3.3 Proteomic profiling analysis of SI-ALI based on LOC
Proteomic analysis of the chip model identified 104 differentially expressed proteins (DEPs), with 85 upregulated and 19 downregulated. These DEPs were characterized by a fold change of ≤ 0.83 or ≥ 1.2 and a p-value of < 0.05 (Supplementary Text 2). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis highlighted the enrichment of these proteins in several biological processes, including cysteine and methionine metabolism, amino acid biosynthesis, mineral absorption, carbon metabolism, and the functional roles of lysosomes and spliceosomes (Figure 5B and Supplementary Text 2). Gene Ontology Biological Processes (GOBP) analysis indicated involvement in lymphocyte aggregation, cellular response to erythropoietin, CAMKK-AMPK signaling cascade, mitochondrial protein processing, and DNA methylation maintenance. Gene Ontology Cellular Component (GOCC) terms were concentrated in clathrin-coated structures, the COPI vesicle coat, and components of the spliceosome. Gene Ontology Molecular Function (GOMF) analysis revealed associations with T cell receptor binding, G-protein subunit binding, and retromer complex binding (Figure 5A and Supplementary Text 2).
3.4 Proteomic profiling analysis of SI-ALI in in vivo model
The same smoke mixture was used to establish the SI-ALI model in C57 mice, enabling a comparative analysis of differences and similarities between the in vivo and lung chip models. The in vivo smoke-exposed group exhibited significantly elevated lung injury scores and wet/dry weight ratios compared to the control group (Supplementary Figures 2A and 2B-a). Additionally, oxidative stress-related and injury markers in the lungs, such as superoxide dismutase (SOD), lactate dehydrogenase (LDH), and glutathione (GSH), showed substantial alterations (Supplementary Figures 2B-b to 2B-d). Further proteomic analysis of lung tissue identified 566 differentially expressed proteins (DEPs), with 465 upregulated and 101 downregulated (fold change ≤ 0.83 or ≥ 1.2 and p-value < 0.05) (Supplementary Text 3). KEGG pathway analysis indicated that these DEPs were enriched in various biological processes, including metabolism, vesicular transport, and tight junction integrity (Supplementary Text 3). Gene Ontology Biological Processes (GOBP) analysis revealed involvement in skeletal muscle satellite cell migration, regulation of mRNA stability in response to oxidative stress, and negative regulation of both ubiquitin-specific protease activity and nitrosative stress-induced apoptotic signaling. Gene Ontology Cellular Component (GOCC) terms were enriched in structures such as collagen type I trimer and mitochondrial complexes. Gene Ontology Molecular Function (GOMF) analysis identified significant enrichment in functions ranging from phosphoserine binding to various oxidoreductase activities (Supplementary Text 3). Overlap of KEGG pathways and GO terms between the animal and lung chip models is detailed in Supplementary Figure 3.