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.