Serum proteome analysis of systemic JIA and related lung disease identifies distinct inflammatory programs and biomarkers. 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. Overall design: 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).

本研究采用SOMAscan（SOMAscan）技术，对健康对照者、全身型幼年特发性关节炎（sJIA）患者、巨噬细胞活化综合征（MAS）患者、sJIA-LD患者及其他相关疾病患者的血清中超过1300种分析物进行检测。
实验设计：本研究共纳入129例患者的162份血清样本，采用SOMAscan技术开展蛋白质组学分析。对于同一患者在不同时间点归属不同疾病组的样本（例如活动期MAS与非活动期sJIA、sJIA-LDFCHi与sJIA-LDFCLo），将其分别归入对应疾病组。
按照生产商SOMAlogic公司（美国科罗拉多州博尔德市）的操作指南，并联合美国国立卫生研究院人类免疫学中心（CHI），将各疾病组的血清样本均匀分配至两块检测板中，随后通过SOMAscan检测完成样本分析。
SOMAscan数据首先经归一化处理以消除单次检测内的杂交变异；随后对所有样本进行中位数归一化，以消除单次检测内的其他检测偏差；最终完成批次校准，以消除不同检测批次间的检测差异。
1305个检测靶点中有187个因板间校准物变异被标记，但仍保留于后续分析中。被标记的SOMAmers未在任何差异表达靶点列表中出现富集。归一化与校准完成后，所有样本均符合预设的合格标准，被纳入后续分析。
归一化与校准流程的完整说明可参阅以下链接：www.somalogic.com/wp-content/uploads/2017/03/SSM-071-Rev-0-Technical-Note-SOMAscan-Data-Standardization.pdf。
靶点丰度的定量评估以相对荧光单位（RFU）表示。