Serum proteome analysis of systemic JIA and related lung disease identifies distinct inflammatory programs and biomarkers

We used SOMAscan to measure >1300 analytes in sera from healthy controls and patients with sJIA, MAS, sJIA-LD and other related diseases. We included 162 serum samples from 129 patients for proteomic profiling using SOMAscan. For samples from a patient belonging to different patient groups at different times (e.g., active MAS and inactive sJIA, sJIA-LDFCHi and sJIA-LDFCLo), the samples were assigned to the separate patient groups. Serum samples were distributed by disease group equally between two plates and measured by SOMAscan assay, according to the manufacturer’s instructions, (SOMAlogic, Boulder, CO) in collaboration with the NIH Center for Human Immunology (CHI). SOMAscan data were first normalized to remove hybridization variation within the run, followed by median normalization across all samples to remove other assay biases within the run and finally calibrated to remove assay differences between runs. 187 of 1305 targets were flagged for between-plate calibrator variation but remained in the analysis. Flagged SOMAmers were not enriched in any differentially expressed target lists. Post-normalization, all samples met predefined acceptance criteria and were included in the analysis. A complete description of the normalization and calibration procedures is available at: www.somalogic.com/wp-content/uploads/2017/03/SSM-071-Rev-0-Technical-Note-SOMAscan-Data-Standardization.pdf. Quantitative assessment of target abundance was expressed as relative fluorescence units (RFU).