{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T15:24:51Z","timestamp":1783524291115,"version":"3.55.0"},"reference-count":70,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2023,8,29]],"date-time":"2023-08-29T00:00:00Z","timestamp":1693267200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["No. 81922042, 82172285, 82241049"],"award-info":[{"award-number":["No. 81922042, 82172285, 82241049"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82273320 and 82072999"],"award-info":[{"award-number":["82273320 and 82072999"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"1\u00b73\u00b75 Project of Excellent Development of Discipline of West China Hospital of Sichuan University","award":["No. ZYYC21001"],"award-info":[{"award-number":["No. ZYYC21001"]}]},{"name":"Innovation Research Project of Sichuan University","award":["No. 2022SCUH0029"],"award-info":[{"award-number":["No. 2022SCUH0029"]}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["CIFMS, 2019-I2M-5-004"],"award-info":[{"award-number":["CIFMS, 2019-I2M-5-004"]}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p><jats:italic>Pseudomonas aeruginosa<\/jats:italic> (<jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic>) can cause severe acute infections, including pneumonia and sepsis, and cause chronic infections, commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic> respiratory infection are largely unknown. Here, we performed assays for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic>-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic>-infected mouse macrophages. To identify the pivotal factors that are involved in host immune defense, we integrated chromatin accessibility and gene expression to investigate molecular changes in <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic>-infected lung tissues combined with proteomics and ubiquitin-proteomics. Our multi-omics investigation discovered a significant concordance for innate immunological and inflammatory responses following <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic> infection between hosts and alveolar macrophages. Furthermore, we discovered that multi-omics changes in pioneer factors Stat1 and Stat3 play a crucial role in the immunological regulation of <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic> infection and that their downstream molecules (e.g., Fas) may be implicated in both immunosuppressive and inflammation-promoting processes. Taken together, these findings indicate that transcription factors and their downstream signaling molecules play a critical role in the mobilization and rebalancing of the host immune response against <jats:italic>P<\/jats:italic>. <jats:italic>aeruginosa<\/jats:italic> infection and may serve as potential targets for bacterial infections and inflammatory diseases, providing insights and resources for omics analyses.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011570","type":"journal-article","created":{"date-parts":[[2023,8,29]],"date-time":"2023-08-29T17:54:24Z","timestamp":1693331664000},"page":"e1011570","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":16,"title":["An integrated multi-omics analysis of identifies distinct molecular characteristics in pulmonary infections of Pseudomonas aeruginosa"],"prefix":"10.1371","volume":"19","author":[{"given":"Yang","family":"Yang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teng","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miao","family":"Tang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaoyu","family":"Zou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yige","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingbo","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueli","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianhua","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yilin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongliang","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing 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