time point. Linear regression analysis was performed using the least-squares method in GraphPad Prism 8.0.2, and the correlation coefficient, r, as well as the coefficient of determination, R2, are reported. Supplementary Material Supplementary FileClick here to view.(397K, pdf) Acknowledgments We thank Christopher Hohmann, Bianca Milles, Jolanta Kozlowski, Damiano M. Rovituso, and Sabine Tacke for help with the ELISpot analysis.