Shan Ou1,2, Guo-Dong Liu3, Yan Tan4, Le-Shun Zhou1, Shu-Rong Bai1, Gang Xue5, Jun Li1, Yong Yang5, Jian Cui6, Jing-Min Cheng2, Jian-Wen Gu2. 1. Department of Anesthesiology, General Hospital of Chengdu Military Command, Chengdu, Sichuan. 2. Department of Neurosurgery, General Hospital of Chengdu Military Command, Chengdu, Sichuan. 3. Department 8, Research Institute of Surgery, Daping Hospital, Third Military Medical University, Chongqing, China. 4. Office of Scientific Research and Training Administration, General Hospital of Chengdu Military Command, Chengdu, Sichuan. 5. Department of Burns and Plastic Surgery, General Hospital of Chengdu Military Command, Chengdu, Sichuan. 6. Department of Anesthesiology, Southwest Hospital, Third Military Medical University, Chongqing, China.
Abstract
BACKGROUND: Burn injury is one of the most common and devastating forms of trauma in daily life. However, the exact sequence of events after burn injury remains unknown. OBJECTIVE: This study aims to investigate gene expression alterations after burn injury. METHODS: Microarray data set GSE8056 was downloaded from the Gene Expression Omnibus (GEO) database, including 12 samples, equally distributed in four groups: normal skin tissue as control and damaged tissues 1-3 days after burn (early period); 4-7 days after burn (middle period); and more than 7 days after burn (late period). Packages in R language were utilized to pre-process the data and filter out the differentially expressed genes (DEGs). Functional annotation of all three groups of DEGs was conducted by using clusters of orthologous groups analysis. The DEGs shared by all three groups were picked out and analyzed with STRING to set up a protein-protein interaction network. CFinder was chosen to implement module analysis, and expression analysis systematic explorer was then adopted to reveal the dysfunctional pathways for each module. RESULTS: A total of 727, 782, and 445 DEGs were identified in the early, middle, and late period after burn, and 234 DEGs were identified as continually differentially expressed throughout all time periods, including genes encoding proinflammatory cytokines, such as interleukin (IL)-6, IL-8, and IL-1β, and genes associated with cell proliferation. Three modules associated with cell proliferation and inflammatory responses were generated from the protein-protein interaction network. CONCLUSION: Our findings are beneficial for understanding the progression of the wound healing response after burn.
BACKGROUND:Burn injury is one of the most common and devastating forms of trauma in daily life. However, the exact sequence of events after burn injury remains unknown. OBJECTIVE: This study aims to investigate gene expression alterations after burn injury. METHODS: Microarray data set GSE8056 was downloaded from the Gene Expression Omnibus (GEO) database, including 12 samples, equally distributed in four groups: normal skin tissue as control and damaged tissues 1-3 days after burn (early period); 4-7 days after burn (middle period); and more than 7 days after burn (late period). Packages in R language were utilized to pre-process the data and filter out the differentially expressed genes (DEGs). Functional annotation of all three groups of DEGs was conducted by using clusters of orthologous groups analysis. The DEGs shared by all three groups were picked out and analyzed with STRING to set up a protein-protein interaction network. CFinder was chosen to implement module analysis, and expression analysis systematic explorer was then adopted to reveal the dysfunctional pathways for each module. RESULTS: A total of 727, 782, and 445 DEGs were identified in the early, middle, and late period after burn, and 234 DEGs were identified as continually differentially expressed throughout all time periods, including genes encoding proinflammatory cytokines, such as interleukin (IL)-6, IL-8, and IL-1β, and genes associated with cell proliferation. Three modules associated with cell proliferation and inflammatory responses were generated from the protein-protein interaction network. CONCLUSION: Our findings are beneficial for understanding the progression of the wound healing response after burn.
Authors: Langni Liu; Katherine E Fahy; Azeezat A Awoyemi; Pariksha Thapa; Lisa E Kelly; Jay Chen; Ji C Bihl; David R Cool; Yanfang Chen; Christine M Rapp; R Michael Johnson; Jeffrey B Travers Journal: J Immunol Date: 2020-05-20 Impact factor: 5.426