Transcriptomic responses to wounding: meta-analysis of gene expression microarray data
Abstract Background A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first...
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doaj-1cc6501db408463ebae23355f4d5402d2020-11-24T21:04:31ZengBMCBMC Genomics1471-21642017-11-0118111210.1186/s12864-017-4202-8Transcriptomic responses to wounding: meta-analysis of gene expression microarray dataPiotr Andrzej Sass0Michał Dąbrowski1Agata Charzyńska2Paweł Sachadyn3Department Molecular Biotechnology and Microbiology, Gdańsk University of TechnologyLaboratory of Bioinformatics, Neurobiology Center, Nencki Institute of Experimental Biology of Polish Academy of SciencesLaboratory of Bioinformatics, Neurobiology Center, Nencki Institute of Experimental Biology of Polish Academy of SciencesDepartment Molecular Biotechnology and Microbiology, Gdańsk University of TechnologyAbstract Background A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. Results We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis & early inflammation, inflammation, early repair, late repair and remodelling. During the initial phases after wounding, haemostasis & early inflammation and inflammation, the transcriptomic responses showed little consistency between different tissues and experiments. For the later phases, wound repair and remodelling, we identified a number of genes displaying similar transcriptional responses in all examined tissues. As revealed by ontological analyses, activation of certain pathways was rather specific for selected phases of wound healing, such as e.g. responses to vitamin D pronounced during inflammation. Conversely, we observed induction of genes encoding inflammatory agents and extracellular matrix proteins in all wound healing phases. Further, we selected several genes differentially upregulated throughout different stages of wound response, including established factors of wound healing in addition to those previously unreported in this context such as PTPRC and AQP4. Conclusions We found that transcriptomic responses to wounding showed similar traits in a diverse selection of tissues including skin, muscles, internal organs and nervous system. Notably, we distinguished transcriptional induction of inflammatory genes not only in the initial response to wounding, but also later, during wound repair and tissue remodelling.http://link.springer.com/article/10.1186/s12864-017-4202-8Wound healingWound repairTissue injury; regenerationGene expression microarrayTranscriptomics |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Piotr Andrzej Sass Michał Dąbrowski Agata Charzyńska Paweł Sachadyn |
spellingShingle |
Piotr Andrzej Sass Michał Dąbrowski Agata Charzyńska Paweł Sachadyn Transcriptomic responses to wounding: meta-analysis of gene expression microarray data BMC Genomics Wound healing Wound repair Tissue injury; regeneration Gene expression microarray Transcriptomics |
author_facet |
Piotr Andrzej Sass Michał Dąbrowski Agata Charzyńska Paweł Sachadyn |
author_sort |
Piotr Andrzej Sass |
title |
Transcriptomic responses to wounding: meta-analysis of gene expression microarray data |
title_short |
Transcriptomic responses to wounding: meta-analysis of gene expression microarray data |
title_full |
Transcriptomic responses to wounding: meta-analysis of gene expression microarray data |
title_fullStr |
Transcriptomic responses to wounding: meta-analysis of gene expression microarray data |
title_full_unstemmed |
Transcriptomic responses to wounding: meta-analysis of gene expression microarray data |
title_sort |
transcriptomic responses to wounding: meta-analysis of gene expression microarray data |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2017-11-01 |
description |
Abstract Background A vast amount of microarray data on transcriptomic response to injury has been collected so far. We designed the analysis in order to identify the genes displaying significant changes in expression after wounding in different organisms and tissues. This meta-analysis is the first study to compare gene expression profiles in response to wounding in as different tissues as heart, liver, skin, bones, and spinal cord, and species, including rat, mouse and human. Results We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis & early inflammation, inflammation, early repair, late repair and remodelling. During the initial phases after wounding, haemostasis & early inflammation and inflammation, the transcriptomic responses showed little consistency between different tissues and experiments. For the later phases, wound repair and remodelling, we identified a number of genes displaying similar transcriptional responses in all examined tissues. As revealed by ontological analyses, activation of certain pathways was rather specific for selected phases of wound healing, such as e.g. responses to vitamin D pronounced during inflammation. Conversely, we observed induction of genes encoding inflammatory agents and extracellular matrix proteins in all wound healing phases. Further, we selected several genes differentially upregulated throughout different stages of wound response, including established factors of wound healing in addition to those previously unreported in this context such as PTPRC and AQP4. Conclusions We found that transcriptomic responses to wounding showed similar traits in a diverse selection of tissues including skin, muscles, internal organs and nervous system. Notably, we distinguished transcriptional induction of inflammatory genes not only in the initial response to wounding, but also later, during wound repair and tissue remodelling. |
topic |
Wound healing Wound repair Tissue injury; regeneration Gene expression microarray Transcriptomics |
url |
http://link.springer.com/article/10.1186/s12864-017-4202-8 |
work_keys_str_mv |
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