Integrated transcriptomic and proteomic analysis reveals innate and adaptive immune dynamics in systemic autoinflammatory diseases

Immune responses in systemic autoinflammatory disease (SAID) were investigated by multi-omics analysis, integrating RNA expression and proteomic data. By identifying the top 10 co-expressed transcripts of IL1B and BLNK, we demonstrated the simultaneous activation of pro- and anti-inflammatory pathways in 338 SAID patients, with less activation in 68 negative controls. Our findings highlight the role of adaptive immune system-related genes in SAID, suggesting a reciprocal relationship between innate and adaptive immunity. Notably, negative controls exhibited active immune responses despite the absence of symptoms, an important consideration for data interpretation. In addition, we demonstrated how transcriptomic and proteomic profiling using heatmaps can verify treatment response, using the top 30 transcripts from 19 ANA-positive SAID patients and the top 30 proteins from 60 SAID patients with follow-up samples. These findings advance our understanding of the pathology of SAID and provide a valuable framework for treatment monitoring.