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A microarray analysis of temporal gene expression profiles in thermally injured human skin.

ABSTRACT: Partial-thickness burns incite a multitude of responses which eventually culminate in cutaneous wound repair. We hypothesized that these events would evoke extensive alterations in gene expression thereby orchestrating the complexity of spatial and temporal events that characterize "normal" human wound healing. In the present study, gene expression from partial-thickness areas at defined temporal periods (1-3 days, 4-6 days, and 7-18 days) after injury were compared to normal non-wounded skin. Gene alterations proved extensive (2286 genes). Statistically significant alterations were noted among increased and decreased genes expressed in the three different temporal groupings. Our foundational data (based on samples from 45 individuals) provide a comprehensive molecular gene expression portrait of the cutaneous reparative responses that are initiated during the first 17 days after injury. Our efforts also represent an initial endeavor to move beyond the historically defined "morphological phases" of wound repair toward reporting molecular clues that define the temporal sequence of healing in human subjects. Further analysis of genes that are either affected or remain not affected following injury to normal skin is expected to identify potential targets for therapeutic augmentation or silencing.

SUBMITTER: Greco JA

PROVIDER: S-EPMC3755600 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature

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A microarray analysis of temporal gene expression profiles in thermally injured human skin.

Greco J A JA Pollins A C AC Boone B E BE Levy S E SE Nanney L B LB

Burns : journal of the International Society for Burn Injuries 20090924 2

Partial-thickness burns incite a multitude of responses which eventually culminate in cutaneous wound repair. We hypothesized that these events would evoke extensive alterations in gene expression thereby orchestrating the complexity of spatial and temporal events that characterize "normal" human wound healing. In the present study, gene expression from partial-thickness areas at defined temporal periods (1-3 days, 4-6 days, and 7-18 days) after injury were compared to normal non-wounded skin. G ...[more]

PMID: 19781859

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Project description:Thermal injury incites inflammatory responses that often transcend the local environment and lead to structural deficiencies in skin that give way to scar formation. We hypothesized that extensive perturbations within burned skin following thermal insult and during subsequent events of wound repair induce vast alterations in gene expression that likely serve as a wound and systemic healing deterrent. A high-throughput microarray experiment was designed to analyze genetic expression patterns and identify potential genes to target for therapeutic augmentation or silencing. The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. Utilizing this design, we report that the totality of gene expression alterations is indeed enormous. Further, we observed that the differential expression of many inflammatory and immune response genes appear to be continually up-regulated in burn wound margins seven days or more after initial thermal insult. As it is well established that the inflammatory process must abate for wound healing to proceed, the finding of ongoing local inflammation is cause for further investigation. To our knowledge, this is the first report of the gene expression alterations induced by thermal injury of human skin. As such, it provides a wealth of data to mine with the ultimate goal of better understanding the local pathophysiologic changes at the site of thermal injury that not only affect wound healing capacity, but may also contribute to systemic derangements within the burn patient. Keywords: time course, disease state analysis The study compares gene expression from burn wound margins at various times following thermal injury to expression observed in normal skin. All skin specimens were obtained in the operating room within minutes of being removed from the patient. Burn specimens were taken from wound margins. Harvested tissue at the burn wound margin maximized the capture of viable cells from the multiple lineages important to the healing process and minimized the inclusion of non-viable cells destroyed by full-thickness injury. After isolation, RNA samples were pooled equally by mass as to contain RNA from 5 tissue specimens for each array replicate.

Project description:BackgroundPineapple (Ananas comosus) is a tropical fruit crop of significant commercial importance. Although the physiological changes that occur during pineapple fruit development have been well characterized, little is known about the molecular events that occur during the fruit ripening process. Understanding the molecular basis of pineapple fruit ripening will aid the development of new varieties via molecular breeding or genetic modification. In this study we developed a 9277 element pineapple microarray and used it to profile gene expression changes that occur during pineapple fruit ripening.ResultsMicroarray analyses identified 271 unique cDNAs differentially expressed at least 1.5-fold between the mature green and mature yellow stages of pineapple fruit ripening. Among these 271 sequences, 184 share significant homology with genes encoding proteins of known function, 53 share homology with genes encoding proteins of unknown function and 34 share no significant homology with any database accession. Of the 237 pineapple sequences with homologs, 160 were up-regulated and 77 were down-regulated during pineapple fruit ripening. DAVID Functional Annotation Cluster (FAC) analysis of all 237 sequences with homologs revealed confident enrichment scores for redox activity, organic acid metabolism, metalloenzyme activity, glycolysis, vitamin C biosynthesis, antioxidant activity and cysteine peptidase activity, indicating the functional significance and importance of these processes and pathways during pineapple fruit development. Quantitative real-time PCR analysis validated the microarray expression results for nine out of ten genes tested.ConclusionsThis is the first report of a microarray based gene expression study undertaken in pineapple. Our bioinformatic analyses of the transcript profiles have identified a number of genes, processes and pathways with putative involvement in the pineapple fruit ripening process. This study extends our knowledge of the molecular basis of pineapple fruit ripening and non-climacteric fruit ripening in general.

Project description:Liver ischemia and reperfusion (I/R) injury is of primary concern in cases of liver disease worldwide and is associated with hemorrhagic shock, resection and transplantation. Numerous studies have previously been conducted to investigate the underlying mechanisms of liver I/R injury, however these have not yet been fully elucidated. To determine the difference between ischemia and reperfusion in signaling pathways and the relative pathological mechanisms, the present study downloaded microarray data GSE10657 from the Gene Expression Omnibus database. A total of two data groups from 1‑year‑old mice were selected for further analysis: i) A total of 90 min ischemia; ii) 90 min ischemia followed by 1 h of reperfusion, n=3 for each group. The Limma package was first used to identify the differentially expressed genes (DEGs). DEGs were subsequently uploaded to the Database for Annotation Visualization and Integrated Discovery online tool for Functional enrichment analysis. A protein‑protein interaction (PPI) network was then constructed via STRING version 10.0 and analyzed using Cytoscape software. A total of 114 DEGs were identified, including 21 down and 93 upregulated genes. These DEGs were primarily enriched in malaria and influenza A, in addition to the tumor necrosis factor and mitogen activated protein kinase signaling pathways. Hub genes identified in the PPI network were C‑X‑C motif chemokine ligand (CXCL) 1, C‑C motif chemokine ligand (CCL) 2, interleukin 6, Jun proto‑oncogene, activator protein (AP)‑1 transcription factor subunit, FOS proto‑oncogene, AP‑1 transcription factor subunit and dual specificity phosphatase 1. CXCL1 and CCL2 may exhibit important roles in liver I/R injury, with involvement in the immune and inflammatory responses and the chemokine‑mediated signaling pathway, particularly at the reperfusion stage. However, further experiments to elucidate the specific roles of these mediators are required in the future.

Dataset Information

A microarray analysis of temporal gene expression profiles in thermally injured human skin.

Publications

A microarray analysis of temporal gene expression profiles in thermally injured human skin.

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