INVESTIGATING PREDICTIVE SERUM SOLUBLE MEDIATORS SPECIFIC TO ANA+ INDIVIDUALS AT RISK OF SYSTEMIC LUPUS ERYTHEMATOSUS WITH HIGH-THROUGHPUT PROTEOMICS

O060 / #518 Topic: AS08 - Cytokines and Cell Trafficking ABSTRACT CONCURRENT SESSION 10: INTEGRATING PROTEOMIC & TRANSCRIPTOMICS IN SLE 24-05-2025 10:40 AM - 11:40 AM Background/Purpose Anti-nuclear autoantibodies (ANAs) are detected years before SLE classification. However, most healthy ANA+ individuals will never develop clinical illness. Patients with incomplete lupus (ILE) exhibit some clinical symptoms with most never progressing to SLE. It is unknown what triggers ANA+ individuals to progress to clinical disease. We sought to identify molecular profiles of serum proteome driving transitions to full immune cell dysregulation. Methods Over 5400 proteins were measured in serum of 67 subjects (ANA-, ANA+ healthy; ILE; SLE) with Proximity Extension Assay (Olink Explore HT). Logistic regression with adjustment for age and genetic ancestry and machine learning approaches (random forest, GENIE3) were used to identify proteomic signatures specific for disease progression. Results Gene set enrichment analysis reveals involvement of pathways related to cellular homeostasis, lymphocyte activation, nucleic acid sensing, cytokine production and apoptosis (Figure 1A). Comparison of serum protein levels found the largest number of differences between ANA+ and ILE (745 proteins, p adj ≤ 0.05), associated with upregulation (in ANA+) of ubiquitin related proteins (ITCH, TAX1BP1, TRIM25, UBE2L6, USP8, USP26, UBL4A, UBE2B, UBOX5), MAPK Signaling (MAP2K6, MAP3K5, MAPKAPK2, MAP7D2, MAPKAP1), pathways related to cell adhesion and cellular regulation (KIT, TGFB2, TNFRSF14, CD46, LGALS1, CD40, IL17D, IL33, TNFSF12) and mitochondrial proteins (MAVS). Significant proteins between ANA-/ANA+ healthy controls (197 proteins, p adj ≤ 0.05) were related to decreased levels of IL7, transcription regulation pathways and increased cell adhesion molecules in ANA+. The lowest variability was found between ILE and SLE (140 proteins, p adj ≤ 0.05) with increase of TNF, BANK1, IL33, IL4R (Figure 1B) Overall, random forest predictions indicate involvement of mitochondrial proteins, dysregulation of ubiquitin related pathways, Th2 Signaling and vesicular trafficking, specific to ANA+ (Figure 1C). Mitochondrial and intracellular sensing proteins, determined with above approaches, are associated with innate cytokine IL1B, mostly in early stages of disease progression (Figure 1D). Inference of gene regulatory networks reveals interactions between pattern recognition proteins driven by mitochondrial MAVS, with variations in disease progression. Those interactions, as well as expression of related proteins, appear to be increased in ANA+, which might highlight MAVS as an initial mitochondrial modulator affecting regulation in early stages of disease (Figure 2A,B) Trajectory of pattern recognition proteins indicates increase in ANA+ and reduction in ILE and SLE, suggesting their potential role in regulating immune response before appearance of clinical symptoms. On the contrary, expression of IFN, CXCL10, IL6, IL10, IL13 gradually increase with disease progression, indicating importance of proinflammatory component during SLE development (Figure 2C). Figure 1. Figure 2. Conclusions Proteomic signatures specific to ANA+ are associated with disruption of cellular homeostasis and dysregulation of proteins related to pattern recognition, antiviral response and ubiquitination. These abnormalities may define important events in the trajectory of preclinical autoimmunity development.