The mass spectrometry-based proteomics analysis of macrophages

Defective autophagy is linked to proinflammatory diseases. However, the mechanisms by which autophagy limits inflammation remain elusive. Here, we found that the pan-FGFR inhibitor LY2874455 efficiently activated autophagy and suppressed innate inflammation in macrophages stimulated by lipopolysaccharide (LPS). The mass spectrometry-based proteomics analysis of RAW264.7 cells treated with LPS (20ng/ml) and LY2874455 was performed. The protein levels of macrophages were systematically analyzed and quantified. Then, the protein levels were compared. The fold change and significance were analyzed. Multiplex proteomic profiling identified the immunoproteasome, a specific isoform of the 20s constitutive proteasome, as substrates that are degraded by selective autophagy. SQSTM1/p62 was found to be a selective autophagy-related receptor that mediated this degradation. Autophagy deficiency or p62 knockdown blocked the effects of LY2874455, leading to the accumulation of immunoproteasomes and increases in inflammatory reactions.