An integrated multi-omics analysis of identifies distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa

Pseudomonas aeruginosa (P. aeruginosa) can cause severe acute infections, including pneumonia and sepsis, and also cause chronic infections commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of P. aeruginosa respiratory infection are largely unknown. Here, we profiled performed to assay for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in P. aeruginosa-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in P. aeruginosa-infected mouse macrophages. To find the pivotal transcription factors that are likely involved in host immune defense, we integrally investigated systematic changes in chromatin accessibility and gene expression in P. aeruginosa-infected lung tissues combined with proteomics and ubiquitin-proteomics studies. We discovered that Stat1 and Stat3 were altered in various omics and found similar results in mouse alveolar macrophages. Taken together, these findings indicate that these crucial transcription factors and their downstream signaling molecules play a critical role in the mobilization of host immune response against P. aeruginosa infection and may serve as potential targets for bacterial infections and inflammatory diseases, as well as provide clear insights and resources for using integrative histological analyses. RNA-seq_TC1, RNA-seq_TC2,RNA-seq_TC3, RNA-seq_CC1, RNA-seq_CC2, and RNA-seq_CC3 served as the control group. RNA-seq_TP1 and RNA-seq_TP2,RNA-seq_TP3, RNA-seq_CP1, RNA-seq_CP2, and RNA-seq_CP3 served as the infection group. ATAC-seq_TC1, ATAC-seq _TC2, ATAC-seq_CC1, and ATAC-seq_CC2 served as the control group. ATAC-seq_TP1, ATAC-seq_TP2, ATAC-seq_CP1, and ATAC-seq_CP2 served as the infection group.