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38 Discovery and evaluation of a multiplexed mass spectrometry panel for measuring candidate peptide biomarkers in urine from patients with lupus nephritis

Background and aims Lupus nephritis (LN) is a clinical manifestation of systemic lupus erythematosus (SLE) associated with significant morbidity and mortality. Although proteinuria is highly correlated with disease progression in LN, the composition of the LN urinary proteome remains poorly characterised. To address this issue, complementary mass spectrometry (MS)-based approaches were used to identify candidate urinary biomarkers and a targeted proteomics panel was developed to further assess levels in LN samples. Methods LN urine samples were profiled using three MS-based methods: 2D SDS-PAGE, chemical labelling using isobaric mass tags, and data-independent acquisition (DIA). A quantitative, multiple reaction monitoring method was developed to further evaluate levels of these candidate peptide biomarkers in a larger cohort. Results Using these discovery proteomic approaches>2600 proteins were identified, 290 of which are up-regulated in LN samples. While chemical labelling enabled identification of more total proteins, DIA outperformed chemical labelling in identification of proteins significantly up-regulated in LN samples. Further evaluation of a selected panel revealed increases in the majority of candidate peptide biomarkers in LN samples compared to healthy controls, including peptides from proteins involved in inflammation and adaptive immunity. Conclusions These results indicate that peptides from proteins involved in inflammation and adaptive immunity can be quantified in urine of LN patients using a multiplexed MS-based method. Results from this study will be used to inform longitudinal and interventional studies focused on understanding the biological implications of these candidate biomarkers and to direct development of novel tools to evaluate disease progression and treatment efficacy of current and future LN therapeutics.