Maarten Cozijnsen

74 PM Arrays (Affymetrix). Washing, staining and scanning was performed using the GeneTitan Hybridization, Wash, and Stain Kit for 3’IVT Arrays, and the GeneTitan Instrument (Affymetrix). Quality and overall comparability of the arrays was verified using the R affyQCReport package. Raw intensity values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO, USA). The normalized data was analyzed pairwise using the web-based Significance of Microarray Analysis (SAM). Cut-off values for significance were false discovery rate (FDR) ≤ 0.05 and fold change ≥ 1.5. Table 1. Baseline patient characteristics infliximab (n=6)* Prednisolone (n=5)* Age 14.5 (12.3-17.4) 12.8 (8.8-14.3) Gender (female) 3 (50%) 2 (40%) Location Ileocecal (L1) 1 (17%) 0 (0%) Colonic (L2) 0 (0%) 3 (60%) Both Ileal and colonic (L3) 5 (83%) 2 (40%) Behavior Not stricturing nor penetrating (B1) 6 (100%) 5 (100%) Perianal disease 0 (0%) 1 (20%) Clinical disease activity (PCDAI) 45 (32.5-62.5) 41.5 (32.5-50.0) Erythrocyte Sedimentation Rate (ESR) 40 (22-81) 47 (21-77) C-reactive protein (CRP) 24 (10-64) 42 (5-86) Fecal calprotectin 1215 (665-1800) 582 (564-1800) Endoscopic disease activity (SESCD) 22 (9-31) 23 (9-25) Histologic disease activity (GHAS) 7 (4-13) 7.5 (7-9) *Median (range) or number (percentage) Protein profiling using PEA methodology Serum was collected before the start of treatment and after 14 weeks of treatment. Serum proteins were measured with a high-throughput technique using the Proseek Multiplex Inflammation panel from OLINK Proteomics (Uppsala, Sweden), which simultaneously measures 92 selected inflammation-related proteins in 1 μl plasma samples. The kit uses a proximity extension assay (PEA) technology, where 92 oligonucleotide-labelled antibody probe pairs can bind to their respective target present in the sample. A PCR reporter sequence is formed by a proximity-dependent DNA polymerization event and is subsequently detected and quantified using real-time PCR. The amplicons are subsequently quantified using a Fluidigm BioMark™ HD real-time PCR platform. The platform provides normalized protein expression (NPX) data where a high protein value corresponds to a high protein concentration, but not an absolute quantification. Four internal controls and two