title: RNA-Seq Transcriptomic Responses of Full-Thickness Dermal Excision Wounds to Pseudomonas aeruginosa Acute and Biofilm Infection.
abstract: Pseudomonas aeruginosa infections of wounds in clinical settings are major complications whose outcomes are influenced by host responses that are not completely understood. Herein we evaluated transcriptomic changes of wounds as they counter P. aeruginosa infection-first active infection, and then chronic biofilm infection. We used the dermal full-thickness, rabbit ear excisional wound model. We studied the wound response: towards acute infection at 2, 6, and 24 hrs after inoculating 106 bacteria into day-3 wounds; and, towards more chronic biofilm infection of wounds similarly infected for 24 hrs but then treated with topical antibiotic to coerce biofilm growth and evaluated at day 5 and 9 post-infection. The wounds were analyzed for bacterial counts, expression of P. aeruginosa virulence and biofilm-synthesis genes, biofilm morphology, infiltrating immune cells, re-epithelialization, and genome-wide gene expression (RNA-Seq transcriptome). This analysis revealed that 2 hrs after bacterial inoculation into day-3 wounds, the down-regulated genes (infected vs. non-infected) of the wound edge were nearly all non-coding RNAs (ncRNAs), comprised of snoRNA, miRNA, and RNU6 pseudogenes, and their down-regulation preceded a general down-regulation of skin-enriched coding gene expression. As the active infection intensified, ncRNAs remained overrepresented among down-regulated genes; however, at 6 and 24 hrs they changed to a different set, which overlapped between these times, and excluded RNU6 pseudogenes but included snRNA components of the major and minor spliceosomes. Additionally, the raw counts of multiple types of differentially-expressed ncRNAs increased on post-wounding day 3 in control wounds, but infection suppressed this increase. After 5 and 9 days, these ncRNA counts in control wounds decreased, whereas they increased in the infected, healing-impaired wounds. These data suggest a sequential and coordinated change in the levels of transcripts of multiple major classes of ncRNAs in wound cells transitioning from inflammation to the proliferation phase of healing.
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: S L Rajasekhar
authors: SL
authors: Karna
authors: US Army Center for Environmental Health Research, Fort Detrick, Maryland, United States of America.|The Geneva Foundation, Tacoma, Washington, United States of America.
authors: Peter
authors: P
authors: D'Arpa
authors: The Forsyth Institute, Cambridge, Massachusetts, United States of America.
authors: Tsute
authors: T
authors: Chen
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Li-Wu
authors: LW
authors: Qian
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Andrea B
authors: AB
authors: Fourcaudot
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Kazuyoshi
authors: K
authors: Yamane
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Ping
authors: P
authors: Chen
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Johnathan J
authors: JJ
authors: Abercrombie
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Tao
authors: T
authors: You
authors: Dental and Craniofacial Trauma Research and Tissue Regeneration Directorate, US Army Institute of Surgical Research, JBSA Fort Sam Houston, Texas, United States of America.
authors: Kai P
authors: KP
authors: Leung
mesh_terms: D000818:Animals; D018441:Biofilms; D005260:Female; D005786:Gene Expression Regulation / Q000502:physiology; D011552:Pseudomonas Infections / Q000503:physiopathology*; D011550:Pseudomonas aeruginosa; D012313:RNA / Q000235:genetics / Q000502:physiology; D011817:Rabbits; D017192:Skin Diseases, Bacterial / Q000382:microbiology / Q000503:physiopathology*; D059467:Transcriptome / Q000502:physiology*; D014947:Wounds and Injuries / Q000382:microbiology* / Q000503:physiopathology
chemical_list: D012313:RNA